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Khichi A, Jakhar R, Dahiya S, Arya J, Dangi M, Chhillar AK. In silico and in vitro evaluation of designed fluconazole analogues as lanosterol 14α-demethylase inhibitors. J Biomol Struct Dyn 2024; 42:4553-4566. [PMID: 37293950 DOI: 10.1080/07391102.2023.2220808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/29/2023] [Indexed: 06/10/2023]
Abstract
The drugs fighting against aggressive fungal infections are in limited number, therefore, extensive research is obligatory to develop new therapeutic strategies. Fluconazole (FLZ) is a clinically approved drug, but resistant drug against most fungal pathogens, thus it is vital to identify more compounds that can better check the fungal growth. Analogue-based drug designing is a quick and economical way since it has inherent drug-like properties of marketed drugs. This study aims to generate and evaluate analogues of FLZ with better potency against fungal-borne infections. A total of 3307 analogues of FLZ were developed from six scaffold structures. Only 390 compounds passed Lipinski's rule, of which 247 analogues exhibited lower docking scores than FLZ with 5FSA. These inhibitors were further subjected to pharmacokinetics property evaluation and cytotoxicity test and it was found that only 46 analogues were suitable for further evaluation. Based on the molecular docking score of the best two analogues, 6f (-12.7 kcal/mol) and 8f (-12.8 kcal/mol) were selected for molecular dynamics and in-vitro studies. Antifungal activities of both compounds against 4 strains of Candida albicans were evaluated by disc diffusion assay and micro broth dilution assay and Minimum inhibitory concentrations (MICs) for 6f and 8f were observed as 256 µg/ml against 4719, 4918 and 5480 strains but the MIC was extended to 512 µg/ml for strain 3719. Both analogues exhibited low antifungal activities as compared to FLZ (8-16 µg/ml). The interaction of 6f with Mycostatin was also performed using a chequerboard assay that was found additive.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alka Khichi
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, India
| | - Ritu Jakhar
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, India
| | - Sweety Dahiya
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Jasmine Arya
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Mehak Dangi
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, India
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Majoumo-Mbe F, Sangbong NA, Tadjong Tcho A, Namba-Nzanguim CT, Simoben CV, Eni DB, Alhaji Isa M, Poli ANR, Cassel J, Salvino JM, Montaner LJ, Tietjen I, Ntie-Kang F. 5-chloro-3-(2-(2,4-dinitrophenyl) hydrazono)indolin-2-one: synthesis, characterization, biochemical and computational screening against SARS-CoV-2. CHEMICKE ZVESTI 2024; 78:3431-3441. [PMID: 38685970 PMCID: PMC11055700 DOI: 10.1007/s11696-023-03274-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 12/04/2023] [Indexed: 05/02/2024]
Abstract
Chemical prototypes with broad-spectrum antiviral activity are important toward developing new therapies that can act on both existing and emerging viruses. Binding of the SARS-CoV-2 spike protein to the host angiotensin-converting enzyme 2 (ACE2) receptor is required for cellular entry of SARS-CoV-2. Toward identifying new chemical leads that can disrupt this interaction, including in the presence of SARS-CoV-2 adaptive mutations found in variants like omicron that can circumvent vaccine, immune, and therapeutic antibody responses, we synthesized 5-chloro-3-(2-(2,4-dinitrophenyl)hydrazono)indolin-2-one (H2L) from the condensation reaction of 5-chloroisatin and 2,4-dinitrophenylhydrazine in good yield. H2L was characterised by elemental and spectral (IR, electronic, Mass) analyses. The NMR spectrum of H2L indicated a keto-enol tautomerism, with the keto form being more abundant in solution. H2L was found to selectively interfere with binding of the SARS-CoV-2 spike receptor-binding domain (RBD) to the host angiotensin-converting enzyme 2 receptor with a 50% inhibitory concentration (IC50) of 0.26 μM, compared to an unrelated PD-1/PD-L1 ligand-receptor-binding pair with an IC50 of 2.06 μM in vitro (Selectivity index = 7.9). Molecular docking studies revealed that the synthesized ligand preferentially binds within the ACE2 receptor-binding site in a region distinct from where spike mutations in SARS-CoV-2 variants occur. Consistent with these models, H2L was able to disrupt ACE2 interactions with the RBDs from beta, delta, lambda, and omicron variants with similar activities. These studies indicate that H2L-derived compounds are potential inhibitors of multiple SARS-CoV-2 variants, including those capable of circumventing vaccine and immune responses. Supplementary Information The online version contains supplementary material available at 10.1007/s11696-023-03274-5.
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Affiliation(s)
- Felicite Majoumo-Mbe
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Neba Abongwa Sangbong
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Alain Tadjong Tcho
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Cyril T. Namba-Nzanguim
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
- Center for Drug Discovery, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Conrad V. Simoben
- Center for Drug Discovery, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Donatus B. Eni
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
- Center for Drug Discovery, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Mustafa Alhaji Isa
- Department of Microbiology, Faculty of Sciences, University of Maiduguri, PMB 1069, Maiduguri, Borno State Nigeria
| | | | - Joel Cassel
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104 USA
| | - Joseph M. Salvino
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104 USA
| | - Luis J. Montaner
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104 USA
| | - Ian Tietjen
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104 USA
| | - Fidele Ntie-Kang
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
- Center for Drug Discovery, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
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Chen M, Cui Y, Chen X, Shang R, Zhang X. C-F bond activation enables synthesis of aryl difluoromethyl bicyclopentanes as benzophenone-type bioisosteres. Nat Commun 2024; 15:419. [PMID: 38199996 PMCID: PMC10781780 DOI: 10.1038/s41467-023-44653-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Bioisosteric design has become an essential approach in the development of drug molecules. Recent advancements in synthetic methodologies have enabled the rapid adoption of this strategy into drug discovery programs. Consequently, conceptionally innovative practices would be appreciated by the medicinal chemistry community. Here we report an expeditous synthetic method for synthesizing aryl difluoromethyl bicyclopentane (ADB) as a bioisostere of the benzophenone core. This approach involves the merger of light-driven C-F bond activation and strain-release chemistry under the catalysis of a newly designed N-anionic-based organic photocatalyst. This defluorinative coupling methodology enables the direct conversion of a wide variety of commercially available trifluoromethylaromatic C-F bonds (more than 70 examples) into the corresponding difluoromethyl bicyclo[1.1.1]pentanes (BCP) arenes/difluoromethyl BCP boronates in a single step. The strategy can also be applied to [3.1.1]and [4.1.1]propellane systems, providing access to analogues with different geometries. Moreover, we have successfully used this protocol to rapidly prepare ADB-substituted analogues of the bioactive molecule Adiporon. Biological testing has shown that the ADB scaffold has the potential to enhance the pharmacological properties of benzophenone-type drug candidates.
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Affiliation(s)
- Mingshuo Chen
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, 310024, Hangzhou, People's Republic of China
| | - Yuang Cui
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, 310024, Hangzhou, People's Republic of China
| | - Xiaoping Chen
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, 310024, Hangzhou, People's Republic of China
| | - Rui Shang
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Xiaheng Zhang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, 310024, Hangzhou, People's Republic of China.
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Chapman CA, Fernandez-Patel S, Jahan N, Cuttaz EA, Novikov A, Goding JA, Green RA. Controlled electroactive release from solid-state conductive elastomer electrodes. Mater Today Bio 2023; 23:100883. [PMID: 38144517 PMCID: PMC10746364 DOI: 10.1016/j.mtbio.2023.100883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023] Open
Abstract
This work highlights the development of a conductive elastomer (CE) based electrophoretic platform that enables the transfer of charged molecules from a solid-state CE electrode directly to targeted tissues. Using an elastomer-based electrode containing poly (3,4-ethylenedioxythiophene) nanowires, controlled electrophoretic delivery of methylene blue (MB) and fluorescein (FLSC) was achieved with applied voltage. Electroactive release of positively charged MB and negatively charged FLSC achieved 33.19 ± 6.47 μg release of MB and 22.36 ± 3.05 μg release of FLSC, a 24 and 20-fold increase in comparison to inhibitory voltages over 1 h. Additionally, selective, and sequential release of the two oppositely charged molecules from a single CE device was demonstrated, showing the potential of this device to be used in multi-drug treatments.
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Affiliation(s)
- Christopher A.R. Chapman
- School of Engineering and Materials Science, Queen Mary University of London, Mile End, London, E1 4NS, UK
- Department of Bioengineering, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Shanila Fernandez-Patel
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Nusrat Jahan
- Department of Bioengineering, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Estelle A. Cuttaz
- Department of Bioengineering, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Alexey Novikov
- Department of Bioengineering, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Josef A. Goding
- Department of Bioengineering, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Rylie A. Green
- Department of Bioengineering, Imperial College London, South Kensington, London, SW7 2AZ, UK
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Meanwell NA. Applications of Bioisosteres in the Design of Biologically Active Compounds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18087-18122. [PMID: 36961953 DOI: 10.1021/acs.jafc.3c00765] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The design of bioisosteres represents a creative and productive approach to improve a molecule, including by enhancing potency, addressing pharmacokinetic challenges, reducing off-target liabilities, and productively modulating physicochemical properties. Bioisosterism is a principle exploited in the design of bioactive compounds of interest to both medicinal and agricultural chemists, and in this review, we provide a synopsis of applications where this kind of molecular editing has proved to be advantageous in molecule optimization. The examples selected for discussion focus on bioisosteres of carboxylic acids, applications of fluorine and fluorinated motifs in compound design, some applications of the sulfoximine functionality, the design of bioisosteres of drug-H2O complexes, and the design of bioisosteres of the phenyl ring.
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Affiliation(s)
- Nicholas A Meanwell
- The Baruch S. Blumberg Institute, 3805 Old Easton Rd, Doylestown, Pennsylvania 18902, United States
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Quan X, Xu L, Li Z, Maienfisch P. Design, Synthesis, and Properties of Silicon-Containing meta-Diamide Insecticides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18188-18196. [PMID: 37191337 DOI: 10.1021/acs.jafc.3c01342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Silicon-containing compounds are sporadically used in crop protection and drug discovery and have demonstrated to increase the biological efficacy as well as to reduce toxicity, improve physicochemical properties, and favorably impact the environmental profile. As part of our research, we have investigated the application of bioisosteric silicon replacements in meta-diamide insecticides and studied the biological activity and molecular properties of the corresponding novel compounds. At all meaningful structural elements of the meta-diamides, silicon-containing substituents were introduced and synthetic methodology was developed for their syntheses. As the most promising compound, silicon-containing meta-diamide II-18 emerged, which exhibits a very low LC50 value of 2.00 mg/L against Mythimna separata and compares well to the reference compounds 28 (LC50 = 0.17 mg/L) and II-20 (LC50 = 0.27 mg/L). Our research on silicon-containing crop protection compounds once again confirmed that the biological activity can be beneficially affected by the insertion of silicone substituents and that the introduction of well-chosen silicone motifs is an excellent strategy for agrochemical research.
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Affiliation(s)
- Xiaocao Quan
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Liu Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Peter Maienfisch
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- CreInSol Consulting & Biocontrols, CH-4118 Rodersdorf, Switzerland
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7
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Buehler Y, Reymond JL. Molecular Framework Analysis of the Generated Database GDB-13s. J Chem Inf Model 2023; 63:484-492. [PMID: 36533982 PMCID: PMC9875802 DOI: 10.1021/acs.jcim.2c01107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Indexed: 12/23/2022]
Abstract
The generated databases (GDBs) list billions of possible molecules from systematic enumeration following simple rules of chemical stability and synthetic feasibility. To assess the originality of GDB molecules, we compared their Bemis and Murcko molecular frameworks (MFs) with those in public databases. MFs result from molecules by converting all atoms to carbons, all bonds to single bonds, and removing terminal atoms iteratively until none remain. We compared GDB-13s (99,394,177 molecules up to 13 atoms containing simplified functional groups, 22,130 MFs) with ZINC (885,905,524 screening compounds, 1,016,597 MFs), PubChem50 (100,852,694 molecules up to 50 atoms, 1,530,189 MFs), and COCONUT (401,624 natural products, 42,734 MFs). While MFs in public databases mostly contained linker bonds and six-membered rings, GDB-13s MFs had diverse ring sizes and ring systems without linker bonds. Most GDB-13s MFs were exclusive to this database, and many were relatively simple, representing attractive targets for synthetic chemistry aiming at innovative molecules.
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Affiliation(s)
- Ye Buehler
- Department of Chemistry, Biochemistry
and Pharmaceutical Sciences, University
of Bern, Freiestrasse 3, 3012Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry
and Pharmaceutical Sciences, University
of Bern, Freiestrasse 3, 3012Bern, Switzerland
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Molecular insights on ar-turmerone as a structural, functional and pharmacophoric analogue of synthetic mosquito repellent DEET by comprehensive computational assessment. Sci Rep 2022; 12:15564. [PMID: 36114273 PMCID: PMC9481521 DOI: 10.1038/s41598-022-19901-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 09/06/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractMosquitoes are vectors for a variety of infectious illnesses, and chemical synthetic insecticides have made it possible to control them effectively. Mosquito repellents are a typical means of keeping mosquitos at bay. Because of its main effectiveness of skin permeability, N,N-Diethyl-meta-toluamide (DEET) is one of the most extensively used mosquito repellents but a dangerous synthetic chemical. DEET was identified about a decade ago to inhibit mosquito's Odorant Binding Protein 1 (OBP1), impairing the mosquito's ability to recognise the host body odour. OBP1 has been identified as a possible target for the development of new mosquito repellents since its discovery. Essential oils from different plants, on the other hand, have been used to repel mosquitos since antiquity. One essential oil from the Curcuma longa (Zingiberales: Zingiberaceae) rhizome display mosquito repellent properties, according to the literature. Furthermore, one of the phytochemicals found in abundance in C. longa essential oil, ar-turmerone, exhibits mosquito repellency as comparable to synthetic DEET. Till date studies on in-silico interaction of natural ar-turmerone with OBP1, which we depict in our current work are scarce. Further, there exist no published reports demonstrating the literary evidence on detailed insights of interaction of DEET with OBP1 along with Molecular Dynamics (MD) simulation studies. We further performed detailed molecular investigations using pharmacophore analysis of ar-turmerone and compared it with DEET, where our findings in the current manuscript unveils for the first time that ar-turmerone is a functional, structural and pharmacophoric analogue of DEET.
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Chen M, Li Z, Shao X, Maienfisch P. Bioisosteric-Replacement-Driven Lead Optimization of Tyclopyrazoflor. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11123-11137. [PMID: 35561416 DOI: 10.1021/acs.jafc.2c00654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A heterocyclic replacement strategy has been applied attempting to further optimize the biological properties of the new insecticide tyclopyrazoflor, a pyridinyl-pyrazole compound with excellent activity against sap-feeding insects recently discovered by Corteva. Our research program on this novel chemical class of insecticide was targeted to evaluate the importance of both the pyridyl and pyrazole moieties on the biological activity, properties, and structure-activity. Synthetic methodologies have been developed delivering our designed target compounds in moderate to good yields. In our attempt to rationalize the biological activity differences of tyclopyrazoflor analogues, a potential surface analysis based on a density functional theory (DFT) calculation and DFT-derived Multiwfn and VMD program model was performed. Furthermore, the SwissBioisostere online database was applied as a great source for inspiration for bioisosteric replacements.
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Affiliation(s)
- Meijun Chen
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Xusheng Shao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Peter Maienfisch
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- CreInSol Consulting & Biocontrols, CH-4118 Rodersdorf, Switzerland
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Literature-based drug-drug similarity for drug repurposing: impact of Medical Subject Headings term refinement and hierarchical clustering. Future Med Chem 2022; 14:1309-1323. [PMID: 36017692 DOI: 10.4155/fmc-2022-0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: We describe herein, an improved procedure for drug repurposing based on refined Medical Subject Headings (MeSH) terms and hierarchical clustering method. Materials & methods: In the present study, we have employed MeSH data from MEDLINE (2019), 1669 US FDA approved drugs from Open FDA and a refined set of MeSH terms. Refinement of MeSH terms was performed to include terms related to mechanistic information of drugs and diseases. Results and Conclusions: In-depth analysis of the results obtained, demonstrated greater efficiency of the proposed approach, based on refined MeSH terms and hierarchical clustering, in terms of number of selected drug candidates for repurposing. Further, analysis of misclustering and size of noise clusters suggest that the proposed approach is reliable and can be employed in drug repurposing.
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Bernacchia L, Paris A, Gupta A, Moores A, Kad N. Identification of the target and mode of action for the prokaryotic nucleotide excision repair inhibitor ATBC. Biosci Rep 2022; 42:BSR20220403. [PMID: 35546304 PMCID: PMC9152706 DOI: 10.1042/bsr20220403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/27/2022] [Accepted: 05/12/2022] [Indexed: 11/17/2022] Open
Abstract
In bacteria, nucleotide excision repair (NER) plays a major role in repairing DNA damage from a wide variety of sources. Therefore, its inhibition offers potential to develop a new antibacterial in combination with adjuvants, such as UV light. To date, only one known chemical inhibitor of NER is 2-(5-amino-1,3,4-thiadiazol-2-yl)benzo(f)chromen-3-one (ATBC) exists and targets Mycobacterium tuberculosis NER. To enable the design of future drugs, we need to understand its mechanism of action. To determine the mechanism of action, we used in silico structure-based prediction, which identified the ATP-binding pocket of Escherichia coli UvrA as a probable target. Growth studies in E. coli showed it was nontoxic alone, but able to impair growth when combined with DNA-damaging agents, and as we predicted, it reduced by an approximately 70% UvrA's ATPase rate. Since UvrA's ATPase activity is necessary for effective DNA binding, we used single-molecule microscopy to directly observe DNA association. We measured an approximately sevenfold reduction in UvrA molecules binding to a single molecule of dsDNA suspended between optically trapped beads. These data provide a clear mechanism of action for ATBC, and show that targeting UvrA's ATPase pocket is effective and ATBC provides an excellent framework for the derivation of more soluble inhibitors that can be tested for activity.
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Affiliation(s)
- Lorenzo Bernacchia
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, U.K
| | - Antoine Paris
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, U.K
| | - Arya Gupta
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, U.K
| | | | - Neil M. Kad
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, U.K
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Christensen E, Hirsch NC, Andersen JV, Ehlers LH. The Analogue Substitution Model: Introducing Competition in the Absence of Generic Substitution in Danish Hospitals. Health Policy 2022; 126:844-852. [DOI: 10.1016/j.healthpol.2022.05.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 10/11/2021] [Accepted: 05/30/2022] [Indexed: 11/04/2022]
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Dangi M, Khichi A, Jakhar R, Chhillar AK. Growing Preferences towards Analog-based Drug Discovery. Curr Pharm Biotechnol 2021; 22:1030-1045. [PMID: 32900347 DOI: 10.2174/1389201021666200908121409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/29/2020] [Accepted: 08/21/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The major concern of today's time is the developing resistance in most of the clinically derived pathogenic micro-organisms for available drugs through several mechanisms. Therefore, there is a dire need to develop novel molecules with drug-like properties that can be effective against the otherwise resistant micro-organisms. METHODS New drugs can be developed using several methods like structure-based drug design, ligandbased drug design, or by developing analogs of the available drugs to further improve their effects. However, the smartness is to opt for the techniques that have comparatively less expenditure, lower failure rates, and faster discovery rates. RESULTS Analog-Based Drug Design (ABDD) is one such technique that researchers worldwide are opting to develop new drug-like molecules with comparatively lower market values. They start by first designing the analogs sharing structural and pharmacological similarities to the existing drugs. This method embarks on scaffold structures of available drugs already approved by the clinical trials, but are left ineffective because of resistance developed by the pathogens. CONCLUSION In this review, we have discussed some recent examples of anti-fungal and anti-bacterial (antimicrobial) drugs that were designed based on the ABDD technique. Also, we have tried to focus on the in silico tools and techniques that can contribute to the designing and computational screening of the analogs, so that these can be further considered for in vitro screening to validate their better biological activities against the pathogens with comparatively reduced rates of failure.
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Affiliation(s)
- Mehak Dangi
- Centre for Bioinformatics, M.D. University, Rohtak-124001, Haryana, India
| | - Alka Khichi
- Centre for Bioinformatics, M.D. University, Rohtak-124001, Haryana, India
| | - Ritu Jakhar
- Centre for Bioinformatics, M.D. University, Rohtak-124001, Haryana, India
| | - Anil K Chhillar
- Centre for Bioinformatics, M.D. University, Rohtak-124001, Haryana, India
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Wieczorek D, Kaczorowska E, Wiśniewska M, Madura ID, Leśniak M, Lipok J, Adamczyk-Woźniak A. Synthesis and Influence of 3-Amino Benzoxaboroles Structure on Their Activity against Candida albicans. Molecules 2020; 25:E5999. [PMID: 33352986 PMCID: PMC7766895 DOI: 10.3390/molecules25245999] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 11/16/2022] Open
Abstract
Benzoxaboroles emerged recently as molecules of high medicinal potential with Kerydin® (Tavaborole) and Eucrisa® (Crisaborole) currently in clinical practice as antifungal and anti-inflammatory drugs, respectively. Over a dozen of 3-amino benzoxaboroles, including Tavaborole's derivatives, have been synthetized and characterized in terms of their activity against Candida albicans as a model pathogenic fungus. The studied compounds broaden considerably the structural diversity of reported benzoxaboroles, enabling determination of the influence of the introduction of a heterocyclic amine, a fluorine substituent as well as the formyl group on antifungal activity of those compounds. The determined zones of the growth inhibition of examined microorganism indicate high diffusion of majority of the studied compounds within the applied media as well as their reasonable activity. The Minimum Inhibitory Concentration (MIC) values show that the introduction of an amine substituent in position "3" of the benzoxaborole heterocyclic ring results in a considerable drop in activity in comparison with Tavaborole (AN2690) as well as unsubstituted benzoxaborole (AN2679). In all studied cases the presence of a fluorine substituent at position para to the boron atom results in lower MIC values (higher activity). Interestingly, introduction of a fluorine substituent in the more distant piperazine phenyl ring does not influence MIC values. As determined by X-ray studies, introduction of a formyl group in proximity of the boron atom results in a considerable change of the boronic group geometry. The presence of a formyl group next to the benzoxaborole unit is also detrimental for activity against Candida albicans.
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Affiliation(s)
- Dorota Wieczorek
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland; (D.W.); (J.L.)
| | - Ewa Kaczorowska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (E.K.); (M.W.); (I.D.M.); (M.L.)
| | - Marta Wiśniewska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (E.K.); (M.W.); (I.D.M.); (M.L.)
| | - Izabela D. Madura
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (E.K.); (M.W.); (I.D.M.); (M.L.)
| | - Magdalena Leśniak
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (E.K.); (M.W.); (I.D.M.); (M.L.)
| | - Jacek Lipok
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland; (D.W.); (J.L.)
| | - Agnieszka Adamczyk-Woźniak
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (E.K.); (M.W.); (I.D.M.); (M.L.)
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15
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Discovery and Preclinical Development of Antigiardiasis Fumagillol Derivatives. Antimicrob Agents Chemother 2020; 64:AAC.00582-20. [PMID: 32778548 PMCID: PMC7508583 DOI: 10.1128/aac.00582-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/03/2020] [Indexed: 11/23/2022] Open
Abstract
Giardiasis, caused by the intestinal parasite Giardia lamblia, is a severe diarrheal disease, endemic in poverty-stricken regions of the world, and also a common infection in developed countries. The available therapeutic options are associated with adverse effects, and G. lamblia resistance to the standard-of-care drugs is spreading. Fumagillin, an antimicrosporidiosis drug, is a therapeutic agent with potential for the treatment of giardiasis. However, it exhibits considerable, albeit reversible, toxicity when used to treat immunocompromised microsporidiosis patients. Giardiasis, caused by the intestinal parasite Giardia lamblia, is a severe diarrheal disease, endemic in poverty-stricken regions of the world, and also a common infection in developed countries. The available therapeutic options are associated with adverse effects, and G. lamblia resistance to the standard-of-care drugs is spreading. Fumagillin, an antimicrosporidiosis drug, is a therapeutic agent with potential for the treatment of giardiasis. However, it exhibits considerable, albeit reversible, toxicity when used to treat immunocompromised microsporidiosis patients. Fumagillin is also a highly unstable compound. To address these liabilities, we designed and synthesized stable fumagillol derivatives with lower levels of permeation across polarized epithelial Caco-2 cells and better potency against G. lamblia trophozoites than fumagillin. Metronidazole-resistant G. lamblia strains were also susceptible to the new fumagillol derivatives. In addition, these compounds were more potent against the amebiasis-causing parasite Entamoeba histolytica than fumagillin. Two compounds exhibited better thermal and acid stability than fumagillin, which should prolong the drug shelf life and reduce compound degradation in the stomach. Studies with a mouse model of giardiasis with the most stable compound, 4-(((((3R,4S,5S,6R)-5-methoxy-4-((2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl)-1-oxaspiro[2.5]octan-6-yl)oxy)carbonyl)amino)benzoic acid (compound 9), revealed that it had better efficacy (effective dose [ED]) than fumagillin at both the fully curative dose (the 100% ED) of 6.6 mg/kg of body weight and a 50% ED of 0.064 mg/kg. Plasma pharmacokinetics revealed the slow absorption of compound 9 through the gut, consistent with the in vitro characterization in Caco-2 cells. An acute-dose study yielded a maximum tolerated dose (MTD) of 1,500 mg/kg, 227-fold higher than the fully curative dose. Thus, along with improved stability, compound 9 also exhibited an excellent therapeutic window.
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16
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Li B, Dai C, Wang L, Deng H, Li Y, Guan Z, Ni H. A novel drug repurposing approach for non-small cell lung cancer using deep learning. PLoS One 2020; 15:e0233112. [PMID: 32525938 PMCID: PMC7289363 DOI: 10.1371/journal.pone.0233112] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/28/2020] [Indexed: 01/02/2023] Open
Abstract
Drug repurposing is an attractive and pragmatic way offering reduced risks and development time in the complicated process of drug discovery. In the past, drug repurposing has been largely accidental and serendipitous. The most successful examples so far have not involved a systematic approach. Nowadays, remarkable advances in drugs, diseases and bioinformatic knowledge are offering great opportunities for designing novel drug repurposing approach through comprehensive understanding of drug information. In this study, we introduced a novel drug repurposing approach based on transcriptomic data and chemical structures using deep learning. One strong candidate for repurposing has been identified. Pimozide is an anti-dyskinesia agent that is used for the suppression of motor and phonic tics in patients with Tourette's Disorder. However, our pipeline proposed it as a strong candidate for treating non-small cell lung cancer. The cytotoxicity of pimozide against A549 cell lines has been validated.
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Affiliation(s)
- Bingrui Li
- Beijing Deep Intelligent Pharma Technologies Co., Ltd, Beijing, China
| | - Chan Dai
- Beijing Deep Intelligent Pharma Technologies Co., Ltd, Beijing, China
| | - Lijun Wang
- Beijing Deep Intelligent Pharma Technologies Co., Ltd, Beijing, China
| | - Hailong Deng
- Beijing Deep Intelligent Pharma Technologies Co., Ltd, Beijing, China
| | - Yingying Li
- Beijing Deep Intelligent Pharma Technologies Co., Ltd, Beijing, China
- * E-mail: (YL); (ZG); (HN)
| | - Zheng Guan
- Beijing Deep Intelligent Pharma Technologies Co., Ltd, Beijing, China
- * E-mail: (YL); (ZG); (HN)
| | - Haihong Ni
- Beijing Deep Intelligent Pharma Technologies Co., Ltd, Beijing, China
- * E-mail: (YL); (ZG); (HN)
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17
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Deep SAR matrix: SAR matrix expansion for advanced analog design using deep learning architectures. FUTURE DRUG DISCOVERY 2020. [DOI: 10.4155/fdd-2020-0005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aim: Enhancing the structure–activity relationship matrix (SARM) methodology through integration of deep learning and expansion of chemical space coverage. Background: Analog design is of critical importance for medicinal chemistry. The SARM approach, which combines systematic structural organization of compound series with analog design, is put into scientific context. Methodology: The new DeepSARM concept is introduced. The architecture of SARM-integrated deep generative models is detailed and the workflow for advanced analog design and matrix expansion described. Exemplary application: The DeepSARM approach is applied to design analogs of kinase inhibitors taking kinome-wide chemical space into account. Future perspective: Practical applications of DeepSARM will be a major focal point. Different applications are discussed. New computational features will be added to prioritize virtual candidate compounds.
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18
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Meanwell NA. Fluorine and Fluorinated Motifs in the Design and Application of Bioisosteres for Drug Design. J Med Chem 2018; 61:5822-5880. [PMID: 29400967 DOI: 10.1021/acs.jmedchem.7b01788] [Citation(s) in RCA: 1292] [Impact Index Per Article: 215.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The electronic properties and relatively small size of fluorine endow it with considerable versatility as a bioisostere and it has found application as a substitute for lone pairs of electrons, the hydrogen atom, and the methyl group while also acting as a functional mimetic of the carbonyl, carbinol, and nitrile moieties. In this context, fluorine substitution can influence the potency, conformation, metabolism, membrane permeability, and P-gp recognition of a molecule and temper inhibition of the hERG channel by basic amines. However, as a consequence of the unique properties of fluorine, it features prominently in the design of higher order structural metaphors that are more esoteric in their conception and which reflect a more sophisticated molecular construction that broadens biological mimesis. In this Perspective, applications of fluorine in the construction of bioisosteric elements designed to enhance the in vitro and in vivo properties of a molecule are summarized.
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Affiliation(s)
- Nicholas A Meanwell
- Discovery Chemistry and Molecular Technologies Bristol-Myers Squibb Research and Development P.O. Box 4000, Princeton , New Jersey 08543-4000 , United States
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19
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Ligand binding cooperativity: Bioisosteric replacement of CO with SO2 among thrombin inhibitors. Bioorg Med Chem Lett 2016; 26:3850-4. [DOI: 10.1016/j.bmcl.2016.07.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 01/22/2023]
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20
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Haslam B, Perez-Breva L. Learning disease relationships from clinical drug trials. J Am Med Inform Assoc 2016; 24:13-23. [PMID: 27189012 DOI: 10.1093/jamia/ocw003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 12/23/2015] [Accepted: 01/03/2016] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Our objective is to test the limits of the assumption that better learning from data in medicine requires more granular data. We hypothesize that clinical trial metadata contains latent scientific, clinical, and regulatory expert knowledge that can be accessed to draw conclusions about the underlying biology of diseases. We seek to demonstrate that this latent information can be uncovered from the whole body of clinical trials. MATERIALS AND METHODS We extract free-text metadata from 93 654 clinical drug trials and introduce a representation that allows us to compare different trials. We then construct a network of diseases using only the trial metadata. We view each trial as the summation of expert knowledge of biological mechanisms and medical evidence linking a disease to a drug believed to modulate the pathways of that disease. Our network representation allows us to visualize disease relationships based on this underlying information. RESULTS Our disease network shows surprising agreement with another disease network based on genetic data and on the Medical Subject Headings (MeSH) taxonomy, yet also contains unique disease similarities. DISCUSSION AND CONCLUSION The agreement of our results with other sources indicates that our premise regarding latent expert knowledge holds. The disease relationships unique to our network may be used to generate hypotheses for future biological and clinical research as well as drug repurposing and design. Our results provide an example of using experimental data on humans to generate biologically useful information and point to a set of new and promising strategies to link clinical outcomes data back to biological research.
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Affiliation(s)
- Bryan Haslam
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Luis Perez-Breva
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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21
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Wang Y, Zhang S, Breitbach ZS, Petersen H, Ellegaard P, Armstrong DW. Enantioseparation of citalopram analogues with sulfated β-cyclodextrin by capillary electrophoresis. Electrophoresis 2016; 37:841-8. [DOI: 10.1002/elps.201500541] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/22/2015] [Accepted: 12/22/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Yadi Wang
- Department of Chemistry and Biochemistry; University of Texas at Arlington; Arlington TX USA
| | - Shusheng Zhang
- Department of Chemistry and Biochemistry; University of Texas at Arlington; Arlington TX USA
- College of Chemistry & Molecular Engineering; Zhengzhou University; Zhengzhou P. R. China
| | - Zachary S. Breitbach
- Department of Chemistry and Biochemistry; University of Texas at Arlington; Arlington TX USA
| | - Hans Petersen
- H. Lundbeck A/S, Chemical Process Research; Valby Denmark
| | | | - Daniel W. Armstrong
- Department of Chemistry and Biochemistry; University of Texas at Arlington; Arlington TX USA
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22
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Baviskar AT, Amrutkar SM, Trivedi N, Chaudhary V, Nayak A, Guchhait SK, Banerjee UC, Bharatam PV, Kundu CN. Switch in Site of Inhibition: A Strategy for Structure-Based Discovery of Human Topoisomerase IIα Catalytic Inhibitors. ACS Med Chem Lett 2015; 6:481-5. [PMID: 25941559 DOI: 10.1021/acsmedchemlett.5b00040] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 02/23/2015] [Indexed: 11/29/2022] Open
Abstract
A study of structure-based modulation of known ligands of hTopoIIα, an important enzyme involved in DNA processes, coupled with synthesis and in vitro assays led to the establishment of a strategy of rational switch in mode of inhibition of the enzyme's catalytic cycle. 6-Arylated derivatives of known imidazopyridine ligands were found to be selective inhibitors of hTopoIIα, while not showing TopoI inhibition and DNA binding. Interestingly, while the parent imidazopyridines acted as ATP-competitive inhibitors, arylated derivatives inhibited DNA cleavage similar to merbarone, indicating a switch in mode of inhibition from ATP-hydrolysis to the DNA-cleavage stage of catalytic cycle of the enzyme. The 6-aryl-imidazopyridines were relatively more cytotoxic than etoposide in cancer cells and less toxic to normal cells. Such unprecedented strategy will encourage research on "choice-based change" in target-specific mode of action for rapid drug discovery.
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Affiliation(s)
| | | | | | | | - Anmada Nayak
- School
of Biotechnology, KIIT University, Campus-11, Patia, Bhubaneswar, Orissa 751024, India
| | | | | | | | - Chanakya N. Kundu
- School
of Biotechnology, KIIT University, Campus-11, Patia, Bhubaneswar, Orissa 751024, India
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23
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Abstract
![]()
The
pharmaceutical industry has significantly contributed to improving
human health. Drugs have been attributed to both increasing life expectancy
and decreasing health care costs. Unfortunately, there has been a
recent decline in the creativity and productivity of the pharmaceutical
industry. This is a complex issue with many contributing factors resulting
from the numerous mergers, increase in out-sourcing, and the heavy
dependency on high-throughput screening (HTS). While a simple solution
to such a complex problem is unrealistic and highly unlikely, the
inclusion of metabolomics as a routine component of the drug discovery
process may provide some solutions to these problems. Specifically,
as the binding affinity of a chemical lead is evolved during the iterative
structure-based drug design process, metabolomics can provide feedback
on the selectivity and the in vivo mechanism of action. Similarly,
metabolomics can be used to evaluate and validate HTS leads. In effect,
metabolomics can be used to eliminate compounds with potential efficacy
and side effect problems while prioritizing well-behaved leads with
druglike characteristics.
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Affiliation(s)
- Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln , 722 Hamilton Hall, Lincoln, Nebraska 68588-0304, United States
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24
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Xiao D, Zhu X, Yu Y, Shao N, Wu J, McCormick KD, Dhondi P, Qin J, Mazzola R, Tang H, Rao A, Siliphaivanh P, Qiu H, Yang X, Rivelli M, Garlisi CG, Eckel S, Mukhopadhyay G, Correll C, Rindgen D, Aslanian R, Palani A. Quality by design (QbD) of amide isosteres: 5,5-Disubstituted isoxazolines as potent CRTh2 antagonists with favorable pharmacokinetic and drug-like properties. Bioorg Med Chem Lett 2014; 24:1615-20. [PMID: 24556380 DOI: 10.1016/j.bmcl.2014.01.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/10/2014] [Accepted: 01/14/2014] [Indexed: 01/07/2023]
Abstract
Isoxazoles are frequently used amide isosteres, as shown in the context of discovery of CRTh2 antagonists from amide 1 to isoxazole 2. However, persistent agonism and poor solubility in isoxazole series presented challenges to its further development. Based on the concept of quality by design (QbD), 5,5-disubstituted isoxazolines 3 were introduced. The chirality at 5 position of isoxazolines controlled the switch between two modes of actions, which led to a novel series of pure antagonists. This non-planar motif also conferred a change of shape of these molecules, which avoided flat structures and improved their physical properties.
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Affiliation(s)
- Dong Xiao
- Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
| | - Xiaohong Zhu
- Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Younong Yu
- Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Ning Shao
- Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Jie Wu
- Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Kevin D McCormick
- Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Pawan Dhondi
- Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Jun Qin
- Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Robert Mazzola
- Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Haiqun Tang
- Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Ashwin Rao
- Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Phieng Siliphaivanh
- Discovery Chemistry, Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Hongchen Qiu
- In vitro Pharmacology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Xiaoxin Yang
- In vitro Pharmacology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Maria Rivelli
- In vitro Pharmacology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Charles G Garlisi
- In vitro Pharmacology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Steve Eckel
- Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Gitali Mukhopadhyay
- Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Craig Correll
- Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Diane Rindgen
- Pharmacokinetics, Pharmacodynamics & Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Robert Aslanian
- Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Anandan Palani
- Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
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25
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Meanwell NA. The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems. TACTICS IN CONTEMPORARY DRUG DESIGN 2014; 9. [PMCID: PMC7416817 DOI: 10.1007/7355_2013_29] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.
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26
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Physicochemical, Spectral, and Biological Studies of Mn(II), Cu(II), Cd(II), Zr(OH) 2(IV), and UO 2(VI) Compounds with Ligand Containing Thiazolidin-4-one Moiety. J CHEM-NY 2014. [DOI: 10.1155/2014/286136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The Schiff base (I) upon reacting with mercaptoacetic acid in dry benzene undergoes cyclization and forms N-(2-carbamoylthienyl)-C-(3′-carboxy-2′-hydroxyphenyl)thiazolidin-4-one, LH3(II). A MeOH solution ofIIreacts with Mn(II), Cu(II), Cd(II), Zr(OH)2(IV), and UO2(VI) ions and forms the coordination compounds, [Mn(LH)(MeOH)2], [Cu(LH)]2, [Cd(LH)], [Zr(OH)2(OAc)2(LH3)], and [UO2(NO3)(LH2)(MeOH)]. The compounds have been characterized on the basis of elemental analyses, molar conductance, molecular weight, spectral (IR, reflectance, and EPR) studies and magnetic susceptibility measurements. LH3behaves as a neutral tridentate ONS donor ligand in [Zr(OH)2(OAc)2(LH3)], monobasic tridentate ONS donor ligand in [UO2(NO3)(LH2)(MeOH)], dibasic tridentate OOS donor ligand in [Cu(LH)]2and dibasic tetradentate OONO donor ligand in [Mn(LH)(MeOH)2] and [Cd(LH)]. [Cu(LH)]2is dimer, while all other compounds are monomers in diphenyl. A square-planar structure for [Cu(LH)]2, a tetrahedral structure for [Cd(LH)], an octahedral structure for [Mn(LH)(MeOH)2], a pentagonal-bipyramidal structure for [Zr(OH)2(OAc)2(LH3)], and an eight-coordinate structure for [UO2(NO3)(LH2)(MeOH)] are proposed. The ligand (II) and its compounds show antibacterial activities towardsE. coli. (Gram negative) andS. aureus(Gram positive).
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27
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Buckle DR, Erhardt PW, Ganellin CR, Kobayashi T, Perun TJ, Proudfoot J, Senn-Bilfinger J. Glossary of terms used in medicinal chemistry. Part II (IUPAC Recommendations 2013). PURE APPL CHEM 2013. [DOI: 10.1351/pac-rec-12-11-23] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The evolution that has taken place in medicinal chemistry practice as a result of
major advances in genomics and molecular biology arising from the Human Genome
Project has carried with it an extensive additional working vocabulary that has
become both integrated and essential terminology for the medicinal chemist. Some
of this augmented terminology has been adopted from the many related and
interlocked scientific disciplines with which the modern medicinal chemist must
be conversant, but many other terms have been introduced to define new concepts
and ideas as they have arisen. In this supplementary Glossary, we have attempted
to collate and define many of the additional terms that are now considered to be
essential components of the medicinal chemist’s expanded repertoire.
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Affiliation(s)
- Derek R. Buckle
- 1DRB Associates, 18 Hillfield Road, Redhill, Surrey, RH1 4AP, UK
| | - Paul W. Erhardt
- 2University of Toledo, College of Pharmacy, Center for Drug Design and Development, 2801 West Bancroft Street, Toledo, OH 43606-3390, USA
| | - C. Robin Ganellin
- 3Department of Chemistry, Christopher Ingold Laboratory, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Toshi Kobayashi
- 4PhRMA, 4th Floor, Landic II Toranomon Building, 3-7-8 Minato-ku, 105-000 Japan
| | | | - John Proudfoot
- 6Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, CT 06877, USA
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28
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Watterson DM, Grum-Tokars VL, Roy SM, Schavocky JP, Bradaric BD, Bachstetter AD, Xing B, Dimayuga E, Saeed F, Zhang H, Staniszewski A, Pelletier JC, Minasov G, Anderson WF, Arancio O, Van Eldik LJ. Development of Novel In Vivo Chemical Probes to Address CNS Protein Kinase Involvement in Synaptic Dysfunction. PLoS One 2013; 8:e66226. [PMID: 23840427 PMCID: PMC3694096 DOI: 10.1371/journal.pone.0066226] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/02/2013] [Indexed: 12/23/2022] Open
Abstract
Serine-threonine protein kinases are critical to CNS function, yet there is a dearth of highly selective, CNS-active kinase inhibitors for in vivo investigations. Further, prevailing assumptions raise concerns about whether single kinase inhibitors can show in vivo efficacy for CNS pathologies, and debates over viable approaches to the development of safe and efficacious kinase inhibitors are unsettled. It is critical, therefore, that these scientific challenges be addressed in order to test hypotheses about protein kinases in neuropathology progression and the potential for in vivo modulation of their catalytic activity. Identification of molecular targets whose in vivo modulation can attenuate synaptic dysfunction would provide a foundation for future disease-modifying therapeutic development as well as insight into cellular mechanisms. Clinical and preclinical studies suggest a critical link between synaptic dysfunction in neurodegenerative disorders and the activation of p38αMAPK mediated signaling cascades. Activation in both neurons and glia also offers the unusual potential to generate enhanced responses through targeting a single kinase in two distinct cell types involved in pathology progression. However, target validation has been limited by lack of highly selective inhibitors amenable to in vivo use in the CNS. Therefore, we employed high-resolution co-crystallography and pharmacoinformatics to design and develop a novel synthetic, active site targeted, CNS-active, p38αMAPK inhibitor (MW108). Selectivity was demonstrated by large-scale kinome screens, functional GPCR agonist and antagonist analyses of off-target potential, and evaluation of cellular target engagement. In vitro and in vivo assays demonstrated that MW108 ameliorates beta-amyloid induced synaptic and cognitive dysfunction. A serendipitous discovery during co-crystallographic analyses revised prevailing models about active site targeting of inhibitors, providing insights that will facilitate future kinase inhibitor design. Overall, our studies deliver highly selective in vivo probes appropriate for CNS investigations and demonstrate that modulation of p38αMAPK activity can attenuate synaptic dysfunction.
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Affiliation(s)
- D. Martin Watterson
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
- * E-mail:
| | - Valerie L. Grum-Tokars
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
| | - Saktimayee M. Roy
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
| | - James P. Schavocky
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
| | - Brinda Desai Bradaric
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
| | - Adam D. Bachstetter
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - Bin Xing
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - Edgardo Dimayuga
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - Faisal Saeed
- Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
| | - Hong Zhang
- Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
| | - Agnieszka Staniszewski
- Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
| | - Jeffrey C. Pelletier
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
| | - George Minasov
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
| | - Wayne F. Anderson
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, United States of America
| | - Ottavio Arancio
- Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
| | - Linda J. Van Eldik
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
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Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments. J Mol Graph Model 2013; 41:20-30. [DOI: 10.1016/j.jmgm.2013.01.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 01/11/2013] [Accepted: 01/16/2013] [Indexed: 01/15/2023]
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Synthesis of a new series of 2-(2-oxo-2H-chromen-3-yl)-5H-chromeno[4,3-b]pyridin-5-ones by two facile methods and evaluation of their antimicrobial activity. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0489-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Emery AC. Catecholamine receptors: prototypes for GPCR-based drug discovery. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2013; 68:335-56. [PMID: 24054152 DOI: 10.1016/b978-0-12-411512-5.00016-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Drugs acting at G protein-coupled receptors (GPCRs) constitute ~40% of those in current clinical use. GPCR-based drug discovery remains at the forefront of drug development, especially for new treatments for psychiatric illness and neurological disease. Here, the basic framework of GPCR signaling learned through the elucidation of catecholamine receptor signaling through G proteins and β-arrestins, and X-ray crystallographic structure determination is reviewed. In silico docking studies developed in tandem with confirmatory empirical data gathering from binding and signaling experiments have allowed this basic framework to be expanded to drug hunting through predictive in silico searching as well as high-throughput and high-content screening approaches. For efforts moving forward for the deployment of new GPCR-acting drugs, collaborative efforts between industry and government/academic research in target validation at the molecular and cellular levels have become progressively more common. Polypharmacological approaches have become increasingly available for learning more about the mechanisms of GPCR-targeted drugs, based on interaction not with a single, but with a wide range of GPCR targets. These approaches are likely to aid in drug repurposing efforts, yield valuable insight on the side effects of currently employed drugs, and allow for a clearer picture of the actual targets of "atypical" drugs used in a variety of therapeutic contexts.
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Affiliation(s)
- Andrew C Emery
- Section on Molecular Neuroscience, Laboratory of Cellular and Molecular Regulation, National Institute of Mental Health Intramural Research Program, Bethesda, Maryland, USA.
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Awale M, Reymond JL. Cluster analysis of the DrugBank chemical space using molecular quantum numbers. Bioorg Med Chem 2012; 20:5372-8. [DOI: 10.1016/j.bmc.2012.03.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/01/2012] [Accepted: 03/05/2012] [Indexed: 11/15/2022]
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Behbehani H, Ibrahim HM. 4-Thiazolidinones in heterocyclic synthesis: synthesis of novel enaminones, azolopyrimidines and 2-arylimino-5-arylidene-4-thiazolidinones. Molecules 2012; 17:6362-85. [PMID: 22634845 PMCID: PMC6268424 DOI: 10.3390/molecules17066362] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 05/18/2012] [Accepted: 05/22/2012] [Indexed: 12/05/2022] Open
Abstract
The 4-thiazolidinones 3a–d were used as a key intermediates for the synthesis of 2-arylimino-5-arylidene-4-thiazolidinones derivatives 7a–pvia nucleophilic addition reactions with the arylidene malononitrile. Moreover the 4-thiazolidinones 3a and 3c condensed with the DMF-DMA to form the corresponding enamines 8 and 9 depending on the reaction conditions. Otherwise the 4-thiazolidinone 3b reacts regioselectively with DMF-DMA to afford the enaminones 10 and 11, respectively. The latter reacts with many heterocyclic amines affording polyfunctionally substituted fused pyrimidine derivatives 13–18. The enamine 8b was also reacted with the 3-amino-1,2,4-triazole to afford the acyclic product 19, which could not be further cyclized to the corresponding tricyclic system 20. Moreover the 4-thiazolidinone 3c reacted with the benzenediazonium chloride to afford the arylhydrazones 12. The X-ray single crystal technique was employed in this study for structure elucidation and Z/E potential isomerism configuration determination. The X-ray crystallographic analyses of eight products could be obtained, thus establishing with certainty the structures proposed in this work.
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Affiliation(s)
- Haider Behbehani
- Chemistry Department, Faculty of Science, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +965-990-630-62; Fax: +965-248-164-82
| | - Hamada Mohamed Ibrahim
- Chemistry Department, Faculty of Science, Fayoum University, Fayoum 63514, A. R., Egypt; E-Mail:
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Bréthous L, Garcia-Delgado N, Schwartz J, Bertrand S, Bertrand D, Reymond JL. Synthesis and Nicotinic Receptor Activity of Chemical Space Analogues of N-(3R)-1-Azabicyclo[2.2.2]oct-3-yl-4-chlorobenzamide (PNU-282,987) and 1,4-Diazabicyclo[3.2.2]nonane-4-carboxylic Acid 4-Bromophenyl Ester (SSR180711). J Med Chem 2012; 55:4605-18. [DOI: 10.1021/jm300030r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lise Bréthous
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Noemi Garcia-Delgado
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Julian Schwartz
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Sonia Bertrand
- HiQScreen, 15 rue de l'Athénée, 1206 Geneva, Switzerland
| | | | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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Duffy BC, Zhu L, Decornez H, Kitchen DB. Early phase drug discovery: cheminformatics and computational techniques in identifying lead series. Bioorg Med Chem 2012; 20:5324-42. [PMID: 22938785 DOI: 10.1016/j.bmc.2012.04.062] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 04/24/2012] [Accepted: 04/27/2012] [Indexed: 01/31/2023]
Abstract
Early drug discovery processes rely on hit finding procedures followed by extensive experimental confirmation in order to select high priority hit series which then undergo further scrutiny in hit-to-lead studies. The experimental cost and the risk associated with poor selection of lead series can be greatly reduced by the use of many different computational and cheminformatic techniques to sort and prioritize compounds. We describe the steps in typical hit identification and hit-to-lead programs and then describe how cheminformatic analysis assists this process. In particular, scaffold analysis, clustering and property calculations assist in the design of high-throughput screening libraries, the early analysis of hits and then organizing compounds into series for their progression from hits to leads. Additionally, these computational tools can be used in virtual screening to design hit-finding libraries and as procedures to help with early SAR exploration.
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Affiliation(s)
- Bryan C Duffy
- AMRI, 26 Corporate Circle, PO Box 15098, Albany, NY 12212-5098, USA
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Meanwell NA. Synopsis of Some Recent Tactical Application of Bioisosteres in Drug Design. J Med Chem 2011; 54:2529-91. [DOI: 10.1021/jm1013693] [Citation(s) in RCA: 1876] [Impact Index Per Article: 144.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicholas A. Meanwell
- Department of Medicinal Chemistry, Bristol-Myers Squibb Pharmaceutical Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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Abstract
This chapter provides a brief overview of chemoinformatics and its applications to chemical library design. It is meant to be a quick starter and to serve as an invitation to readers for more in-depth exploration of the field. The topics covered in this chapter are chemical representation, chemical data and data mining, molecular descriptors, chemical space and dimension reduction, quantitative structure-activity relationship, similarity, diversity, and multiobjective optimization.
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Cao L, Sui J, Kong D, Li Z, Lin H. Generic Immunoassay of Quinolones: Production and Characterization of Anti-pefloxacin Antibodies as Broad Selective Receptors. FOOD ANAL METHOD 2011. [DOI: 10.1007/s12161-011-9196-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Garcia-Delgado N, Bertrand S, Nguyen KT, van Deursen R, Bertrand D, Reymond JL. Exploring α7-Nicotinic Receptor Ligand Diversity by Scaffold Enumeration from the Chemical Universe Database GDB. ACS Med Chem Lett 2010; 1:422-6. [PMID: 24900227 DOI: 10.1021/ml100125f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 07/13/2010] [Indexed: 02/08/2023] Open
Abstract
Virtual analogues (1167860 compounds) of the nicotinic α7-receptor (α7 nAChR) ligands PNU-282,987 and SSR180711 were generated from the chemical universe database GDB-11 by extracting all aliphatic diamine analogues of the aminoquinuclidine and 1,4-diazabicyclo[3.2.2]nonane scaffolds of these ligands and converting them to the corresponding aryl amides using five different aromatic acyl groups. The library was ranked by docking to the nicotinic binding site of the acetylcholine binding protein (AChBP, 1UW6.pdb) using Autodock and Glide. Thirty-eight ligands derived from the best docking hits were synthesized and tested for modulation of the acetylcholine signal at the human α7 nAChR receptor expressed in Xenopus oocytes, leading to competitive and noncompetitive antagonists with IC50 = 5-7 μM. These experiments demonstrate the first example of using GDB in a fragment-based approach by diversifying the scaffold of known drugs.
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Affiliation(s)
- Noemi Garcia-Delgado
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Sonia Bertrand
- Department of Neuroscience, Medical Faculty, 1, rue Michel Servet CH-1211 Geneva 4, Switzerland
| | - Kong T. Nguyen
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Ruud van Deursen
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Daniel Bertrand
- Department of Neuroscience, Medical Faculty, 1, rue Michel Servet CH-1211 Geneva 4, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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40
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De Franchi E, Schalon C, Messa M, Onofri F, Benfenati F, Rognan D. Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements. PLoS One 2010; 5:e12214. [PMID: 20808948 PMCID: PMC2922380 DOI: 10.1371/journal.pone.0012214] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 07/26/2010] [Indexed: 11/18/2022] Open
Abstract
Predicting off-targets by computational methods is getting increasing importance in early drug discovery stages. We herewith present a computational method based on binding site three-dimensional comparisons, which prompted us to investigate the cross-reaction of protein kinase inhibitors with synapsin I, an ATP-binding protein regulating neurotransmitter release in the synapse. Systematic pair-wise comparison of the staurosporine-binding site of the proto-oncogene Pim-1 kinase with 6,412 druggable protein-ligand binding sites suggested that the ATP-binding site of synapsin I may recognize the pan-kinase inhibitor staurosporine. Biochemical validation of this hypothesis was realized by competition experiments of staurosporine with ATP-gamma(35)S for binding to synapsin I. Staurosporine, as well as three other inhibitors of protein kinases (cdk2, Pim-1 and casein kinase type 2), effectively bound to synapsin I with nanomolar affinities and promoted synapsin-induced F-actin bundling. The selective Pim-1 kinase inhibitor quercetagetin was shown to be the most potent synapsin I binder (IC50 = 0.15 microM), in agreement with the predicted binding site similarities between synapsin I and various protein kinases. Other protein kinase inhibitors (protein kinase A and chk1 inhibitor), kinase inhibitors (diacylglycerolkinase inhibitor) and various other ATP-competitors (DNA topoisomerase II and HSP-90alpha inhibitors) did not bind to synapsin I, as predicted from a lower similarity of their respective ATP-binding sites to that of synapsin I. The present data suggest that the observed downregulation of neurotransmitter release by some but not all protein kinase inhibitors may also be contributed by a direct binding to synapsin I and phosphorylation-independent perturbation of synapsin I function. More generally, the data also demonstrate that cross-reactivity with various targets may be detected by systematic pair-wise similarity measurement of ligand-annotated binding sites.
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Affiliation(s)
- Enrico De Franchi
- Department of Neuroscience and Brain Technologies, The Italian Institute of Technology, Genova, Italy
| | - Claire Schalon
- Structural Chemogenomics, Laboratory of Therapeutic Innovation, CNRS UMR 7200, Université de Strasbourg, Illkirch, France
| | - Mirko Messa
- Department of Neuroscience and Brain Technologies, The Italian Institute of Technology, Genova, Italy
| | - Franco Onofri
- Department of Experimental Medicine, University of Genova and Istituto Nazionale di Neuroscienze, Genova, Italy
| | - Fabio Benfenati
- Department of Neuroscience and Brain Technologies, The Italian Institute of Technology, Genova, Italy
- Department of Experimental Medicine, University of Genova and Istituto Nazionale di Neuroscienze, Genova, Italy
| | - Didier Rognan
- Structural Chemogenomics, Laboratory of Therapeutic Innovation, CNRS UMR 7200, Université de Strasbourg, Illkirch, France
- * E-mail:
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41
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Rando DG, Giarolla J, Pasqualoto KFM, Ferreira EI. Chalcones and N-acylhydrazones: direct analogues? Exploratory data analysis applied to potential novel antileishmanial agents. BRAZ J PHARM SCI 2010. [DOI: 10.1590/s1984-82502010000200019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Leishmaniasis is an important health and social problem for which there is limited effective therapy. Chalcones and N-acylhydrazones have been studied as promising antileishmanial agents in enzymatic inhibition and in vitro assays. Since these chemical classes of compounds also resemble each other structurally, it would be useful to investigate whether they share direct analogy. Exploratory data analysis was applied to a library of chalcones and nitrated N-acylhydrazones assayed against Leishmania donovani to investigate their similarity. Under the conditions applied in the present study, the two classes did not present functional or structural analogy.
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42
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Omar K, Geronikaki A, Zoumpoulakis P, Camoutsis C, Soković M, Cirić A, Glamoclija J. Novel 4-thiazolidinone derivatives as potential antifungal and antibacterial drugs. Bioorg Med Chem 2010; 18:426-32. [PMID: 19914077 DOI: 10.1016/j.bmc.2009.10.041] [Citation(s) in RCA: 202] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 10/23/2009] [Indexed: 11/16/2022]
Affiliation(s)
- Kouatli Omar
- Department of Pharmaceutical Chemistry of Aristotle, School of Pharmacy, University of Thessaloniki, Thessaloniki, Greece
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43
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Vijayan RSK, Bera I, Prabu M, Saha S, Ghoshal N. Combinatorial Library Enumeration and Lead Hopping using Comparative Interaction Fingerprint Analysis and Classical 2D QSAR Methods for Seeking Novel GABAA α3 Modulators. J Chem Inf Model 2009; 49:2498-511. [PMID: 19891421 DOI: 10.1021/ci900309s] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. S. K. Vijayan
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (a unit of CSIR), 4, Raja S.C. Mullick Road, Kolkata-700 032, West Bengal, India and Department of Bioinformatics, West Bengal University of Technology, BF - 142 Salt Lake, Kolkata-700 064
| | - Indrani Bera
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (a unit of CSIR), 4, Raja S.C. Mullick Road, Kolkata-700 032, West Bengal, India and Department of Bioinformatics, West Bengal University of Technology, BF - 142 Salt Lake, Kolkata-700 064
| | - M. Prabu
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (a unit of CSIR), 4, Raja S.C. Mullick Road, Kolkata-700 032, West Bengal, India and Department of Bioinformatics, West Bengal University of Technology, BF - 142 Salt Lake, Kolkata-700 064
| | - Sangita Saha
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (a unit of CSIR), 4, Raja S.C. Mullick Road, Kolkata-700 032, West Bengal, India and Department of Bioinformatics, West Bengal University of Technology, BF - 142 Salt Lake, Kolkata-700 064
| | - Nanda Ghoshal
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (a unit of CSIR), 4, Raja S.C. Mullick Road, Kolkata-700 032, West Bengal, India and Department of Bioinformatics, West Bengal University of Technology, BF - 142 Salt Lake, Kolkata-700 064
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Abstract
BACKGROUND: Drug discovery is a complex and unpredictable endeavor with a high failure rate. Current trends in the pharmaceutical industry have exasperated these challenges and are contributing to the dramatic decline in productivity observed over the last decade. The industrialization of science by forcing the drug discovery process to adhere to assembly-line protocols is imposing unnecessary restrictions, such as short project time-lines. Recent advances in nuclear magnetic resonance are responding to these self-imposed limitations and are providing opportunities to increase the success rate of drug discovery. OBJECTIVE/METHOD: A review of recent advancements in NMR technology that have the potential of significantly impacting and benefiting the drug discovery process will be presented. These include fast NMR data collection protocols and high-throughput protein structure determination, rapid protein-ligand co-structure determination, lead discovery using fragment-based NMR affinity screens, NMR metabolomics to monitor in vivo efficacy and toxicity for lead compounds, and the identification of new therapeutic targets through the functional annotation of proteins by FAST-NMR. CONCLUSION: NMR is a critical component of the drug discovery process, where the versatility of the technique enables it to continually expand and evolve its role. NMR is expected to maintain this growth over the next decade with advancements in automation, speed of structure calculation, in-cell imaging techniques, and the expansion of NMR amenable targets.
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Affiliation(s)
- Robert Powers
- Department of Chemistry, University of Nebraska Lincoln, Lincoln, NE 68588
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45
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Triggle DJ. The chemist as astronaut: Searching for biologically useful space in the chemical universe. Biochem Pharmacol 2009; 78:217-23. [DOI: 10.1016/j.bcp.2009.02.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 02/19/2009] [Accepted: 02/19/2009] [Indexed: 12/21/2022]
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Cao L, Kong D, Sui J, Jiang T, Li Z, Ma L, Lin H. Broad-specific antibodies for a generic immunoassay of quinolone: development of a molecular model for selection of haptens based on molecular field-overlapping. Anal Chem 2009; 81:3246-51. [PMID: 19338269 DOI: 10.1021/ac802403a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new molecular model for quinolone haptens was developed based on molecular field-overlapping. The quanlitive modeling of 3-D conformations showed that the conformation difference among quinolones is caused mainly by the different substitutes at the 1 and 7 positions. The 8-substitute also showed some effect by its inter-reaction with the 1-substitute. The conformational similarity of 27 quinolones to each other was for the first time calculated and exploited for a selection of haptens according to desired broad specificity of corresponding antibodies. The developed model was preliminarily validated with antibodies against different quinolones. A significant positive correlation (R = 0.7793) was observed between calculated overlapping coefficients of haptens and the cross-reactivity of corresponding polyclonal antibodies (Pabs), which confirmed the overall accuracy of the developed model and its application in quantitative structure-activity relationship analysis. On the basis of molecular modeling results, the strategy for the production of broad specific antibodies against quinolones was suggested and the potentiality of several candidates was predicted.
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Affiliation(s)
- Limin Cao
- Food Safety Laboratory, Ocean University of China, Qingdao, 266003, PR China
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47
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Medicinal chemistry strategies in follow-on drug discovery. Drug Discov Today 2009; 14:516-22. [DOI: 10.1016/j.drudis.2009.02.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 02/17/2009] [Accepted: 02/23/2009] [Indexed: 11/22/2022]
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Márquez-Navarro A, Nogueda-Torres B, Hernández-Campos A, Soria-Arteche O, Castillo R, Rodríguez-Morales S, Yépez-Mulia L, Hernández-Luis F. Anthelmintic activity of benzimidazole derivatives against Toxocara canis second-stage larvae and Hymenolepis nana adults. Acta Trop 2009; 109:232-5. [PMID: 19073130 DOI: 10.1016/j.actatropica.2008.11.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 11/18/2008] [Accepted: 11/18/2008] [Indexed: 10/21/2022]
Abstract
The anthelmintic activity of 11 benzimidazole derivatives (A1-A11) and 2 thioureides N,N'-disubstituted (B1-B2) was determined. Each compound and albendazole was tested in vitro against Toxocara canis larvae and in vivo against Hymenolepis nana adult. Compounds A1-A6 and B1-B2 were designed as albendazole prodrugs. Compounds A8-A11 were designed as direct analogues of A7, which had previously proved to be an effective agent against Fasciola hepatica. Results of the in vitro screening showed that A6 was more active than albendazole at 0.18 microM (relative mobility 40% and 80%, respectively). Whereas that the in vivo evaluation against H. nana, compounds A7-A11 demonstrated significant activity in terms of removing cestode adults in the range of 88-97%, displaying better efficacy than albendazole (83%).
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Munoz L, Ranaivo HR, Roy SM, Hu W, Craft JM, McNamara LK, Chico LW, Van Eldik LJ, Watterson DM. A novel p38 alpha MAPK inhibitor suppresses brain proinflammatory cytokine up-regulation and attenuates synaptic dysfunction and behavioral deficits in an Alzheimer's disease mouse model. J Neuroinflammation 2007; 4:21. [PMID: 17784957 PMCID: PMC2014744 DOI: 10.1186/1742-2094-4-21] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Accepted: 09/04/2007] [Indexed: 11/22/2022] Open
Abstract
Background An accumulating body of evidence is consistent with the hypothesis that excessive or prolonged increases in proinflammatory cytokine production by activated glia is a contributor to the progression of pathophysiology that is causally linked to synaptic dysfunction and hippocampal behavior deficits in neurodegenerative diseases such as Alzheimer's disease (AD). This raises the opportunity for the development of new classes of potentially disease-modifying therapeutics. A logical candidate CNS target is p38α MAPK, a well-established drug discovery molecular target for altering proinflammatory cytokine cascades in peripheral tissue disorders. Activated p38 MAPK is seen in human AD brain tissue and in AD-relevant animal models, and cell culture studies strongly implicate p38 MAPK in the increased production of proinflammatory cytokines by glia activated with human amyloid-beta (Aβ) and other disease-relevant stressors. However, the vast majority of small molecule drugs do not have sufficient penetrance of the blood-brain barrier to allow their use as in vivo research tools or as therapeutics for neurodegenerative disorders. The goal of this study was to test the hypothesis that brain p38α MAPK is a potential in vivo target for orally bioavailable, small molecules capable of suppressing excessive cytokine production by activated glia back towards homeostasis, allowing an improvement in neurologic outcomes. Methods A novel synthetic small molecule based on a molecular scaffold used previously was designed, synthesized, and subjected to analyses to demonstrate its potential in vivo bioavailability, metabolic stability, safety and brain uptake. Testing for in vivo efficacy used an AD-relevant mouse model. Results A novel, CNS-penetrant, non-toxic, orally bioavailable, small molecule inhibitor of p38α MAPK (MW01-2-069A-SRM) was developed. Oral administration of the compound at a low dose (2.5 mg/kg) resulted in attenuation of excessive proinflammatory cytokine production in the hippocampus back towards normal in the animal model. Animals with attenuated cytokine production had reductions in synaptic dysfunction and hippocampus-dependent behavioral deficits. Conclusion The p38α MAPK pathway is quantitatively important in the Aβ-induced production of proinflammatory cytokines in hippocampus, and brain p38α MAPK is a viable molecular target for future development of potential disease-modifying therapeutics in AD and related neurodegenerative disorders.
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Affiliation(s)
- Lenka Munoz
- Center for Drug Discovery and Chemical Biology, Northwestern University, 303 E Chicago Ave, Mailcode W896, Chicago, IL 60611, USA
- Faculty of Pharmacy A15, University of Sydney, NSW2006, Sydney, Australia
| | - Hantamalala Ralay Ranaivo
- Center for Drug Discovery and Chemical Biology, Northwestern University, 303 E Chicago Ave, Mailcode W896, Chicago, IL 60611, USA
| | - Saktimayee M Roy
- Center for Drug Discovery and Chemical Biology, Northwestern University, 303 E Chicago Ave, Mailcode W896, Chicago, IL 60611, USA
| | - Wenhui Hu
- Center for Drug Discovery and Chemical Biology, Northwestern University, 303 E Chicago Ave, Mailcode W896, Chicago, IL 60611, USA
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Science Park, 510663, Guangzhou, China
| | - Jeffrey M Craft
- Center for Drug Discovery and Chemical Biology, Northwestern University, 303 E Chicago Ave, Mailcode W896, Chicago, IL 60611, USA
- Barnes-Jewish Hospital, Washington University in St Louis, St Louis, MO 63110, USA
| | - Laurie K McNamara
- Center for Drug Discovery and Chemical Biology, Northwestern University, 303 E Chicago Ave, Mailcode W896, Chicago, IL 60611, USA
| | - Laura Wing Chico
- Center for Drug Discovery and Chemical Biology, Northwestern University, 303 E Chicago Ave, Mailcode W896, Chicago, IL 60611, USA
| | - Linda J Van Eldik
- Center for Drug Discovery and Chemical Biology, Northwestern University, 303 E Chicago Ave, Mailcode W896, Chicago, IL 60611, USA
| | - D Martin Watterson
- Center for Drug Discovery and Chemical Biology, Northwestern University, 303 E Chicago Ave, Mailcode W896, Chicago, IL 60611, USA
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Geldenhuys WJ, Van der Schyf CJ. Triquinane-based compounds as possible serotonin 5-HT6 receptor antagonists for the treatment of Alzheimer’s disease. Med Hypotheses 2007; 68:81-6. [PMID: 16962723 DOI: 10.1016/j.mehy.2006.06.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Accepted: 06/21/2006] [Indexed: 11/28/2022]
Abstract
The recently discovered serotonin 5-HT(6) receptor is a novel target for the treatment of cognitive decline associated with neurodegenerative diseases such as Alzheimer's disease (AD). Several studies have shown that antagonism of this receptor leads to improved learning and memory. Two serotonin 5-HT(6) receptor antagonists are currently in Phase II clinical trials for cognitive enhancement. Striking structural similarities between the polycyclic features of some 5-HT(6) antagonists and those of the cis-syn-cis triquinane ring system led us to propose that triquinane-derived compounds may represent a novel class of 5-HT(6) receptor antagonists. Using computational methodologies, we propose a structure with features that may impart potent 5-HT(6) receptor antagonistic activities to the triquinane ring complex. Related compounds, once synthesized, may have possible utility in the treatment of cognitive decline associated with AD.
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Affiliation(s)
- Werner J Geldenhuys
- Texas Tech University Health Sciences Center, School of Pharmacy, 1300 Coulter Drive, Amarillo, TX 79106, USA
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