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Rees S, Rees T, van Rensburg M, Walker C, Pilkington L, Barker D. Investigation into novel mukanadin B, mukanadin D and mukanadin F derivatives as antagonists of 5-HT1A signalling. ChemMedChem 2024:e202400102. [PMID: 38661010 DOI: 10.1002/cmdc.202400102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 04/26/2024]
Abstract
Marine bromopyrrole alkaloids are a diverse family of natural products with a large array of biological applications. The mukanadin family is a group of molecules consisting of seven members (mukanadin A - G) that possess a range of biological activities. Inhibition of serotonergic signaling has been demonstrated by mukanadin B derivatives, presenting this chemical scaffold as a candidate for further SAR exploration. A library of thirteen novel mukanadin B and D derivatives with structural variation targeted at the pyrrole ring, central linker and hydantoin ring, were synthesized. These analogues were subsequently assessed for serotonergic antagonism, in addition to natural products, mukanadin B, D, F and 9-hydroxy mukanadin B. A collection of compounds exhibited significant 5-HT1A signaling, including five of the novel derivatives and two of the naturally occurring bromopyrroles, mukanadin B and F. Particular SAR information could be determined from these results, such as modification of the pyrrole ring being a well-tolerated strategy for improving serotonergic inhibition. Other changes to the pharmacophore led to significant reduction in activity such as saturation of the linker region, or no conclusive improvement in inhibitory activity such as a 9-OH group or replacement of the hydantoin ring with a triazole moiety.
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Affiliation(s)
- Shaun Rees
- University of Auckland, School of Chemical Sciences, NEW ZEALAND
| | - Tayla Rees
- University of Auckland, School of Biological Sciences, NEW ZEALAND
| | | | | | - Lisa Pilkington
- University of Auckland, School of Chemical Sciences, 23 Symonds Street, 1010, Auckland, NEW ZEALAND
| | - David Barker
- University of Auckland, School of Chemical Sciences, NEW ZEALAND
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2
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Prysiazhniuk K, Datsenko OP, Polishchuk O, Shulha S, Shablykin O, Nikandrova Y, Horbatok K, Bodenchuk I, Borysko P, Shepilov D, Pishel I, Kubyshkin V, Mykhailiuk PK. Spiro[3.3]heptane as a Saturated Benzene Bioisostere. Angew Chem Int Ed Engl 2024; 63:e202316557. [PMID: 38251921 DOI: 10.1002/anie.202316557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Indexed: 01/23/2024]
Abstract
The spiro[3.3]heptane core, with the non-coplanar exit vectors, was shown to be a saturated benzene bioisostere. This scaffold was incorporated into the anticancer drug sonidegib (instead of the meta-benzene), the anticancer drug vorinostat (instead of the phenyl ring), and the anesthetic drug benzocaine (instead of the para-benzene). The patent-free saturated analogs obtained showed a high potency in the corresponding biological assays.
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Affiliation(s)
| | | | | | | | - Oleh Shablykin
- Enamine Ltd., Winston Churchill Str. 78, 02094, Kyiv, Ukraine
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry NAS of Ukraine, 02094, Kyiv, Ukraine
| | | | | | | | - Petro Borysko
- Bienta, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
| | | | - Iryna Pishel
- Bienta, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
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3
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Kirichok AA, Tkachuk H, Kozyriev Y, Shablykin O, Datsenko O, Granat D, Yegorova T, Bas YP, Semirenko V, Pishel I, Kubyshkin V, Lesyk D, Klymenko-Ulianov O, Mykhailiuk PK. 1-Azaspiro[3.3]heptane as a Bioisostere of Piperidine. Angew Chem Int Ed Engl 2023:e202311583. [PMID: 37819253 DOI: 10.1002/anie.202311583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023]
Abstract
1-Azaspiro[3.3]heptanes were synthesized, characterized, and validated biologically as bioisosteres of piperidine. The key synthesis step was thermal [2+2] cycloaddition between endocyclic alkenes and the Graf isocyanate, ClO2 S-NCO, to give spirocyclic β-lactams. Reduction of the β-lactam ring with alane produced 1-azaspiro[3.3]heptanes. Incorporation of this core into the anesthetic drug bupivacaine instead of the piperidine fragment resulted in a new patent-free analogue with high activity.
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Affiliation(s)
- Alexander A Kirichok
- Enamine Ltd, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, Faculty of Chemistry, Volodymyrska 60, 01601, Kyiv, Ukraine
| | | | - Yevhenii Kozyriev
- Enamine Ltd, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
- Oles Honchar Dnipro National University, Faculty of Chemistry, 72 Gagarina Ave., 49010, Dnipro, Ukraine
| | - Oleh Shablykin
- Enamine Ltd, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the NAS of Ukraine, Akademika Kukharya 1, 02094, Kyiv, Ukraine
| | | | - Dmitry Granat
- Enamine Ltd, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
| | - Tetyana Yegorova
- Taras Shevchenko National University of Kyiv, Faculty of Chemistry, Volodymyrska 60, 01601, Kyiv, Ukraine
| | - Yuliya P Bas
- Taras Shevchenko National University of Kyiv, Faculty of Chemistry, Volodymyrska 60, 01601, Kyiv, Ukraine
| | | | - Iryna Pishel
- Enamine Ltd, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
| | | | - Dmytro Lesyk
- Bienta, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
| | | | - Pavel K Mykhailiuk
- Enamine Ltd, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, Faculty of Chemistry, Volodymyrska 60, 01601, Kyiv, Ukraine
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4
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Ferreira N, DE Araújo I, Lustosa T, da Silva PR, Paiva J, Scotti MT, Scotti L. Proposition of In silico Pharmacophore Models for Malaria: A Review. Comb Chem High Throughput Screen 2023:CCHTS-EPUB-134859. [PMID: 37815185 DOI: 10.2174/0113862073247691230925062440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/23/2023] [Accepted: 08/09/2023] [Indexed: 10/11/2023]
Abstract
In the field of medicinal chemistry, the concept of pharmacophore refers to the specific region of a molecule that possesses essential structural and chemical characteristics for binding to a receptor and eliciting biological activity. Understanding the pharmacophore is crucial for drug research and development, as it allows the design of new drugs. Malaria, a widespread disease, is commonly treated with chloroquine and artemisinin, but the emergence of parasite resistance limits their effectiveness. This study aims to explore computer simulations to discover a specific pharmacophore for Malaria, providing new alternatives for its treatment. A literature review was conducted, encompassing articles proposing a pharmacophore for Malaria, gathered from the "Web of Science" database, with a focus on recent publications to ensure up-to-date analysis. The selected articles employed diverse methods, including ligand-based and structurebased approaches, integrating molecular structure and biological activity data to yield comprehensive analyses. Affinity evaluation between the proposed pharmacophore and the target receptor involved calculating free energy to quantify their interaction. Multiple linear regression was commonly utilized, though it is sensitive to multicollinearity issues. Another recurrent methodology was the use of the Schrödinger package, employing tools such as the Phase module and the OPLS force field for interaction analysis. Pharmacophore model proposition allows threedimensional representations guiding the synthesis and design of new biologically active compounds, offering a promising avenue for discovering therapeutic agents to combat Malaria.
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Affiliation(s)
- Natália Ferreira
- Federal University of Paraíba Department of Pharmacy, João Pessoa Brazil
| | - Igor DE Araújo
- Federal University of Paraíba Postgraduate Programa in Natural and Synthetic Bioactive Compounds, Federal University of Paraiba, João Pessoa Brazil
| | - Teresa Lustosa
- Federal University of Paraíba Postgraduate Programa in Natural and Synthetic Bioactive Compounds, Federal University of Paraiba, João Pessoa Brazil
| | | | - Jéssica Paiva
- Federal University of Paraíba Postgraduate Programa in Natural and Synthetic Bioactive Compounds, Federal University of Paraiba, João Pessoa Brazil
| | - Marcus Tullius Scotti
- Federal University of Paraíba Postgraduate Programa in Natural and Synthetic Bioactive Compounds, Federal University of Paraiba, João Pessoa Brazil
| | - Luciana Scotti
- Federal University of Paraíba Postgraduate Programa in Natural and Synthetic Bioactive Compounds, Federal University of Paraiba João Pessoa Brazil
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5
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Angyal P, Hegedüs K, Mészáros BB, Daru J, Dudás Á, Galambos AR, Essmat N, Al-Khrasani M, Varga S, Soós T. Total Synthesis and Structural Plasticity of Kratom Pseudoindoxyl Metabolites. Angew Chem Int Ed Engl 2023; 62:e202303700. [PMID: 37332089 DOI: 10.1002/anie.202303700] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
Mitragynine pseudoindoxyl, a kratom metabolite, has attracted increasing attention due to its favorable side effect profile as compared to conventional opioids. Herein, we describe the first enantioselective and scalable total synthesis of this natural product and its epimeric congener, speciogynine pseudoindoxyl. The characteristic spiro-5-5-6-tricyclic system of these alkaloids was formed through a protecting-group-free cascade relay process in which oxidized tryptamine and secologanin analogues were used. Furthermore, we discovered that mitragynine pseudoindoxyl acts not as a single molecular entity but as a dynamic ensemble of stereoisomers in protic environments; thus, it exhibits structural plasticity in biological systems. Accordingly, these synthetic, structural, and biological studies provide a basis for the planned design of mitragynine pseudoindoxyl analogues, which can guide the development of next-generation analgesics.
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Affiliation(s)
- Péter Angyal
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary
| | - Kristóf Hegedüs
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary
| | - Bence Balázs Mészáros
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - János Daru
- Department of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary
| | - Ádám Dudás
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary
| | - Anna Rita Galambos
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Nagyvárad tér 4, 1089, Budapest, Hungary
| | - Nariman Essmat
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Nagyvárad tér 4, 1089, Budapest, Hungary
| | - Mahmoud Al-Khrasani
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Nagyvárad tér 4, 1089, Budapest, Hungary
| | - Szilárd Varga
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Tibor Soós
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
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6
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Ali A, Bauser M, Bertrand S, Blackaby W, Boss C, Bossart M, Hall A, Binch H, Czechtizky W, Gijsen H, Haning H, Hartung IV, Kilburn P, Lassalle G, Lücking U, Mack J, Missbach M, Otsomaa L, Torrens A, Wagner M, Walter M, Weinstabl H, van Hijfte L, von Nussbaum F. European Medicinal Chemistry Leaders in Industry (EMCL) - On the Status and Future of Medicinal Chemistry Research in Europe. ChemMedChem 2023; 18:e202300127. [PMID: 37276375 DOI: 10.1002/cmdc.202300127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/16/2023] [Indexed: 07/18/2023]
Abstract
The status of industrial Medicinal Chemistry was discussed with European Medicinal Chemistry Leaders from large to mid-sized pharma and CRO companies as well as biotechs. The chemical modality space has expanded recently from small molecules to address new challenging targets. Besides the classical SAR/SPR optimization of drug molecules also their 'greenness' has increasing importance. The entire pharma discovery ecosystem has developed significantly. Beyond pharma and academia new key players such as Biotech and integrated CROs as well as Digital companies have appeared and are now to a large extend fueled by VC money. Digitalization is happening everywhere but surprisingly did not change speed and success rates of projects so far. Future Medicinal Chemists will still have to be excellent synthetic chemists but in addition they must be knowledgeable in new computational areas such as data sciences. Their ability to collaborate and to work in teams is key.
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Affiliation(s)
- Amjad Ali
- External Discovery Chemistry, Merck and Co. Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Marcus Bauser
- Research & Early Development, Global R&D, Leo Pharma, Industriparken 55, 2750, Ballerup, Denmark
| | - Sophie Bertrand
- Medicinal Chemistry, Medicine Design, R&D, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Wesley Blackaby
- Chemistry and Analytical Sciences, Drug Design and Small Molecule Unit, Servier Research Institute, 125 Chemin de Ronde, 78290, Croissy sur Seine, France
| | - Christoph Boss
- Drug Discovery Chemistry, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 4123, Allschwil/BK, Switzerland
| | - Martin Bossart
- Synthetic Medicinal Modalities, Sanofi, Industriepark Höchst G838, 65926, Frankfurt, Germany
| | - Adrian Hall
- Medicinal Chemistry, UCB Pharma, Chemin Du Foriest 1, 1420, Braine-l'Alleud, Belgium
| | - Hayley Binch
- Medicinal Chemistry, Roche Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Werngard Czechtizky
- Medicinal Chemistry, Respiratory and Immunology, AstraZeneca, Pepparedsleden 1, 43183, Göteborg, Sweden
| | - Harrie Gijsen
- Discovery Chemistry, Therapeutics Discovery, Janssen Research & Development, A division of Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Helmut Haning
- Research & Development, Drug Discovery Sciences, Medicinal Chemistry, Bayer AG, Pharmaceuticals, < postCode/>42096, Wuppertal, Germany
| | - Ingo V Hartung
- Medicinal Chemistry & Drug Design, Merck Healthcare KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Paul Kilburn
- Medicinal Chemistry and Translational DMPK, Lundbeck, Ottiliavej 9, 2500, Valby, Denmark
| | - Gilbert Lassalle
- Medicinal Chemistry, Evotec (France), SAS, Campus Curie, 195 Route d'Espagne, 31036, Toulouse Cedex, France
| | - Ulrich Lücking
- Chemistry, FoRx Therapeutics, Lichtstrasse 35, 4056, Basel, Switzerland
| | - Jürgen Mack
- Medicinal Chemistry, Boehringer Ingelheim, Birkendorfer Str. 65, 88400, Biberach, Germany
| | - Martin Missbach
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), 4002, Basel, Switzerland
| | - Leena Otsomaa
- Medicine Design, R&D, Orion Corporation, Orion Pharma, Orionintie 1, 02200, Espoo, Finland
| | - Antoni Torrens
- Chemical Collaborations & Strategic Alliances, ABAC Therapeutics S.L., Joan XXIII, 10, 08950, Esplugues de Llobregat. Barcelona, Spain
| | - Michael Wagner
- Chemistry and Drug Discovery, Dewpoint Therapeutics GmbH, Industriepark Hoechst, G830, 65926, Frankfurt, Germany
| | - Magnus Walter
- Chemical Sciences and Process Development, Monte Rosa Therapeutics AG, Klybeckstrasse 191, WKL-136.3, 4057, Basel, Switzerland
| | - Harald Weinstabl
- Medicinal Chemistry, Boehringer Ingelheim, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Luc van Hijfte
- Drug Discovery, Symeres, Kerkenbos 1013, 6546, BB Nijmegen, The Netherlands
| | - Franz von Nussbaum
- Life Science Chemistry, Nuvisan ICB GmbH, Müllerstr. 178, 13353, Berlin, Germany
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7
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Lu T, Li T, Wu MK, Zheng CC, He XM, Zhu HL, Li L, Man RJ. Molecular simulations required to target novel and potent inhibitors of cancer invasion. Expert Opin Drug Discov 2023; 18:1367-1377. [PMID: 37676052 DOI: 10.1080/17460441.2023.2254695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
INTRODUCTION Computer-aided drug design (CADD) is a computational approach used to discover, develop, and analyze drugs and active molecules with similar biochemical properties. Molecular simulation technology has significantly accelerated drug research and reduced manufacturing costs. It is an optimized drug discovery method that greatly improves the efficiency of novel drug development processes. AREASCOVERED This review discusses the development of molecular simulations of effective cancer inhibitors and traces the main outcomes of in silico studies by introducing representative categories of six important anticancer targets. The authors provide views on this topic from the perspective of both medicinal chemistry and artificial intelligence, indicating the major challenges and predicting trends. EXPERT OPINION The goal of introducing CADD into cancer treatment is to realize a highly efficient, accurate, and desired approach with a high success rate for identifying potent drug candidates. However, the major challenge is the lack of a sophisticated data-filtering mechanism to verify bottom data from mixed-quality references. Consequently, despite the continuous development of algorithms, computer power, and interface optimization, specific data filtering mechanisms will become an urgent and crucial issue in the future.
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Affiliation(s)
| | - Tong Li
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi University for Nationalities, Nanning, China
| | - Meng-Ke Wu
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi University for Nationalities, Nanning, China
| | - Chi-Chong Zheng
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi University for Nationalities, Nanning, China
| | - Xue-Mei He
- Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Science, Nanning, China
| | - Hai-Liang Zhu
- School of Life Sciences, Nanjing University, Nanjing, China
| | - Li Li
- Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Science, Nanning, China
| | - Ruo-Jun Man
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi University for Nationalities, Nanning, China
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Dincer B, Yazici AB, Cinar I, Toktay E, Selli J, Cadirci E, Bayraktutan Z, Yazici E. Antipsychotics Induced Reproductive Toxicity by Stimulating Oxidative Stress: A Comparative In Vivo and In Silico Study. Chem Biodivers 2023; 20:e202201190. [PMID: 37005228 DOI: 10.1002/cbdv.202201190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/22/2023] [Accepted: 03/31/2023] [Indexed: 04/04/2023]
Abstract
The pathophysiological mechanism behind the link between antipsychotic drugs and sexual dysfunction is still unknown. The goal of this research is to compare the potential effects of antipsychotics on the male reproductive system. Fifty rats were randomly assigned into the five groups indicated: Control, Haloperidol, Risperidone, Quetiapine and Aripiprazole. Sperm parameters were significantly impaired in all antipsychotics-treated groups. Haloperidol and Risperidone significantly decreased the level of testosterone. All antipsychotics had significantly reduced inhibin B level. A significant reduction was observed in SOD activity in all antipsychotics-treated groups. While GSH levels diminished, MDA levels were rising in the Haloperidol and Risperidone groups. Also, the GSH level was significantly elevated in the Quetiapine and Aripiprazole groups. By causing oxidative stress and altering hormone levels, Haloperidol and Risperidone are damaging to male reproductivity. This study represents useful starting point for exploring further aspects of the underlying mechanisms reproductive toxicity of antipsychotics.
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Affiliation(s)
- Busra Dincer
- Ondokuz Mayis University: Ondokuz Mayis Universitesi, Pharmacology, Samsun, 55020, Samsun, TURKEY
| | - Ahmet Bulent Yazici
- Sakarya University: Sakarya Universitesi, Department of Psychiatry, Sakarya University, Sakarya, TURKEY
| | - Irfan Cinar
- Kastamonu University: Kastamonu Universitesi, Pharmacology, Kastamonu University, Kastamonu, TURKEY
| | - Erdem Toktay
- Kafkas University Faculty of Medicine: Kafkas Universitesi Tip Fakultesi, Histology and embryology, Kafkas University, Kars, TURKEY
| | - Jale Selli
- Alanya Alaaddin Keykubat Üniversitesi: Alanya Alaaddin Keykubat Universitesi, Histology and embryology, Alanya Alaaddin Keykubat Üniversitesi:, Alanya/Antalya, TURKEY
| | - Elif Cadirci
- Ataturk University: Ataturk Universitesi, pharmacolgy, Ataturk University, Erzurum, TURKEY
| | - Zafer Bayraktutan
- Ataturk University: Ataturk Universitesi, Biochemistry, Ataturk University, Erzurum, TURKEY
| | - Esra Yazici
- Sakarya University: Sakarya Universitesi, Psychiatry, Sakarya University, Sakarya, TURKEY
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9
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Yazdani K, Jordan D, Yang M, Fullenkamp CR, Calabrese DR, Boer R, Hilimire T, Allen TEH, Khan RT, Schneekloth JS. Machine Learning Informs RNA-Binding Chemical Space. Angew Chem Int Ed Engl 2023; 62:e202211358. [PMID: 36584293 PMCID: PMC9992102 DOI: 10.1002/anie.202211358] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023]
Abstract
Small molecule targeting of RNA has emerged as a new frontier in medicinal chemistry, but compared to the protein targeting literature our understanding of chemical matter that binds to RNA is limited. In this study, we reported Repository Of BInders to Nucleic acids (ROBIN), a new library of nucleic acid binders identified by small molecule microarray (SMM) screening. The complete results of 36 individual nucleic acid SMM screens against a library of 24 572 small molecules were reported (including a total of 1 627 072 interactions assayed). A set of 2 003 RNA-binding small molecules was identified, representing the largest fully public, experimentally derived library of its kind to date. Machine learning was used to develop highly predictive and interpretable models to characterize RNA-binding molecules. This work demonstrates that machine learning algorithms applied to experimentally derived sets of RNA binders are a powerful method to inform RNA-targeted chemical space.
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Affiliation(s)
- Kamyar Yazdani
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Deondre Jordan
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Mo Yang
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Christopher R. Fullenkamp
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - David R. Calabrese
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Robert Boer
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Thomas Hilimire
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | | | | | - John S. Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
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10
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Somprasong S, Reis MC, Harutyunyan SR. Catalytic Access to Chiral δ-Lactams via Nucleophilic Dearomatization of Pyridine Derivatives. Angew Chem Int Ed Engl 2023; 62:e202217328. [PMID: 36522289 DOI: 10.1002/anie.202217328] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
Nitrogen-bearing rings are common features in the molecular structures of modern drugs, with chiral δ-lactams being an important subclass due to their known pharmacological properties. Catalytic dearomatization of preactivated pyridinium ion derivatives emerged as a powerful method for the rapid construction of chiral N-heterocycles. However, direct catalytic dearomatization of simple pyridine derivatives are scarce and methodologies yielding chiral δ-lactams are yet to be developed. Herein, we describe an enantioselective C4-dearomatization of methoxypyridine derivatives for the preparation of functionalised enantioenriched δ-lactams using chiral copper catalysis. Experimental 13 C kinetic isotope effects and density functional theory calculations shed light on the reaction mechanism and the origin of enantioselectivity.
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Affiliation(s)
- Siriphong Somprasong
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Marta Castiñeira Reis
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Syuzanna R Harutyunyan
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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11
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Clayton AD, Pyzer-Knapp EO, Purdie M, Jones MF, Barthelme A, Pavey J, Kapur N, Chamberlain TW, Blacker AJ, Bourne RA. Bayesian Self-Optimization for Telescoped Continuous Flow Synthesis. Angew Chem Int Ed Engl 2023; 62:e202214511. [PMID: 36346840 PMCID: PMC10108149 DOI: 10.1002/anie.202214511] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/28/2022] [Accepted: 11/08/2022] [Indexed: 11/09/2022]
Abstract
The optimization of multistep chemical syntheses is critical for the rapid development of new pharmaceuticals. However, concatenating individually optimized reactions can lead to inefficient multistep syntheses, owing to chemical interdependencies between the steps. Herein, we develop an automated continuous flow platform for the simultaneous optimization of telescoped reactions. Our approach is applied to a Heck cyclization-deprotection reaction sequence, used in the synthesis of a precursor for 1-methyltetrahydroisoquinoline C5 functionalization. A simple method for multipoint sampling with a single online HPLC instrument was designed, enabling accurate quantification of each reaction, and an in-depth understanding of the reaction pathways. Notably, integration of Bayesian optimization techniques identified an 81 % overall yield in just 14 h, and revealed a favorable competing pathway for formation of the desired product.
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Affiliation(s)
- Adam D Clayton
- Institute of Process Research and Development, Schools of Chemistry & Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | | | - Mark Purdie
- ISEL, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield, UK
| | - Martin F Jones
- Chemical Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield, UK
| | | | - John Pavey
- UCB Pharma SA, All. de la Recherche 60, 1070, Anderlecht, Belgium
| | - Nikil Kapur
- Institute of Process Research and Development, School of Mechanical Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Thomas W Chamberlain
- Institute of Process Research and Development, Schools of Chemistry & Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - A John Blacker
- Institute of Process Research and Development, Schools of Chemistry & Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Richard A Bourne
- Institute of Process Research and Development, Schools of Chemistry & Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, UK
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12
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Abstract
Cyclophilins, enzymes with peptidyl-prolyl cis/trans isomerase activity, are relevant to a large variety of biological processes. The most abundant member of this enzyme family, cyclophilin A, is the cellular receptor of the immunosuppressive drug cyclosporine A (CsA). As a consequence of the pathophysiological role of cyclophilins, particularly in viral infections, there is a broad interest in cyclophilin inhibition devoid of immunosuppressive activity. This Review first gives an introduction into the physiological and pathophysiological roles of cyclophilins. The presentation of non-immunosuppressive cyclophilin inhibitors will commence with drugs based on chemical modifications of CsA. The naturally occurring macrocyclic sanglifehrins have become other lead structures for cyclophilin-inhibiting drugs. Finally, de novo designed compounds, whose structures are not derived from or inspired by natural products, will be presented. Relevant synthetic concepts will be discussed, but the focus will also be on biochemical studies, structure-activity relationships, and clinical studies.
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Affiliation(s)
- Cordelia Schiene‐Fischer
- Institute of Biochemistry and BiotechnologyMartin-Luther-University Halle-Wittenberg06099Halle (Saale)Germany
| | - Gunter Fischer
- Max Planck Institute for Biophysical Chemistry37077GöttingenGermany
| | - Manfred Braun
- Institute of Organic and Macromolecular ChemistryHeinrich-Heine-University Düsseldorf40225DüsseldorfGermany
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13
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Camberlein V, Fléau C, Sierocki P, Li L, Gealageas R, Bosc D, Guillaume V, Warenghem S, Leroux F, Rosell M, Cheng K, Medve L, Prigent M, Decanter M, Piveteau C, Biela A, Eveque M, Dumont J, Mpakali A, Giastas P, Herledan A, Couturier C, Haupenthal J, Lesire L, Hirsch AKH, Deprez B, Stratikos E, Bouvier M, Deprez‐Poulain R. Discovery of the First Selective Nanomolar Inhibitors of ERAP2 by Kinetic Target-Guided Synthesis. Angew Chem Int Ed Engl 2022; 61:e202203560. [PMID: 35904863 PMCID: PMC9558494 DOI: 10.1002/anie.202203560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Indexed: 01/07/2023]
Abstract
Endoplasmic reticulum aminopeptidase 2 (ERAP2) is a key enzyme involved in the trimming of antigenic peptides presented by Major Histocompatibility Complex class I. It is a target of growing interest for the treatment of autoimmune diseases and in cancer immunotherapy. However, the discovery of potent and selective ERAP2 inhibitors is highly challenging. Herein, we have used kinetic target-guided synthesis (KTGS) to identify such inhibitors. Co-crystallization experiments revealed the binding mode of three different inhibitors with increasing potency and selectivity over related enzymes. Selected analogues engage ERAP2 in cells and inhibit antigen presentation in a cellular context. 4 d (BDM88951) displays favorable in vitro ADME properties and in vivo exposure. In summary, KTGS allowed the discovery of the first nanomolar and selective highly promising ERAP2 inhibitors that pave the way of the exploration of the biological roles of this enzyme and provide lead compounds for drug discovery efforts.
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Affiliation(s)
- Virgyl Camberlein
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Charlotte Fléau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Pierre Sierocki
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Lenong Li
- Department of Microbiology and ImmunologyUniversity of Illinois at Chicago909 S Wolcott AvenueChicagoIL 60612USA
| | - Ronan Gealageas
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Damien Bosc
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Valentin Guillaume
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Sandrine Warenghem
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Melissa Rosell
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Keguang Cheng
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Laura Medve
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Mathilde Prigent
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Myriam Decanter
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Alexandre Biela
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Maxime Eveque
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Julie Dumont
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Anastasia Mpakali
- National Center for Scientific Research DemokritosAgia Paraskevi15341Greece
| | - Petros Giastas
- National Center for Scientific Research DemokritosAgia Paraskevi15341Greece
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Cyril Couturier
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
| | - Laetitia Lesire
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany,Department for Pharmacy, Saarland UniversityCampus E8 166123SaarbrückenGermany
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
| | - Efstratios Stratikos
- National Center for Scientific Research DemokritosAgia Paraskevi15341Greece,Laboratory of BiochemistryDepartment of ChemistryNational and Kapodistrian University of AthensPanepistimiopolisZographou15784Greece
| | - Marlene Bouvier
- Department of Microbiology and ImmunologyUniversity of Illinois at Chicago909 S Wolcott AvenueChicagoIL 60612USA
| | - Rebecca Deprez‐Poulain
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems3 rue du Pr Laguesse59000LilleFrance,European Genomic Institute for Diabetes, EGID, Pôle Recherche1 place de Verdun59045Lille CedexFrance
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14
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Grygorenko OO, Melnykov KP, Holovach S, Demchuk O. Fluorinated Cycloalkyl Building Blocks for Drug Discovery. ChemMedChem 2022; 17:e202200365. [PMID: 36031924 DOI: 10.1002/cmdc.202200365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Indexed: 11/06/2022]
Abstract
The review covers various aspects of fluorinated cycloalkyl (C 3 -C 7 ) building blocks for drug discovery, including their synthesis, key physicochemical properties, and biological and medicinal applications of their derivatives. The discussed synthetic methods include classical nucleophilic fluorinations of various substrates, the addition of fluorine and another heteroatom to double bonds, cycloadditions and other transformations of fluorine-containing substrates, as well as some newer reactions like fluorination of non-activated and remotely activated C-H bonds, decarboxylative and deborylative fluorinations, etc. The known data on the effect of introducing the fluorinated cycloalkyl groups on the compound's key in vitro parameters (such as acidity/basicity, lipophilicity, conformational behavior, and short contact capabilities) are surveyed. Finally, applications of fluorinated cycloalkyl building block derivatives in the design of biologically active compounds (including marketed drugs Maraviroc, Ivosidenib, and Sitafloxacin) are covered, with a focus on the fluorination impact.
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Affiliation(s)
- Oleksandr O Grygorenko
- Taras Shevchenko National University of Kyiv: Kiivs'kij nacional'nij universitet imeni Tarasa Sevcenka, Chemical Faculty, UKRAINE
| | - Kostiantyn P Melnykov
- Taras Shevchenko National University of Kyiv: Kiivs'kij nacional'nij universitet imeni Tarasa Sevcenka, Chemical Faculty, UKRAINE
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15
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Jouaneh TMM, Rosario ME, Li Y, Leibovitz E, Bertin MJ. Incorporating LC-MS/MS Analysis and the Dereplication of Natural Product Samples into an Upper-Division Undergraduate Laboratory Course. J Chem Educ 2022; 99:2636-2642. [PMID: 37654737 PMCID: PMC10468906 DOI: 10.1021/acs.jchemed.1c01212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Growth in the biomedical and biotechnology sectors requires a highly trained and highly skilled workforce to answer the next great scientific questions. Undergraduate laboratory courses incorporating hands-on training based in authentic research position soon-to-be graduates to learn in environments that mirror that of academic, industrial, and government laboratories. Mass spectrometry is one of the most broadly applied analyses carried out in the biomedical and pharmaceutical sciences and thus it is essential that upper-division students gain hands-on experience in techniques and analytical workflows in mass spectrometry. Our pre-course assessments identified weaknesses in student experience and knowledge in the fundamentals of mass spectrometry, supporting that it was a necessary area for improvement. We incorporated a laboratory experiment focused on tandem mass spectrometry and database searching into a preexisting mini-semester project devoted to identifying metabolites from medicinal plants. Implementation of the experiment allowed students to make more confident metabolite identifications, introduced them to a cutting-edge database analysis platform (GNPS: Global Natural Products Social Molecular Networking), and increased student experience and knowledge of mass spectrometry in addition to the principle of dereplication of samples derived from nature.
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Affiliation(s)
- Terra Marie M. Jouaneh
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Margaret E. Rosario
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Yibo Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Elizabeth Leibovitz
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Matthew J. Bertin
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
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16
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Wang H, Hetzer F, Huang W, Qu Q, Meyerowitz J, Kaindl J, Hübner H, Skiniotis G, Kobilka BK, Gmeiner P. Structure-Based Evolution of G Protein-Biased μ-Opioid Receptor Agonists. Angew Chem Int Ed Engl 2022; 61:e202200269. [PMID: 35385593 PMCID: PMC9322534 DOI: 10.1002/anie.202200269] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Indexed: 01/14/2023]
Abstract
The μ-opioid receptor (μOR) is the major target for opioid analgesics. Activation of μOR initiates signaling through G protein pathways as well as through β-arrestin recruitment. μOR agonists that are biased towards G protein signaling pathways demonstrate diminished side effects. PZM21, discovered by computational docking, is a G protein biased μOR agonist. Here we report the cryoEM structure of PZM21 bound μOR in complex with Gi protein. Structure-based evolution led to multiple PZM21 analogs with more pronounced Gi protein bias and increased lipophilicity to improve CNS penetration. Among them, FH210 shows extremely low potency and efficacy for arrestin recruitment. We further determined the cryoEM structure of FH210 bound to μOR in complex with Gi protein and confirmed its expected binding pose. The structural and pharmacological studies reveal a potential mechanism to reduce β-arrestin recruitment by the μOR, and hold promise for developing next-generation analgesics with fewer adverse effects.
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Affiliation(s)
- Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Florian Hetzer
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Strasse 10, 91058, Erlangen, Germany
| | - Weijiao Huang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Qianhui Qu
- Department of Molecular and Cellular Physiology, Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Present address: Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Justin Meyerowitz
- Department of Molecular and Cellular Physiology, Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonas Kaindl
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Strasse 10, 91058, Erlangen, Germany
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Strasse 10, 91058, Erlangen, Germany
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Strasse 10, 91058, Erlangen, Germany
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17
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Moghadam ES, Mireskandari K, Abdel-Jalil R, Amini M. An approach to pharmacological targets of pyrrole family from a medicinal chemistry viewpoint. Mini Rev Med Chem 2022; 22:2486-2561. [PMID: 35339175 DOI: 10.2174/1389557522666220325150531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/12/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022]
Abstract
Pyrrole is one of the most widely used heterocycles in the pharmaceutical industry. Due to the importance of pyrrole structure in drug design and development, herein, we tried to conduct an extensive review of the bioactive pyrrole based compounds reported recently. The bioactivity of pyrrole derivatives varies, so in the review, we categorized them based on their direct pharmacologic targets. Therefore, readers are able to find the variety of biologic targets for pyrrole containing compounds easily. This review explains around seventy different biologic targets for pyrrole based derivatives, so, it is helpful for medicinal chemists in design and development novel bioactive compounds for different diseases. This review presents an extensive meaningful structure activity relationship for each reported structure as much as possible. The review focuses on papers published between 2018 and 2020.
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Affiliation(s)
- Ebrahim Saeedian Moghadam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran14176, Iran.
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.
- Department of Chemistry, College of Science, Sultan Qaboos University, Muscat, P.O. Box 36, P.C. 123, Sultanate of Oman
| | - Katayoon Mireskandari
- Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| | - Raid Abdel-Jalil
- Department of Chemistry, College of Science, Sultan Qaboos University, Muscat, P.O. Box 36, P.C. 123, Sultanate of Oman
| | - Mohsen Amini
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran14176, Iran.
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
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18
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Adamek RN, Ludford P, Duggan SM, Tor Y, Cohen SM. Corrigendum: Identification of Adenosine Deaminase Inhibitors by Metal-binding Pharmacophore Screening. ChemMedChem 2022; 17:e202200087. [PMID: 35182106 DOI: 10.1002/cmdc.202200087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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19
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Yordi EG, Santana L, Uriarte E, Borges F, Matos MJ. Computer-Aided Design of Coumarins for Neurodegenerative diseases: Trends of the Last Decade. Curr Top Med Chem 2021; 21:2245-2257. [PMID: 34635041 DOI: 10.2174/1568026621666211011101429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/31/2021] [Accepted: 08/31/2021] [Indexed: 11/22/2022]
Abstract
Computer-aided design of new drugs is an exponentially growing field, especially in the last decade. The support of theoretical tools may accelerate the drug discovery process, which is a long and very expensive journey. Tools as QSAR and docking calculations are on the top of the list for helping medicinal chemists to find more potent and selective molecules as potential leads for facing challenging diseases. Coumarins have been an important source of inspiration for the design of new drugs. Due to their chemical properties and their affinity to some targets, special attention has been paid to their role against neurodegenerative diseases. Therefore, the authors provide an overview of the scientific reports describing the research and development of new drug design tools supporting the discovery of coumarins as enzymatic inhibitors or receptor ligands involved in these diseases. This review emphasizes the rationale behind the design of new drug candidates, and particular attention is paid to the search for new leads over the last 10 years. QSAR and docking studies are discussed, as well as new technologies applied for the research in this field. The manuscripts discussed in this review have been collected from multiple electronic databases, including Pubmed, SciFinder, and Mendeley.
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Affiliation(s)
- Estela Guardado Yordi
- Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela. Spain
| | - Lourdes Santana
- CIQUP/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto. Portugal
| | - Eugenio Uriarte
- CIQUP/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto. Portugal
| | - Fernanda Borges
- CIQUP/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto. Portugal
| | - Maria J Matos
- Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela. Spain
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20
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Thilgen C, Wennemers H, Carell T. François Diederich (1952-2020): 40 Years of Organic Chemistry. Angew Chem Int Ed Engl 2021; 60:11562-11567. [PMID: 33909942 DOI: 10.1002/anie.202101232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
François Diederich, Professor of Organic Chemistry and long-time Chair of the Editorial Board of Angewandte Chemie, sadly passed away on September 23, 2020. He will be remembered for his groundbreaking research in the chemistry of fullerenes and carbon-rich molecules, in supramolecular and medicinal chemistry, as an engaging teacher, and as a generous and fascinating human being.
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Affiliation(s)
- Carlo Thilgen
- Departement für Chemie und Angewandte Biowissenschaften, ETH Zürich, Switzerland
| | - Helma Wennemers
- Departement für Chemie und Angewandte Biowissenschaften, ETH Zürich, Switzerland
| | - Thomas Carell
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany
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21
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Abstract
An approach of building block (BB) inclusivity and atom efficient library schemes deliver the quality and diversity of DNA-encoded libraries best suited for small molecule drug discovery. In this Perspective, we offer key learnings in DEL design from a decade's worth of DEL-driven screening.
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Affiliation(s)
- Y Zhang
- X-Chem Inc., 100 Beaver Street, Waltham, MA 02453, USA
| | - M A Clark
- X-Chem Inc., 100 Beaver Street, Waltham, MA 02453, USA.
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22
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Adamek RN, Ludford P, Duggan SM, Tor Y, Cohen SM. Identification of Adenosine Deaminase Inhibitors by Metal-binding Pharmacophore Screening. ChemMedChem 2020; 15:2151-2156. [PMID: 32729197 DOI: 10.1002/cmdc.202000271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/25/2020] [Indexed: 12/20/2022]
Abstract
Adenosine deaminase (ADA) is a human mononuclear Zn2+ metalloenzyme that converts adenosine to inosine. ADA is a validated drug target for cancer, but there has been little recent work on the development of new therapeutics against this enzyme. The lack of new advancements can be partially attributed to an absence of suitable assays for high-throughput screening (HTS) against ADA. To facilitate more rapid drug discovery efforts for this target, an in vitro assay was developed that utilizes the enzymatic conversion of a visibly emitting adenosine analogue to the corresponding fluorescent inosine analogue by ADA, which can be monitored via fluorescence intensity changes. Utilizing this assay, a library of ∼350 small molecules containing metal-binding pharmacophores (MBPs) was screened in an HTS format to identify new inhibitor scaffolds against ADA. This approach yielded a new metal-binding scaffold with a Ki value of 26±1 μM.
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Affiliation(s)
- Rebecca N Adamek
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
| | - Paul Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
| | - Stephanie M Duggan
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
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23
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Abstract
The number of publications concerning Pan-Assay Interference Compounds and related problematic structural motifs in screening libraries is constantly growing. In consequence, filter collections are merged, extended but also critically discussed. Due to the complexity of the chemical pattern language SMARTS, an easy-to-use toolbox enabling every chemist to understand, design and modify chemical patterns is urgently needed. Over the past decade, we developed a series of software tools for visualizing, editing, creating, and analysing chemical patterns. Herein, we highlight how most of these tools can now be easily used as part of the novel SMARTS.plus web server (https://smarts.plus/). As a showcase, we demonstrate how researchers can apply the web server tools within minutes to derive novel SMARTS patterns for the filtering of frequent hitters from their screening libraries with only a little experience with the SMARTS language.
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Affiliation(s)
- Christiane Ehrt
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146, Hamburg, Germany
| | - Bennet Krause
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146, Hamburg, Germany
| | - Robert Schmidt
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146, Hamburg, Germany
| | - Emanuel S R Ehmki
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146, Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146, Hamburg, Germany
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24
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Valsecchi C, Grisoni F, Motta S, Bonati L, Ballabio D. NURA: A curated dataset of nuclear receptor modulators. Toxicol Appl Pharmacol 2020; 407:115244. [PMID: 32961130 DOI: 10.1016/j.taap.2020.115244] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 08/27/2020] [Accepted: 09/14/2020] [Indexed: 01/10/2023]
Abstract
Nuclear receptors (NRs) are key regulators of human health and constitute a relevant target for medicinal chemistry applications as well as for toxicological risk assessment. Several open databases dedicated to small molecules that modulate NRs exist; however, depending on their final aim (i.e., adverse effect assessment or drug design), these databases contain a different amount and type of annotated molecules, along with a different distribution of experimental bioactivity values. Stemming from these considerations, in this work we aim to provide a unified dataset, NURA (NUclear Receptor Activity) dataset, collecting curated information on small molecules that modulate NRs, to be intended for both pharmacological and toxicological applications. NURA contains bioactivity annotations for 15,247 molecules and 11 selected NRs, and it was obtained by integrating and curating data from toxicological and pharmacological databases (i.e., Tox21, ChEMBL, NR-DBIND and BindingDB). Our results show that NURA dataset is a useful tool to bridge the gap between toxicology- and medicinal-chemistry-related databases, as it is enriched in terms of number of molecules, structural diversity and covered atomic scaffolds compared to the single sources. To the best of our knowledge, NURA dataset is the most exhaustive collection of small molecules annotated for their modulation of the chosen nuclear receptors. NURA dataset is intended to support decision-making in pharmacology and toxicology, as well as to contribute to data-driven applications, such as machine learning. The dataset and the data curation pipeline can be downloaded free of charge on Zenodo at the following DOI: https://doi.org/10.5281/zenodo.3991561.
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Affiliation(s)
- Cecile Valsecchi
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, P.za della Scienza 1, 20126 Milano, Italy
| | - Francesca Grisoni
- ETH Zurich, Department of Chemistry and Applied Biosciences, RETHINK, Vladimir-Prelog-Weg 4, 8049 Zurich, Switzerland.
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, P.za della Scienza 1, 20126 Milano, Italy
| | - Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, P.za della Scienza 1, 20126 Milano, Italy
| | - Davide Ballabio
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, P.za della Scienza 1, 20126 Milano, Italy
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25
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Jakob CHG, Dominelli B, Hahn EM, Berghausen TO, Pinheiro T, Marques F, Reich RM, Correia JDG, Kühn FE. Antiproliferative Activity of Functionalized Histidine-derived Au(I) bis-NHC Complexes for Bioconjugation. Chem Asian J 2020; 15:2754-2762. [PMID: 32592289 PMCID: PMC7689731 DOI: 10.1002/asia.202000620] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/20/2020] [Indexed: 12/23/2022]
Abstract
A series of histidine derived Au(I) bis-NHC complexes bearing different ester, amide and carboxylic acid functionalities as well as wingtip substituents is synthesized and characterized. The stability in aqueous media, in vitro cytotoxicity in a set of cancer cell lines (MCF7, PC3 and A2780/A2780cisR) along with the cellular uptake are evaluated. Stability tests suggest hydrolysis of the ester within 8 h, which might lead to deactivation. Furthermore, the bis-NHC system shows a sufficient stability against cysteine and the thiol containing peptide GSH. The benzyl ester and amide show the highest activity comparable to the benchmark compound cisplatin, with the ester only displaying a slightly lower cytotoxicity than the amide. A cellular uptake study revealed that the benzyl ester and the amide could have different intracellular distribution profiles but both complexes induce perturbations of the cellular physiological processes. The simple modifiability and high stability of the complexes provides a promising system for upcoming post modifications to enable targeted cancer therapy.
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Affiliation(s)
- Christian H. G. Jakob
- Molecular CatalysisCatalysis Research Center and Department of Chemistry Department Technische Universität MünchenLichtenbergstrasse 4D-85748Garching bei MünchenGermany
| | - Bruno Dominelli
- Molecular CatalysisCatalysis Research Center and Department of Chemistry Department Technische Universität MünchenLichtenbergstrasse 4D-85748Garching bei MünchenGermany
| | - Eva M. Hahn
- Molecular CatalysisCatalysis Research Center and Department of Chemistry Department Technische Universität MünchenLichtenbergstrasse 4D-85748Garching bei MünchenGermany
| | - Tobias O. Berghausen
- Molecular CatalysisCatalysis Research Center and Department of Chemistry Department Technische Universität MünchenLichtenbergstrasse 4D-85748Garching bei MünchenGermany
| | - Teresa Pinheiro
- Institute for Bioengineering and BiosciencesDepartamento de Engenharia e Ciências NuclearesInstituto Superior TécnicoUniversidade de LisboaAv. Rovisco Pais 11049-001LisboaPortugal
| | - Fernanda Marques
- Centro de Ciências e Tecnologias NuclearesDepartamento de Engenharia e Ciências NuclearesInstituto Superior TécnicoUniversidade de LisboaCTN, Estrada Nacional 10 (km 139,7)2695-066Bobadela LRSPortugal
| | - Robert M. Reich
- Molecular CatalysisCatalysis Research Center and Department of Chemistry Department Technische Universität MünchenLichtenbergstrasse 4D-85748Garching bei MünchenGermany
| | - João D. G. Correia
- Centro de Ciências e Tecnologias NuclearesDepartamento de Engenharia e Ciências NuclearesInstituto Superior TécnicoUniversidade de LisboaCTN, Estrada Nacional 10 (km 139,7)2695-066Bobadela LRSPortugal
| | - Fritz E. Kühn
- Molecular CatalysisCatalysis Research Center and Department of Chemistry Department Technische Universität MünchenLichtenbergstrasse 4D-85748Garching bei MünchenGermany
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26
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Abstract
Pannexin 1 (Panx1) channels are transmembrane proteins that release adenosine triphosphate and play an important role in intercellular communication. They are widely expressed in somatic and nervous system tissues, and their activity has been associated with many pathologies such as stroke, epilepsy, inflammation, and chronic pain. While there are a variety of small molecules known to inhibit Panx1, currently little is known about the mechanism of channel inhibition, and there is a dearth of sufficiently potent and selective drugs targeting Panx1. Herein we provide a review of the current literature on Panx1 structural biology and known pharmacological agents that will help provide a basis for rational development of Panx1 chemical modulators.
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Affiliation(s)
- Kathleen E. Navis
- Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Churmy Y. Fan
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Tuan Trang
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Roger J. Thompson
- Department of Cell Biology and Anatomy, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Darren J. Derksen
- Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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27
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Dawidowski M, Król M, Szulczyk B, Chodkowski A, Podsadni P, Konopelski P, Ufnal M, Szuberski P, Wróbel MZ, Zhang Y, El Harchi A, Hancox JC, Jarkovska D, Mistrova E, Sviglerova J, Štengl M, Popowicz GM, Turło J. Structure-activity relationship and cardiac safety of 2-aryl-2-(pyridin-2-yl)acetamides as a new class of broad-spectrum anticonvulsants derived from Disopyramide. Bioorg Chem 2020; 98:103717. [PMID: 32171994 DOI: 10.1016/j.bioorg.2020.103717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/23/2019] [Accepted: 02/28/2020] [Indexed: 10/24/2022]
Abstract
A series of 2-aryl-2-(pyridin-2-yl)acetamides were synthesized and screened for their anticonvulsant activity in animal models of epilepsy. The compounds were broadly active in the 'classical' maximal electroshock seizure (MES) and subcutaneous Metrazol (scMET) tests as well as in the 6 Hz and kindling models of pharmacoresistant seizures. Furthermore, the compounds showed good therapeutic indices between anticonvulsant activity and motor impairment. Structure-activity relationship (SAR) trends clearly showed the highest activity resides in unsubstituted phenyl derivatives or compounds having ortho- and meta- substituents on the phenyl ring. The 2-aryl-2-(pyridin-2-yl)acetamides were derived by redesign of the cardiotoxic sodium channel blocker Disopyramide (DISO). Our results show that the compounds preserve the capability of the parent compound to inhibit voltage gated sodium currents in patch-clamp experiments; however, in contrast to DISO, a representative compound from the series 1 displays high levels of cardiac safety in a panel of in vitro and in vivo experiments.
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Affiliation(s)
- Maciej Dawidowski
- Department of Drug Technology and Pharmaceutical Biotechnology, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland.
| | - Marek Król
- Department of Drug Technology and Pharmaceutical Biotechnology, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Bartłomiej Szulczyk
- Department of Drug Technology and Pharmaceutical Biotechnology, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland; Laboratory of Physiology and Pathophysiology, Centre for Preclinical Research, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland
| | - Andrzej Chodkowski
- Department of Drug Technology and Pharmaceutical Biotechnology, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Piotr Podsadni
- Department of Drug Technology and Pharmaceutical Biotechnology, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Piotr Konopelski
- Department of Experimental Physiology and Pathophysiology, Centre for Preclinical Research, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland
| | - Marcin Ufnal
- Department of Experimental Physiology and Pathophysiology, Centre for Preclinical Research, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland
| | - Piotr Szuberski
- Department of Drug Technology and Pharmaceutical Biotechnology, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Martyna Zofia Wróbel
- Department of Drug Technology and Pharmaceutical Biotechnology, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Yihong Zhang
- School of Physiology, Pharmacology and Neuroscience, Faculty of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Aziza El Harchi
- School of Physiology, Pharmacology and Neuroscience, Faculty of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Jules C Hancox
- School of Physiology, Pharmacology and Neuroscience, Faculty of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Dagmar Jarkovska
- Department of Physiology, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Pilsen, Czech Republic
| | - Eliska Mistrova
- Department of Physiology, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Pilsen, Czech Republic
| | - Jitka Sviglerova
- Department of Physiology, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Pilsen, Czech Republic
| | - Milan Štengl
- Department of Physiology, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Pilsen, Czech Republic
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Jadwiga Turło
- Department of Drug Technology and Pharmaceutical Biotechnology, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
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28
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De Vita E, Smits N, van den Hurk H, Beck EM, Hewitt J, Baillie G, Russell E, Pannifer A, Hamon V, Morrison A, McElroy SP, Jones P, Ignatenko NA, Gunkel N, Miller AK. Synthesis and Structure-Activity Relationships of N-(4-Benzamidino)-Oxazolidinones: Potent and Selective Inhibitors of Kallikrein-Related Peptidase 6. ChemMedChem 2020; 15:79-95. [PMID: 31675166 PMCID: PMC7004151 DOI: 10.1002/cmdc.201900536] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/23/2019] [Indexed: 12/16/2022]
Abstract
Kallikrein-related peptidase 6 (KLK6) is a secreted serine protease that belongs to the family of tissue kallikreins. Aberrant expression of KLK6 has been found in different cancers and neurodegenerative diseases, and KLK6 is currently studied as a potential target in these pathologies. We report a novel series of KLK6 inhibitors discovered in a high-throughput screen within the European Lead Factory program. Structure-guided design based on docking studies enabled rapid progression of a hit cluster to inhibitors with improved potency, selectivity and pharmacokinetic properties. In particular, inhibitors 32 ((5R)-3-(4-carbamimidoylphenyl)-N-((S)-1-(naphthalen-1-yl)propyl)-2-oxooxazolidine-5-carboxamide) and 34 ((5R)-3-(6-carbamimidoylpyridin-3-yl)-N-((1S)-1-(naphthalen-1-yl)propyl)-2-oxooxazolidine-5-carboxamide) have single-digit nanomolar potency against KLK6, with over 25-fold and 100-fold selectivities against the closely related enzyme trypsin, respectively. The most potent compound, 32, effectively reduces KLK6-dependent invasion of HCT116 cells. The high potency in combination with good solubility and low clearance of 32 make it a good chemical probe for KLK6 target validation in vitro and potentially in vivo.
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Affiliation(s)
- Elena De Vita
- Cancer Drug Development GroupGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120HeidelbergGermany
- Faculty of BiosciencesUniversity of Heidelberg69120HeidelbergGermany
| | - Niels Smits
- Pivot Park Screening CentreKloosterstraat 95349 ABOss (TheNetherlands
| | | | - Elizabeth M. Beck
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Joanne Hewitt
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Gemma Baillie
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Emily Russell
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Andrew Pannifer
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Véronique Hamon
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Angus Morrison
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Stuart P. McElroy
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Philip Jones
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Natalia A. Ignatenko
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZ 85721USA
- Department of Cellular and Molecular MedicineUniversity of ArizonaTucsonAZ 85721USA
| | - Nikolas Gunkel
- Cancer Drug Development GroupGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120HeidelbergGermany
- German Cancer Consortium (DKTK)69120HeidelbergGermany
| | - Aubry K. Miller
- Cancer Drug Development GroupGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120HeidelbergGermany
- German Cancer Consortium (DKTK)69120HeidelbergGermany
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29
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Pedreira JGB, Franco LS, Barreiro EJ. Chemical Intuition in Drug Design and Discovery. Curr Top Med Chem 2019; 19:1679-1693. [PMID: 31258088 DOI: 10.2174/1568026619666190620144142] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 12/14/2022]
Abstract
The medicinal chemist plays the most important role in drug design, discovery and development. The primary goal is to discover leads and optimize them to develop clinically useful drug candidates. This process requires the medicinal chemist to deal with large sets of data containing chemical descriptors, pharmacological data, pharmacokinetics parameters, and in silico predictions. The modern medicinal chemist has a large number of tools and technologies to aid him in creating strategies and supporting decision-making. Alongside with these tools, human cognition, experience and creativity are fundamental to drug research and are important for the chemical intuition of medicinal chemists. Therefore, fine-tuning of data processing and in-house experience are essential to reach clinical trials. In this article, we will provide an expert opinion on how chemical intuition contributes to the discovery of drugs, discuss where it is involved in the modern drug discovery process, and demonstrate how multidisciplinary teams can create the optimal environment for drug design, discovery, and development.
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Affiliation(s)
- Júlia G B Pedreira
- Laboratorio de Avaliacao e Sintese de Substancias Bioativas (LASSBio), Instituto de Ciencias Biomedicas (ICB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,Programa de Pós-Graduação em Química, UFRJ, Rio de Janeiro, Brazil
| | - Lucas S Franco
- Laboratorio de Avaliacao e Sintese de Substancias Bioativas (LASSBio), Instituto de Ciencias Biomedicas (ICB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,Programa de Pós-Graduação em Farmacologia e Química Medicinal, ICB-UFRJ, Rio de Janeiro, Brazil
| | - Eliezer J Barreiro
- Laboratorio de Avaliacao e Sintese de Substancias Bioativas (LASSBio), Instituto de Ciencias Biomedicas (ICB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,Programa de Pós-Graduação em Química, UFRJ, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Farmacologia e Química Medicinal, ICB-UFRJ, Rio de Janeiro, Brazil.,Programa de Pesquisas em Desenvolvimento de Fármacos (PPDF), ICB, UFRJ, Rio de Janeiro, Brazil
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30
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Ali R, Guan Y, Leveille AN, Vaughn E, Parelkar S, Thompson PR, Mattson AE. Synthesis and Anticancer Activity of Structure Simplified Naturally-Inspired Dimeric Chromenone Derivatives. European J Org Chem 2019; 2019:6917-6929. [PMID: 33828411 DOI: 10.1002/ejoc.201901026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Select dimeric chromenones exhibit low micromolar cyctotoxicity toward lymphoma and leukemia cell lines, L5178Y and HL60, respectively. The bioactive dimeric chromenones were identified from a focused library of structurally-simplified derivatives of naturally-occurring dimeric chromenones and tetrahydroxanthones that was prepared as part of this study. The simple dimeric chromenone scaffolds contain no stereogenic centers, are easily synthesized, and may be utilized as lead compounds in cancer research and drug discovery.
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Affiliation(s)
- Rameez Ali
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01602
| | - Yong Guan
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01602
| | - Alexandria N Leveille
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01602
| | - Elizabeth Vaughn
- Department of Chemistry, Appalachian State University, 287 Rivers St., Boone, NC 28608
| | - Sangram Parelkar
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA, 01605
| | - Paul R Thompson
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA, 01605
| | - Anita E Mattson
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01602
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31
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Shastri S, Chatterjee B, Thakur SS. Achievements in Cancer Research and its Therapeutics in Hundred Years. Curr Top Med Chem 2019; 19:1545-1562. [PMID: 31362690 DOI: 10.2174/1568026619666190730093034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 12/19/2022]
Abstract
Cancer research has progressed leaps and bounds over the years. This review is a brief overview of the cancer research, milestone achievements and therapeutic studies on it over the one hundred ten years which would give us an insight into how far we have come to understand and combat this fatal disease leading to millions of deaths worldwide. Modern biology has proved that cancer is a very complex disease as still we do not know precisely how it triggers. It involves several factors such as protooncogene, oncogene, kinase, tumor suppressor gene, growth factor, signalling cascade, micro RNA, immunity, environmental factors and carcinogens. However, modern technology now helps the cancer patient on the basis of acquired and established knowledge in the last hundred years to save human lives.
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Affiliation(s)
- Sravanthi Shastri
- Proteomics and Cell Signaling, Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Bhaswati Chatterjee
- National Institute of Pharmaceutical Education and Research, Hyderabad, India
| | - Suman S Thakur
- Proteomics and Cell Signaling, Centre for Cellular and Molecular Biology, Hyderabad, India
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32
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Kumari A, Singh RK. Medicinal chemistry of indole derivatives: Current to future therapeutic prospectives. Bioorg Chem 2019; 89:103021. [PMID: 31176854 DOI: 10.1016/j.bioorg.2019.103021] [Citation(s) in RCA: 227] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/22/2019] [Accepted: 05/29/2019] [Indexed: 12/21/2022]
Abstract
Indole is a versatile pharmacophore, a privileged scaffold and an outstanding heterocyclic compound with wide ranges of pharmacological activities due to different mechanisms of action. It is an superlative moiety in drug discovery with the sole property of resembling different structures of the protein. Plenty of research has been taking place in recent years to synthesize and explore the various therapeutic prospectives of this moiety. This review summarizes some of the recent effective chemical synthesis (2014-2018) for indole ring. This review also emphasized on the structure-activity relationship (SAR) to reveal the active pharmacophores of various indole analogues accountable for anticancer, anticonvulsant, antimicrobial, antitubercular, antimalarial, antiviral, antidiabetic and other miscellaneous activities which have been investigated in the last five years. The precise features with motives and framework of each research topic is introduced for helping the medicinal chemists to understand the perspective of the context in a better way. This review will definitely offer the platform for researchers to strategically design diverse novel indole derivatives having different promising pharmacological activities with reduced toxicity and side effects.
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Affiliation(s)
- Archana Kumari
- Rayat-Bahra Institute of Pharmacy, Dist. Hoshiarpur, 146104 Punjab, India
| | - Rajesh K Singh
- Department of Pharmaceutical Chemistry, Shivalik College of Pharmacy, Nangal, Dist. Rupnagar, 140126 Punjab, India.
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33
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Santoso KT, Cheung CY, Hards K, Cook GM, Stocker BL, Timmer MSM. Synthesis and Investigation of Phthalazinones as Antitubercular Agents. Chem Asian J 2019; 14:1278-1285. [PMID: 30680937 DOI: 10.1002/asia.201801805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/16/2019] [Indexed: 11/08/2022]
Abstract
A series of 2- and 7-substituted phthalazinones was synthesised and their potential as anti-tubercular drugs assessed via Mycobacterium tuberculosis (mc2 6230) growth inhibition assays. All phthalazinones tested showed growth inhibitory activity (MIC <100 μm), and those compounds containing lipophilic and electron-withdrawing groups generally exhibited better anti-tubercular activity. Several lead compounds were identified, including 7-((2-amino-6-(4-fluorophenyl)pyrimidin-4-yl)amino)-2-heptylphthalazin-1(2H)-one (MIC=1.6 μm), 4-tertbutylphthalazin-2(1H)-one (MIC=3 μm), and 7-nitro-phthalazin-1(2H)-one (MIC=3 μm). Mode of action studies indicated that selected pyrimidinyl-phthalazinones may interfere with NADH oxidation, however, the mode of action of the lead compound is independent of this enzyme. MIC=minimum inhibitory concentration.
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Affiliation(s)
- Kristiana T Santoso
- School of Chemical and Physical Sciences, Victoria University of Wellington, P.O. Box 600, 6140, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, P.O. Box 600, 6140, Wellington, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Kiel Hards
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Bridget L Stocker
- School of Chemical and Physical Sciences, Victoria University of Wellington, P.O. Box 600, 6140, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, P.O. Box 600, 6140, Wellington, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Mattie S M Timmer
- School of Chemical and Physical Sciences, Victoria University of Wellington, P.O. Box 600, 6140, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, P.O. Box 600, 6140, Wellington, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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34
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Abstract
Drug design and discovery remains a popular topic of study to many students interested in visible, real-world applications of the chemical sciences. It is important that laboratory experiments detailing the early stages of drug discovery incorporate both compound design and an exploration of ligand/receptor interactions. Molecular modeling is widely employed in research endeavors seeking to predict the activity of potential compounds prior to synthesis and can therefore be used to illustrate these concepts. The following activity therefore details the use of AutoDock to predict the binding affinity and docked pose of a series of CDK2 inhibitors. Students can then compare their docking output to experimentally determined inhibitory activities and crystal structures. Finally, the AutoDock workflow detailed in this activity can be used in research settings, provided the receptor crystal structure is known.
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35
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Abstract
Substructure search (SSS) is a fundamental technique supported by various chemical information systems. Many users apply it in an iterative manner: they modify their queries to shape the composition of the retrieved hit sets according to their needs. We propose and evaluate two heuristic extensions of SSS aimed at simplifying these iterative query modifications by collecting additional information during query processing and visualizing this information in an intuitive way. This gives the user a convenient feedback on how certain changes to the query would affect the retrieved hit set and reduces the number of trial-and-error cycles needed to generate an optimal search result. The proposed heuristics are simple, yet surprisingly effective and can be easily added to existing SSS implementations.
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Affiliation(s)
- Nils Weskamp
- Boehringer Ingelheim Pharma GmbH & Co. KG, Discovery Research, Lead Identification and Optimization Support, Computational Chemistry, Birkendorfer Straße 65, 88397, Biberach an der Riss, Germany.
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36
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Goodrich S, Patel M, Woydziak ZR. Synthesis of a Fluorescent Acridone using a Grignard Addition, Oxidation, and Nucleophilic Aromatic Substitution Reaction Sequence. J Chem Educ 2015; 92:1221-1225. [PMID: 27681671 PMCID: PMC5036523 DOI: 10.1021/ed5009574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A three-pot synthesis oriented for an undergraduate organic chemistry laboratory was developed to construct a fluorescent acridone molecule. This laboratory experiment utilizes Grignard addition to an aldehyde, alcohol oxidation, and iterative nucleophilic aromatic substitution steps to produce the final product. Each of the intermediates and the acridone product of the synthesis are analyzed by common techniques available in most undergraduate chemistry laboratories, such as melting point, TLC, IR spectroscopy, UV-Vis spectroscopy, and fluorescence spectroscopy. Yields for each transformation in the synthesis are generally moderately low to good (20-90%) and nearly all of the students (>90%) who attempted the synthesis were able to produce the final acridone product.
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37
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Harling JD, Deakin AM, Campos S, Grimley R, Chaudry L, Nye C, Polyakova O, Bessant CM, Barton N, Somers D, Barrett J, Graves RH, Hanns L, Kerr WJ, Solari R. Discovery of novel irreversible inhibitors of interleukin (IL)-2-inducible tyrosine kinase (Itk) by targeting cysteine 442 in the ATP pocket. J Biol Chem 2013; 288:28195-206. [PMID: 23935099 DOI: 10.1074/jbc.m113.474114] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
IL-2-inducible tyrosine kinase (Itk) plays a key role in antigen receptor signaling in T cells and is considered an important target for anti-inflammatory drug discovery. In order to generate inhibitors with the necessary potency and selectivity, a compound that targeted cysteine 442 in the ATP binding pocket and with an envisaged irreversible mode of action was designed. We incorporated a high degree of molecular recognition and specific design features making the compound suitable for inhaled delivery. This study confirms the irreversible covalent binding of the inhibitor to the kinase by x-ray crystallography and enzymology while demonstrating potency, selectivity, and prolonged duration of action in in vitro biological assays. The biosynthetic turnover of the kinase was also examined as a critical factor when designing irreversible inhibitors for extended duration of action. The exemplified Itk inhibitor demonstrated inhibition of both TH1 and TH2 cytokines, was additive with fluticasone propionate, and inhibited cytokine release from human lung fragments. Finally, we describe an in vivo pharmacodynamic assay that allows rapid preclinical development without animal efficacy models.
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Affiliation(s)
- John D Harling
- From the Allergic Inflammation Discovery Performance Unit and
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