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Kesharwani S, Eeba, Tandi M, Agarwal N, Sundriyal S. Design and synthesis of non-hydroxamate lipophilic inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR): in silico, in vitro and antibacterial studies. RSC Adv 2024; 14:27530-27554. [PMID: 39221132 PMCID: PMC11362829 DOI: 10.1039/d4ra05083e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
1-Deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) is a key enzyme of the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway operating in several pathogens, including Mycobacterium and Plasmodium. Since a DXR homologue is not present in humans, it is an important antimicrobial target. Fosmidomycin (FSM) and its analogues inhibit DXR function by chelating the divalent metal (Mn2+ or Mg2+) in its active site via a hydroxamate metal binding group (MBG). The latter, however, enhances the polarity of molecules and is known to display metabolic instability and toxicity issues. While attempts have been made to increase the lipophilicity of FSM by substituting the linker chain and prodrug approach, very few efforts have been made to replace the hydroxamate group with other lipophilic MBGs. We report a systematic in silico and experimental investigation to identify novel MBGs for designing non-hydroxamate lipophilic DXR inhibitors. The SAR studies with selected MBG fragments identified novel inhibitors of E. Coli DXR with IC50 values ranging from 0.29 to 106 μM. The promising inhibitors were also screened against ESKAPE pathogens and M. tuberculosis.
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Affiliation(s)
- Sharyu Kesharwani
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani (BITS) Pilani Campus, Vidya Vihar, Pilani Rajasthan 333 031 India
| | - Eeba
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Mile Stone, Gurugram-Faridabad Expressway Faridabad 121001 Haryana India
| | - Mukesh Tandi
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani (BITS) Pilani Campus, Vidya Vihar, Pilani Rajasthan 333 031 India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Mile Stone, Gurugram-Faridabad Expressway Faridabad 121001 Haryana India
| | - Sandeep Sundriyal
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani (BITS) Pilani Campus, Vidya Vihar, Pilani Rajasthan 333 031 India
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2
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Rossi S, Tudino V, Carullo G, Butini S, Campiani G, Gemma S. Metalloenzyme Inhibitors against Zoonotic Infections: Focus on Leishmania and Schistosoma. ACS Infect Dis 2024; 10:1520-1535. [PMID: 38669567 DOI: 10.1021/acsinfecdis.4c00163] [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] [Indexed: 04/28/2024]
Abstract
The term "zoonosis" denotes diseases transmissible among vertebrate animals and humans. These diseases constitute a significant public health challenge, comprising 61% of human pathogens and causing an estimated 2.7 million deaths annually. Zoonoses not only affect human health but also impact animal welfare and economic stability, particularly in low- and middle-income nations. Leishmaniasis and schistosomiasis are two important neglected tropical diseases with a high prevalence in tropical and subtropical areas, imposing significant burdens on affected regions. Schistosomiasis, particularly rampant in sub-Saharan Africa, lacks alternative treatments to praziquantel, prompting concerns regarding parasite resistance. Similarly, leishmaniasis poses challenges with unsatisfactory treatments, urging the development of novel therapeutic strategies. Effective prevention demands a One Health approach, integrating diverse disciplines to enhance diagnostics and develop safer drugs. Metalloenzymes, involved in parasite biology and critical in different biological pathways, emerged in the last few years as useful drug targets for the treatment of human diseases. Herein we have reviewed recent reports on the discovery of inhibitors of metalloenzymes associated with zoonotic diseases like histone deacetylases (HDACs), carbonic anhydrase (CA), arginase, and heme-dependent enzymes.
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Affiliation(s)
- Sara Rossi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Valeria Tudino
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Gabriele Carullo
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-7346, Iran
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
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Schneider NO, Gilreath K, Burkett DJ, St. Maurice M, Donaldson WA. Synthesis and Evaluation of 5-(Heteroarylmethylene)hydantoins as Glycogen Synthase Kinase-3β Inhibitors. Pharmaceuticals (Basel) 2024; 17:570. [PMID: 38794140 PMCID: PMC11123921 DOI: 10.3390/ph17050570] [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: 03/13/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Glycogen synthase kinase-3 (GSK-3) is a serine/threonine kinase which plays a center role in the phosphorylation of a wide variety of proteins, generally leading to their inactivation. As such, GSK-3 is viewed as a therapeutic target. An ever-increasing number of small organic molecule inhibitors of GSK-3 have been reported. Phenylmethylene hydantoins are known to exhibit a wide range of inhibitory activities including for GSK-3β. A family of fourteen 2-heterocycle substituted methylene hydantoins (14, 17-29) were prepared and evaluated for the inhibition of GSK-3β at 25 μM. The IC50 values of five of these compounds was determined; the two best inhibitors are 5-[(4'-chloro-2-pyridinyl)methylene]hydantoin (IC50 = 2.14 ± 0.18 μM) and 5-[(6'-bromo-2-pyridinyl)methylene]hydantoin (IC50 = 3.39 ± 0.16 μM). The computational docking of the compounds with GSK-3β (pdb 1q41) revealed poses with hydrogen bonding to the backbone at Val135. The 5-[(heteroaryl)methylene]hydantoins did not strongly inhibit other metalloenzymes, demonstrating poor inhibitory activity against matrix metalloproteinase-12 at 25 μM and against human carbonic anhydrase at 200 μM, and were not inhibitors for Staphylococcus aureus pyruvate carboxylase at concentrations >1000 μM.
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Affiliation(s)
- Nicholas O. Schneider
- Department of Biological Sciences, Marquette University, P.O. Box 1881, Milwaukee, WI 53201, USA
| | - Kendra Gilreath
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201, USA
| | - Daniel J. Burkett
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201, USA
| | - Martin St. Maurice
- Department of Biological Sciences, Marquette University, P.O. Box 1881, Milwaukee, WI 53201, USA
| | - William A. Donaldson
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201, USA
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4
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Gising J, Honarnejad S, Bras M, Baillie GL, McElroy SP, Jones PS, Morrison A, Beveridge J, Hallberg M, Larhed M. The Discovery of New Inhibitors of Insulin-Regulated Aminopeptidase by a High-Throughput Screening of 400,000 Drug-like Compounds. Int J Mol Sci 2024; 25:4084. [PMID: 38612894 PMCID: PMC11012289 DOI: 10.3390/ijms25074084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/25/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
With the ambition to identify novel chemical starting points that can be further optimized into small drug-like inhibitors of insulin-regulated aminopeptidase (IRAP) and serve as potential future cognitive enhancers in the clinic, we conducted an ultra-high-throughput screening campaign of a chemically diverse compound library of approximately 400,000 drug-like small molecules. Three biochemical and one biophysical assays were developed to enable large-scale screening and hit triaging. The screening funnel, designed to be compatible with high-density microplates, was established with two enzyme inhibition assays employing either fluorescent or absorbance readouts. As IRAP is a zinc-dependent enzyme, the remaining active compounds were further evaluated in the primary assay, albeit with the addition of zinc ions. Rescreening with zinc confirmed the inhibitory activity for most compounds, emphasizing a zinc-independent mechanism of action. Additionally, target engagement was confirmed using a complementary biophysical thermal shift assay where compounds causing positive/negative thermal shifts were considered genuine binders. Triaging based on biochemical activity, target engagement, and drug-likeness resulted in the selection of 50 qualified hits, of which the IC50 of 32 compounds was below 3.5 µM. Despite hydroxamic acid dominance, diverse chemotypes with biochemical activity and target engagement were discovered, including non-hydroxamic acid compounds. The most potent compound (QHL1) was resynthesized with a confirmed inhibitory IC50 of 320 nM. Amongst these compounds, 20 new compound structure classes were identified, providing many new starting points for the development of unique IRAP inhibitors. Detailed characterization and optimization of lead compounds, considering both hydroxamic acids and other diverse structures, are in progress for further exploration.
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Affiliation(s)
- Johan Gising
- The Beijer Laboratory, Science for Life Laboratory, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden; (J.B.); (M.L.)
| | - Saman Honarnejad
- Pivot Park Screening Centre, Kloosterstraat 9, 5349 AB Oss, The Netherlands; (S.H.); (M.B.)
| | - Maaike Bras
- Pivot Park Screening Centre, Kloosterstraat 9, 5349 AB Oss, The Netherlands; (S.H.); (M.B.)
| | - Gemma L. Baillie
- BioAscent Discovery Ltd., Bo‘Ness Road, Newhouse, Motherwell ML1 5UH, UK; (G.L.B.); (S.P.M.); (P.S.J.); (A.M.)
| | - Stuart P. McElroy
- BioAscent Discovery Ltd., Bo‘Ness Road, Newhouse, Motherwell ML1 5UH, UK; (G.L.B.); (S.P.M.); (P.S.J.); (A.M.)
| | - Philip S. Jones
- BioAscent Discovery Ltd., Bo‘Ness Road, Newhouse, Motherwell ML1 5UH, UK; (G.L.B.); (S.P.M.); (P.S.J.); (A.M.)
| | - Angus Morrison
- BioAscent Discovery Ltd., Bo‘Ness Road, Newhouse, Motherwell ML1 5UH, UK; (G.L.B.); (S.P.M.); (P.S.J.); (A.M.)
| | - Julia Beveridge
- The Beijer Laboratory, Science for Life Laboratory, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden; (J.B.); (M.L.)
| | - Mathias Hallberg
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Neuropharmacology and Addiction Research, Biomedical Centre, Uppsala University, P.O. Box 591, SE-751 24 Uppsala, Sweden;
| | - Mats Larhed
- The Beijer Laboratory, Science for Life Laboratory, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden; (J.B.); (M.L.)
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Son S, Song WJ. Programming interchangeable and reversible heterooligomeric protein self-assembly using a bifunctional ligand. Chem Sci 2024; 15:2975-2983. [PMID: 38404387 PMCID: PMC10882485 DOI: 10.1039/d3sc05448a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/10/2024] [Indexed: 02/27/2024] Open
Abstract
Protein design for self-assembly allows us to explore the emergence of protein-protein interfaces through various chemical interactions. Heterooligomers, unlike homooligomers, inherently offer a comprehensive range of structural and functional variations. Besides, the macromolecular repertoire and their applications would significantly expand if protein components could be easily interchangeable. This study demonstrates that a rationally designed bifunctional linker containing an enzyme inhibitor and maleimide can guide the formation of diverse protein heterooligomers in an easily applicable and exchangeable manner without extensive sequence optimizations. As proof of concept, we selected four structurally and functionally unrelated proteins, carbonic anhydrase, aldolase, acetyltransferase, and encapsulin, as building block proteins. The combinations of two proteins with the bifunctional linker yielded four two-component heterooligomers with discrete sizes, shapes, and enzyme activities. Besides, the overall size and formation kinetics of the heterooligomers alter upon adding metal chelators, acidic buffer components, and reducing agents, showing the reversibility and tunability in the protein self-assembly. Given that the functional groups of both the linker and protein components are readily interchangeable, our work broadens the scope of protein-assembled architectures and their potential applications as functional biomaterials.
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Affiliation(s)
- Soyeun Son
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
| | - Woon Ju Song
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
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Palica K, Deufel F, Skagseth S, Di Santo Metzler GP, Thoma J, Andersson Rasmussen A, Valkonen A, Sunnerhagen P, Leiros HKS, Andersson H, Erdelyi M. α-Aminophosphonate inhibitors of metallo-β-lactamases NDM-1 and VIM-2. RSC Med Chem 2023; 14:2277-2300. [PMID: 38020072 PMCID: PMC10650955 DOI: 10.1039/d3md00286a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/31/2023] [Indexed: 12/01/2023] Open
Abstract
The upswing of antibiotic resistance is an escalating threat to human health. Resistance mediated by bacterial metallo-β-lactamases is of particular concern as these enzymes degrade β-lactams, our most frequently prescribed class of antibiotics. Inhibition of metallo-β-lactamases could allow the continued use of existing β-lactam antibiotics, such as penicillins, cephalosporins and carbapenems, whose applicability is becoming ever more limited. The design, synthesis, and NDM-1, VIM-2, and GIM-1 inhibitory activities (IC50 4.1-506 μM) of a series of novel non-cytotoxic α-aminophosphonate-based inhibitor candidates are presented herein. We disclose the solution NMR spectroscopic and computational investigation of their NDM-1 and VIM-2 binding sites and binding modes. Whereas the binding modes of the inhibitors are similar, VIM-2 showed a somewhat higher conformational flexibility, and complexed a larger number of inhibitor candidates in more varying binding modes than NDM-1. Phosphonate-type inhibitors may be potential candidates for development into therapeutics to combat metallo-β-lactamase resistant bacteria.
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Affiliation(s)
- Katarzyna Palica
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University Husargatan 3 752 37 Uppsala Sweden
| | - Fritz Deufel
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University Husargatan 3 752 37 Uppsala Sweden
| | - Susann Skagseth
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway N-9037 Tromsø Norway
| | - Gabriela Paula Di Santo Metzler
- Department of Chemistry & Molecular Biology, University of Gothenburg Medicinaregatan 9C 413 90 Göteborg Sweden
- Center for Antibiotics Resistance Research (CARe) at University of Gothenburg 413 90 Göteborg Sweden
| | - Johannes Thoma
- Department of Chemistry & Molecular Biology, University of Gothenburg Medicinaregatan 9C 413 90 Göteborg Sweden
- Center for Antibiotics Resistance Research (CARe) at University of Gothenburg 413 90 Göteborg Sweden
| | - Anna Andersson Rasmussen
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University Husargatan 3 752 37 Uppsala Sweden
| | - Arto Valkonen
- Department of Chemistry, University of Jyvaskyla Survontie 9B 40014 Finland
| | - Per Sunnerhagen
- Department of Chemistry & Molecular Biology, University of Gothenburg Medicinaregatan 9C 413 90 Göteborg Sweden
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway N-9037 Tromsø Norway
| | - Hanna Andersson
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University Husargatan 3 752 37 Uppsala Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University Husargatan 3 752 37 Uppsala Sweden
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Vasile S, Roos K. Understanding the Structure-Activity Relationship through Density Functional Theory: A Simple Method Predicts Relative Binding Free Energies of Metalloenzyme Fragment-like Inhibitors. ACS OMEGA 2023; 8:21438-21449. [PMID: 37360476 PMCID: PMC10285960 DOI: 10.1021/acsomega.2c08156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/29/2023] [Indexed: 06/28/2023]
Abstract
Despite being involved in several human diseases, metalloenzymes are targeted by a small percentage of FDA-approved drugs. Development of novel and efficient inhibitors is required, as the chemical space of metal binding groups (MBGs) is currently limited to four main classes. The use of computational chemistry methods in drug discovery has gained momentum thanks to accurate estimates of binding modes and binding free energies of ligands to receptors. However, exact predictions of binding free energies in metalloenzymes are challenging due to the occurrence of nonclassical phenomena and interactions that common force field-based methods are unable to correctly describe. In this regard, we applied density functional theory (DFT) to predict the binding free energies and to understand the structure-activity relationship of metalloenzyme fragment-like inhibitors. We tested this method on a set of small-molecule inhibitors with different electronic properties and coordinating two Mn2+ ions in the binding site of the influenza RNA polymerase PAN endonuclease. We modeled the binding site using only atoms from the first coordination shell, hence reducing the computational cost. Thanks to the explicit treatment of electrons by DFT, we highlighted the main contributions to the binding free energies and the electronic features differentiating strong and weak inhibitors, achieving good qualitative correlation with the experimentally determined affinities. By introducing automated docking, we explored alternative ways to coordinate the metal centers and we identified 70% of the highest affinity inhibitors. This methodology provides a fast and predictive tool for the identification of key features of metalloenzyme MBGs, which can be useful for the design of new and efficient drugs targeting these ubiquitous proteins.
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Moianos D, Prifti GM, Makri M, Zoidis G. Targeting Metalloenzymes: The "Achilles' Heel" of Viruses and Parasites. Pharmaceuticals (Basel) 2023; 16:901. [PMID: 37375848 DOI: 10.3390/ph16060901] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Metalloenzymes are central to the regulation of a wide range of essential viral and parasitic functions, including protein degradation, nucleic acid modification, and many others. Given the impact of infectious diseases on human health, inhibiting metalloenzymes offers an attractive approach to disease therapy. Metal-chelating agents have been expansively studied as antivirals and antiparasitics, resulting in important classes of metal-dependent enzyme inhibitors. This review provides the recent advances in targeting the metalloenzymes of viruses and parasites that impose a significant burden on global public health, including influenza A and B, hepatitis B and C, and human immunodeficiency viruses as well as Trypanosoma brucei and Trypanosoma cruzi.
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Affiliation(s)
- Dimitrios Moianos
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Georgia-Myrto Prifti
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Maria Makri
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Grigoris Zoidis
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
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Pyrrolyl and Indolyl α-γ-Diketo Acid Derivatives Acting as Selective Inhibitors of Human Carbonic Anhydrases IX and XII. Pharmaceuticals (Basel) 2023. [DOI: 10.3390/ph16020188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Solid tumors are active tissues containing hypoxic regions and producing metabolic acids. By decreasing pH, cancer cells create a hostile environment for surrounding host cells and foster tumor growth and progression. By governing acid/base regulation, carbonic anhydrases (CAs) are involved in several physiological/pathological processes, including tumors. Indeed, CAs are clinically relevant in cancer therapy as among the fifteen human isoforms, two of them, namely CA IX (overexpressed in solid tumors and associated with increased metastasis and poor prognosis) and CA XII (overexpressed in some tumors) are involved in tumorigenesis. Targeting these two isoforms is considered as a pertinent approach to develop new cancer therapeutics. Several CA inhibitors (CAIs) have been described, even though they are unselective inhibitors of different isoforms. Thus, efforts are needed to find new selective CAIs. In this work, we described new diketo acid derivatives as CAIs, with the best acting compounds 1c and 5 as nanomolar inhibitors of CA IX and XII, being also two orders of magnitude selective over CAs I and II. Molecular modeling studies showed the different binding poses of the best acting CAIs within CA II and IX, highlighting the key structural features that could confer the ability to establish specific interactions within the enzymes. In different tumor cell lines overexpressing CA IX and XII, the tested compounds showed antiproliferative activity already at 24 h treatment, with no effects on somatic not transformed cells.
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A Four-Step Platform to Optimize Growth Conditions for High-Yield Production of Siderophores in Cyanobacteria. Metabolites 2023; 13:metabo13020154. [PMID: 36837773 PMCID: PMC9967094 DOI: 10.3390/metabo13020154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
In response to Iron deprivation and in specific environmental conditions, the cyanobacteria Anabaena flos aquae produce siderophores, iron-chelating molecules that in virtue of their interesting environmental and clinical applications, are recently gaining the interest of the pharmaceutical industry. Yields of siderophore recovery from in vitro producing cyanobacterial cultures are, unfortunately, very low and reach most of the times only analytical quantities. We here propose a four-step experimental pipeline for a rapid and inexpensive identification and optimization of growth parameters influencing, at the transcriptional level, siderophore production in Anabaena flos aquae. The four-steps pipeline consists of: (1) identification of the promoter region of the operon of interest in the genome of Anabaena flos aquae; (2) cloning of the promoter in a recombinant DNA vector, upstream the cDNA coding for the Green Fluorescent Protein (GFP) followed by its stable transformation in Escherichia Coli; (3) identification of the environmental parameters affecting expression of the gene in Escherichia coli and their application to the cultivation of the Anabaena strain; (4) identification of siderophores by the combined use of high-resolution tandem mass spectrometry and molecular networking. This multidisciplinary, sustainable, and green pipeline is amenable to automation and is virtually applicable to any cyanobacteria, or more in general, to any microorganisms.
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A fragment-based drug discovery strategy applied to the identification of NDM-1 β-lactamase inhibitors. Eur J Med Chem 2022; 240:114599. [PMID: 35841882 DOI: 10.1016/j.ejmech.2022.114599] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/26/2022] [Accepted: 07/07/2022] [Indexed: 11/23/2022]
Abstract
Hydrolysis of β-lactam drugs, a major class of antibiotics, by serine or metallo-β-lactamases (SBL or MBL) is one of the main mechanisms for antibiotic resistance. New Delhi Metallo-β-lactamase-1 (NDM-1), an acquired metallo-carbapenemase first reported in 2009, is currently considered one of the most clinically relevant targets for the development of β-lactam-β-lactamase inhibitor combinations active on NDM-producing clinical isolates. Identification of scaffolds that could be further rationally pharmacomodulated to design new and efficient NDM-1 inhibitors is thus urgently needed. Fragment-based drug discovery (FBDD) has become of great interest for the development of new drugs for the past few years and combination of several FBDD strategies, such as virtual and NMR screening, can reduce the drawbacks of each of them independently. Our methodology starting from a high throughput virtual screening on NDM-1 of a large library (more than 700,000 compounds) allowed, after slicing the hit molecules into fragments, to build a targeted library. These hit fragments were included in an in-house untargeted library fragments that was screened by Saturation Transfer Difference (STD) Nuclear Magnetic Resonance (NMR). 37 fragments were finally identified and used to establish a pharmacophore. 10 molecules based on these hit fragments were synthesized to validate our strategy. Indenone 89 that combined two identified fragments shows an inhibitory activity on NDM-1 with a Ki value of 4 μM.
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12
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Hafiz S, Xavierselvan M, Gokalp S, Labadini D, Barros S, Duong J, Foster M, Mallidi S. Eutectic Gallium-Indium Nanoparticles for Photodynamic Therapy of Pancreatic Cancer. ACS APPLIED NANO MATERIALS 2022; 5:6125-6139. [PMID: 35655927 PMCID: PMC9150699 DOI: 10.1021/acsanm.1c04353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/12/2022] [Indexed: 05/04/2023]
Abstract
Developing a cancer theranostic nanoplatform with diagnosis and treatment capabilities to effectively treat tumors and reduce side effects is of great significance. Herein, we present a drug delivery strategy for photosensitizers based on a new liquid metal nanoplatform that leverages the tumor microenvironment to achieve photodynamic therapeutic effects in pancreatic cancer. Eutectic gallium indium (EGaIn) nanoparticles were successfully conjugated with a water-soluble cancer targeting ligand, hyaluronic acid, and a photosensitizer, benzoporphyrin derivative, creating EGaIn nanoparticles (EGaPs) via a simple green sonication method. The prepared sphere-shaped EGaPs, with a core-shell structure, presented high biocompatibility and stability. EGaPs had greater cellular uptake, manifested targeting competence, and generated significantly higher intracellular ROS. Further, near-infrared light activation of EGaPs demonstrated their potential to effectively eliminate cancer cells due to their single oxygen generation capability. Finally, from in vivo studies, EGaPs caused tumor regression and resulted in 2.3-fold higher necrosis than the control, therefore making a good vehicle for photodynamic therapy. The overall results highlight that EGaPs provide a new way to assemble liquid metal nanomaterials with different ligands for enhanced cancer therapy.
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Affiliation(s)
- Sabrina
S. Hafiz
- Department
of Chemistry, University of Massachusetts
Boston, Boston, Massachusetts 02125, United States
| | - Marvin Xavierselvan
- Department
of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Sumeyra Gokalp
- Department
of Chemistry, University of Massachusetts
Boston, Boston, Massachusetts 02125, United States
| | - Daniela Labadini
- Department
of Chemistry, University of Massachusetts
Boston, Boston, Massachusetts 02125, United States
| | - Sebastian Barros
- Department
of Chemistry, University of Massachusetts
Boston, Boston, Massachusetts 02125, United States
| | - Jeanne Duong
- Department
of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Michelle Foster
- Department
of Chemistry, University of Massachusetts
Boston, Boston, Massachusetts 02125, United States
| | - Srivalleesha Mallidi
- Department
of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
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The PDE4 Inhibitor Tanimilast Restrains the Tissue-Damaging Properties of Human Neutrophils. Int J Mol Sci 2022; 23:ijms23094982. [PMID: 35563373 PMCID: PMC9104715 DOI: 10.3390/ijms23094982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
Neutrophils, the most abundant subset of leukocytes in the blood, play a pivotal role in host response against invading pathogens. However, in respiratory diseases, excessive infiltration and activation of neutrophils can lead to tissue damage. Tanimilast-international non-proprietary name of CHF6001—is a novel inhaled phosphodiesterase 4 (PDE4) inhibitor in advanced clinical development for the treatment of chronic obstructive pulmonary disease (COPD), a chronic inflammatory lung disease where neutrophilic inflammation plays a key pathological role. Human neutrophils from healthy donors were exposed to pro-inflammatory stimuli in the presence or absence of tanimilast and budesonide—a typical inhaled corticosteroid drug-to investigate the modulation of effector functions including adherence to endothelial cells, granule protein exocytosis, release of extracellular DNA traps, cytokine secretion, and cell survival. Tanimilast significantly decreased neutrophil-endothelium adhesion, degranulation, extracellular DNA traps casting, and cytokine secretion. In contrast, it promoted neutrophil survival by decreasing both spontaneous apoptosis and cell death in the presence of pro-survival factors. The present work suggests that tanimilast can alleviate the severe tissue damage caused by massive recruitment and activation of neutrophils in inflammatory diseases such as COPD.
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14
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Palica K, Vorácová M, Skagseth S, Andersson Rasmussen A, Allander L, Hubert M, Sandegren L, Schrøder Leiros HK, Andersson H, Erdélyi M. Metallo-β-Lactamase Inhibitor Phosphonamidate Monoesters. ACS OMEGA 2022; 7:4550-4562. [PMID: 35155946 PMCID: PMC8830069 DOI: 10.1021/acsomega.1c06527] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Being the second leading cause of death and the leading cause of disability-adjusted life years worldwide, infectious diseases remain-contrary to earlier predictions-a major consideration for the public health of the 21st century. Resistance development of microbes to antimicrobial drugs constitutes a large part of this devastating problem. The most widely spread mechanism of bacterial resistance operates through the degradation of existing β-lactam antibiotics. Inhibition of metallo-β-lactamases is expected to allow the continued use of existing antibiotics, whose applicability is becoming ever more limited. Herein, we describe the synthesis, the metallo-β-lactamase inhibition activity, the cytotoxicity studies, and the NMR spectroscopic determination of the protein binding site of phosphonamidate monoesters. The expression of single- and double-labeled NDM-1 and its backbone NMR assignment are also disclosed, providing helpful information for future development of NDM-1 inhibitors. We show phosphonamidates to have the potential to become a new generation of antibiotic therapeutics to combat metallo-β-lactamase-resistant bacteria.
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Affiliation(s)
- Katarzyna Palica
- Department
of Chemistry—BMC, Organic Chemistry, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden
| | - Manuela Vorácová
- Department
of Chemistry—BMC, Organic Chemistry, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden
| | - Susann Skagseth
- The
Norwegian Structural Biology Centre (NorStruct), Department of Chemistry,
Faculty of Science and Technology, UiT The
Arctic University of Norway, N-9037 Tromsø, Norway
| | - Anna Andersson Rasmussen
- Department
of Chemistry—BMC, Organic Chemistry, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden
| | - Lisa Allander
- Department
of Medical Biochemistry and Microbiology—BMC, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden
| | - Madlen Hubert
- Department
of Pharmacy—BMC, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden
| | - Linus Sandegren
- Department
of Medical Biochemistry and Microbiology—BMC, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden
| | - Hanna-Kirstirep Schrøder Leiros
- The
Norwegian Structural Biology Centre (NorStruct), Department of Chemistry,
Faculty of Science and Technology, UiT The
Arctic University of Norway, N-9037 Tromsø, Norway
| | - Hanna Andersson
- Department
of Chemistry—BMC, Organic Chemistry, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden
| | - Máté Erdélyi
- Department
of Chemistry—BMC, Organic Chemistry, Uppsala University, Husargatan 3, 752 37 Uppsala, Sweden
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15
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Taily IM, Saha D, Banerjee P. Aza-Oxyallyl Cation Driven 3-Amido Oxetane Rearrangement to 2-Oxazolines: Access to Oxazoline Amide Ethers. J Org Chem 2022; 87:2155-2166. [PMID: 35129349 DOI: 10.1021/acs.joc.1c03108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein, we report a highly facile and unprecedented activation of 3-amido oxetanes to synthesize 2-oxazoline amide ethers using a transient electrophilic aza-oxyallyl cation as an activating as well as an alkylating agent under mild reaction conditions. The aza-oxyallyl cation driven intramolecular rearrangement of 3-amido oxetanes to 2-oxazolines is the hallmark of this transformation and is a new addition to the reactivity profile of aza-oxyallyl cations.
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Affiliation(s)
- Irshad Maajid Taily
- Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
| | - Debarshi Saha
- Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
| | - Prabal Banerjee
- Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
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16
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Choi J, Neupane T, Baral R, Jee JG. Hydroxamic Acid as a Potent Metal-Binding Group for Inhibiting Tyrosinase. Antioxidants (Basel) 2022; 11:antiox11020280. [PMID: 35204163 PMCID: PMC8868331 DOI: 10.3390/antiox11020280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 12/10/2022] Open
Abstract
Tyrosinase, a metalloenzyme containing a dicopper cofactor, plays a central role in synthesizing melanin from tyrosine. Many studies have aimed to identify small-molecule inhibitors of tyrosinase for pharmaceutical, cosmetic, and agricultural purposes. In this study, we report that hydroxamic acid is a potent metal-binding group for interacting with dicopper atoms, thereby inhibiting tyrosinase. Hydroxamate-containing molecules, including anticancer drugs targeting histone deacetylase, vorinostat and panobinostat, significantly inhibited mushroom tyrosinase, with inhibitory constants in the submicromolar range. Of the tested molecules, benzohydroxamic acid was the most potent. Its inhibitory constant of 7 nM indicates that benzohydroxamic acid is one of the most potent tyrosinase inhibitors. Results from differential scanning fluorimetry revealed that direct binding mediates inhibition. The enzyme kinetics were studied to assess the inhibitory mechanism of the hydroxamate-containing molecules. Experiments with B16F10 cell lysates confirmed that the new inhibitors are inhibitory against mammalian tyrosinase. Docking simulation data revealed intermolecular contacts between hydroxamate-containing molecules and tyrosinase.
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17
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New Inhibitors of Laccase and Tyrosinase by Examination of Cross-Inhibition between Copper-Containing Enzymes. Int J Mol Sci 2021; 22:ijms222413661. [PMID: 34948458 PMCID: PMC8707586 DOI: 10.3390/ijms222413661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
Coppers play crucial roles in the maintenance homeostasis in living species. Approximately 20 enzyme families of eukaryotes and prokaryotes are known to utilize copper atoms for catalytic activities. However, small-molecule inhibitors directly targeting catalytic centers are rare, except for those that act against tyrosinase and dopamine-β-hydroxylase (DBH). This study tested whether known tyrosinase inhibitors can inhibit the copper-containing enzymes, ceruloplasmin, DBH, and laccase. While most small molecules minimally reduced the activities of ceruloplasmin and DBH, aside from known inhibitors, 5 of 28 tested molecules significantly inhibited the function of laccase, with the Ki values in the range of 15 to 48 µM. Enzyme inhibitory kinetics classified the molecules as competitive inhibitors, whereas differential scanning fluorimetry and fluorescence quenching supported direct bindings. To the best of our knowledge, this is the first report on organic small-molecule inhibitors for laccase. Comparison of tyrosinase and DBH inhibitors using cheminformatics predicted that the presence of thione moiety would suffice to inhibit tyrosinase. Enzyme assays confirmed this prediction, leading to the discovery of two new dual tyrosinase and DBH inhibitors.
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18
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Turner LD, Nielsen AL, Lin L, Pellett S, Sugane T, Olson ME, Johnson EA, Janda KD. Irreversible inhibition of BoNT/A protease: proximity-driven reactivity contingent upon a bifunctional approach. RSC Med Chem 2021; 12:960-969. [PMID: 34223161 PMCID: PMC8221255 DOI: 10.1039/d1md00089f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/03/2021] [Indexed: 12/27/2022] Open
Abstract
Botulinum neurotoxin A (BoNT/A) is categorized as a Tier 1 bioterrorism agent and persists within muscle neurons for months, causing paralysis. A readily available treatment that abrogates BoNT/A's toxicity and longevity is a necessity in the event of a widespread BoNT/A attack and for clinical treatment of botulism, yet remains an unmet need. Herein, we describe a comprehensive warhead screening campaign of bifunctional hydroxamate-based inhibitors for the irreversible inhibition of the BoNT/A light chain (LC). Using the 2,4-dichlorocinnamic hydroxamic acid (DCHA) metal-binding pharmacophore modified with a pendent warhead, a total of 37 compounds, possessing 13 distinct warhead types, were synthesized and evaluated for time-dependent inhibition against the BoNT/A LC. Iodoacetamides, maleimides, and an epoxide were found to exhibit time-dependent inhibition and their k GSH measured as a description of reactivity. The epoxide exhibited superior time-dependent inhibition over the iodoacetamides, despite reacting with glutathione (GSH) 51-fold slower. The proximity-driven covalent bond achieved with the epoxide inhibitor was contingent upon the vital hydroxamate-Zn2+ anchor in placing the warhead in an optimal position for reaction with Cys165. Monofunctional control compounds exemplified the necessity of the bifunctional approach, and Cys165 modification was confirmed through high-resolution mass spectrometry (HRMS) and ablation of time-dependent inhibitory activity against a C165A variant. Compounds were also evaluated against BoNT/A-intoxicated motor neuron cells, and their cell toxicity, serum stability, and selectivity against matrix metalloproteinases (MMPs) were characterized. The bifunctional approach allows the use of less intrinsically reactive electrophiles to intercept Cys165, thus expanding the toolbox of potential warheads for selective irreversible BoNT/A LC inhibition. We envision that this dual-targeted strategy is amenable to other metalloproteases that also possess non-catalytic cysteines proximal to the active-site metal center.
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Affiliation(s)
- Lewis D Turner
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research 10550 N Torrey Pines Road La Jolla CA 92037 USA
| | - Alexander L Nielsen
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research 10550 N Torrey Pines Road La Jolla CA 92037 USA
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Lucy Lin
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research 10550 N Torrey Pines Road La Jolla CA 92037 USA
| | - Sabine Pellett
- Department of Bacteriology, University of Wisconsin 1550 Linden Drive Madison WI 53706 USA
| | - Takashi Sugane
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research 10550 N Torrey Pines Road La Jolla CA 92037 USA
| | - Margaret E Olson
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research 10550 N Torrey Pines Road La Jolla CA 92037 USA
- College of Pharmacy, Roosevelt University Schaumburg IL 60173 USA
| | - Eric A Johnson
- Department of Bacteriology, University of Wisconsin 1550 Linden Drive Madison WI 53706 USA
| | - Kim D Janda
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research 10550 N Torrey Pines Road La Jolla CA 92037 USA
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19
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Binding Free Energy (BFE) Calculations and Quantitative Structure-Activity Relationship (QSAR) Analysis of Schistosoma mansoni Histone Deacetylase 8 ( smHDAC8) Inhibitors. Molecules 2021; 26:molecules26092584. [PMID: 33925246 PMCID: PMC8125515 DOI: 10.3390/molecules26092584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 01/02/2023] Open
Abstract
Histone-modifying proteins have been identified as promising targets to treat several diseases including cancer and parasitic ailments. In silico methods have been incorporated within a variety of drug discovery programs to facilitate the identification and development of novel lead compounds. In this study, we explore the binding modes of a series of benzhydroxamates derivatives developed as histone deacetylase inhibitors of Schistosoma mansoni histone deacetylase (smHDAC) using molecular docking and binding free energy (BFE) calculations. The developed docking protocol was able to correctly reproduce the experimentally established binding modes of resolved smHDAC8–inhibitor complexes. However, as has been reported in former studies, the obtained docking scores weakly correlate with the experimentally determined activity of the studied inhibitors. Thus, the obtained docking poses were refined and rescored using the Amber software. From the computed protein–inhibitor BFE, different quantitative structure–activity relationship (QSAR) models could be developed and validated using several cross-validation techniques. Some of the generated QSAR models with good correlation could explain up to ~73% variance in activity within the studied training set molecules. The best performing models were subsequently tested on an external test set of newly designed and synthesized analogs. In vitro testing showed a good correlation between the predicted and experimentally observed IC50 values. Thus, the generated models can be considered as interesting tools for the identification of novel smHDAC8 inhibitors.
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20
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Kaur N, Singh P, Banerjee P. Vinylogous Aza‐Michael Addition of Urea Derivatives with
p
‐Quinone Methides Followed by Oxidative Dearomative Cyclization: Approach to Spiroimidazolidinone Derivatives. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Navpreet Kaur
- Department of Chemistry Indian Institute of Technology Ropar Rupnagar Punjab 140001 India
| | - Priyanka Singh
- Department of Chemistry Indian Institute of Technology Ropar Rupnagar Punjab 140001 India
| | - Prabal Banerjee
- Department of Chemistry Indian Institute of Technology Ropar Rupnagar Punjab 140001 India
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21
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Ortiz-Meoz RF, Wang L, Matico R, Rutkowska-Klute A, De la Rosa M, Bedard S, Midgett R, Strohmer K, Thomson D, Zhang C, Mebrahtu M, Guss J, Totoritis R, Consler T, Campobasso N, Taylor D, Lewis T, Weaver K, Muelbaier M, Seal J, Dunham R, Kazmierski W, Favre D, Bergamini G, Shewchuk L, Rendina A, Zhang G. Characterization of Apo-Form Selective Inhibition of Indoleamine 2,3-Dioxygenase*. Chembiochem 2020; 22:516-522. [PMID: 32974990 DOI: 10.1002/cbic.202000298] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/23/2020] [Indexed: 01/01/2023]
Abstract
Indoleamine-2,3-dioxygenase 1 (IDO1) is a heme-containing enzyme that catalyzes the rate-limiting step in the kynurenine pathway of tryptophan (TRP) metabolism. As it is an inflammation-induced immunoregulatory enzyme, pharmacological inhibition of IDO1 activity is currently being pursued as a potential therapeutic tool for the treatment of cancer and other disease states. As such, a detailed understanding of the mechanism of action of IDO1 inhibitors with various mechanisms of inhibition is of great interest. Comparison of an apo-form-binding IDO1 inhibitor (GSK5628) to the heme-coordinating compound, epacadostat (Incyte), allows us to explore the details of the apo-binding inhibition of IDO1. Herein, we demonstrate that GSK5628 inhibits IDO1 by competing with heme for binding to a heme-free conformation of the enzyme (apo-IDO1), whereas epacadostat coordinates its binding with the iron atom of the IDO1 heme cofactor. Comparison of these two compounds in cellular systems reveals a long-lasting inhibitory effect of GSK5628, previously undescribed for other known IDO1 inhibitors. Detailed characterization of this apo-binding mechanism for IDO1 inhibition might help design superior inhibitors or could confer a unique competitive advantage over other IDO1 inhibitors vis-à-vis specificity and pharmacokinetic parameters.
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Affiliation(s)
- Rodrigo F Ortiz-Meoz
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Liping Wang
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Rosalie Matico
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | | | - Martha De la Rosa
- Infectious Diseases TAU, GlaxoSmithKline Five Moore Drive, Research Triangle Park, NC 27709, USA
| | - Sabrina Bedard
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Robert Midgett
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Katrin Strohmer
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Douglas Thomson
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Cunyu Zhang
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Makda Mebrahtu
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Jeffrey Guss
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Rachel Totoritis
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Thomas Consler
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Nino Campobasso
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - David Taylor
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Tia Lewis
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Kurt Weaver
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Marcel Muelbaier
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - John Seal
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Richard Dunham
- Infectious Diseases TAU, GlaxoSmithKline Five Moore Drive, Research Triangle Park, NC 27709, USA
| | - Wieslaw Kazmierski
- Infectious Diseases TAU, GlaxoSmithKline Five Moore Drive, Research Triangle Park, NC 27709, USA
| | - David Favre
- Infectious Diseases TAU, GlaxoSmithKline Five Moore Drive, Research Triangle Park, NC 27709, USA
| | - Giovanna Bergamini
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Lisa Shewchuk
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Alan Rendina
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Guofeng Zhang
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
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22
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Roth L, Gotsbacher MP, Codd R. Immobilized Metal Affinity Chromatography as a Drug Discovery Platform for Metalloenzyme Inhibitors. J Med Chem 2020; 63:12116-12127. [PMID: 32940035 DOI: 10.1021/acs.jmedchem.0c01541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Immobilized metal-ion affinity chromatography (IMAC) used to purify recombinant proteins features a resin-bound 1:1 Ni(II)-iminodiacetic acid (IDA) complex. This hemi-saturated Ni(II)-IDA system containing exchangeable sites at the metal ion is re-cast as a surrogate of a coordinatively-unsaturated metalloenzyme active site, with utility for selecting compounds with metal-binding groups from mixtures as potential metalloenzyme inhibitors. Exchanging Ni(II) for other metal ions could broaden the scope of metalloenzyme target. This work examined the performance of Cu(II)-, Fe(III)-, Ga(III)-, Ni(II)-, or Zn(II)-IMAC resins to reversibly bind experimental or clinical metalloenzyme inhibitors of Zn(II)-ACE1, Zn(II)-HDAC, Fe(II)/(III)-5-LO or Cu(II)-tyrosinase from a curated mixture (1-17). Each IMAC system gave a distinct selection profile. The Zn(II)-IMAC system selectively bound the thiol-containing Zn(II)-ACE1 inhibitors captopril and omapatrilat, and the Fe(III)-IMAC system selectively bound the Fe(II)/(III)-5-LO inhibitor licofelone, demonstrating a remarkable IMAC-metalloenzyme metal ion match. IMAC provides a simple, water-compatible platform, which could accelerate metalloenzyme inhibitor discovery.
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Affiliation(s)
- Lukas Roth
- School of Medical Sciences (Pharmacology), The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Michael P Gotsbacher
- School of Medical Sciences (Pharmacology), The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Rachel Codd
- School of Medical Sciences (Pharmacology), The University of Sydney, Sydney, New South Wales 2006, Australia
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23
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The Anticancer Activity for the Bumetanide-Based Analogs via Targeting the Tumor-Associated Membrane-Bound Human Carbonic Anhydrase-IX Enzyme. Pharmaceuticals (Basel) 2020; 13:ph13090252. [PMID: 32961906 PMCID: PMC7558282 DOI: 10.3390/ph13090252] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/05/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022] Open
Abstract
The membrane-bound human carbonic anhydrase (hCA) IX is widely recognized as a marker of tumor hypoxia and a prognostic factor within several human cancers. Being undetected in most normal tissues, hCA-IX implies the pharmacotherapeutic advent of reduced off-target adverse effects. We assessed the potential anticancer activity of bumetanide-based analogues to inhibit the hCA-IX enzymatic activity and cell proliferation of two solid cancer cell lines, namely kidney carcinoma (A-498) and bladder squamous cell carcinoma (SCaBER). Bumetanide analogues efficiently inhibit the target hCA-IX in low nanomolar activity (IC50 = 4.4–23.7 nM) and have an excellent selectivity profile (SI = 14.5–804) relative to the ubiquitous hCA-II isoform. Additionally, molecular docking studies provided insights into the compounds’ structure–activity relationship and preferential binding of small-sized as well as selective bulky ligands towards the hCA-IX pocket. In particular, 2,4-dihydro-1,2,4-triazole-3-thione derivative 9c displayed pronounced hCA-IX inhibitory activity and impressive antiproliferative activity on oncogenic A-498 kidney carcinoma cells and is being considered as a promising anticancer candidate. Future studies will aim to optimize this compound to fine-tune its anticancer activity as well as explore its potential through in-vivo preclinical studies.
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24
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Shirbhate E, Patel P, Patel VK, Veerasamy R, Sharma PC, Rajak H. The combination of histone deacetylase inhibitors and radiotherapy: a promising novel approach for cancer treatment. Future Oncol 2020; 16:2457-2469. [PMID: 32815411 DOI: 10.2217/fon-2020-0385] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
HDAC inhibitors (HDACi) play an essential role in various cellular processes, such as differentiation and transcriptional regulation of key genes and cytostatic factors, cell cycle arrest and apoptosis that facilitates the targeting of epigenome of eukaryotic cells. In the majority of cancers, only a handful of patients receive optimal benefit from chemotherapeutics. Additionally, there is emerging interest in the use of HDACi to modulate the effects of ionizing radiations. The use of HDACi with radiotherapy, with the goal of reaching dissimilar, often distinct pathways or multiple biological targets, with the expectation of synergistic effects, reduced toxicity and diminished intrinsic and acquired resistance, conveys an approach of increasing interest. In this review, the clinical potential of HDACi in combination with radiotherapy is described as an efficient synergy for cancer treatment will be overviewed.
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Affiliation(s)
- Ekta Shirbhate
- Institute of Pharmaceutical Sciences, Guru Ghasidas University, Bilaspur-495 009, Chhattisgarh, India
| | - Preeti Patel
- Institute of Pharmaceutical Sciences, Guru Ghasidas University, Bilaspur-495 009, Chhattisgarh, India
| | - Vijay K Patel
- Institute of Pharmaceutical Sciences, Guru Ghasidas University, Bilaspur-495 009, Chhattisgarh, India
| | - Ravichandran Veerasamy
- Faculty of Pharmacy, AIMST University, Semeling, 08100 Bedong, Kedah Darul Aman, Malaysia
| | - Prabodh C Sharma
- Institute of Pharmaceutical Sciences, Kurukshetra University, Kurukshetra-136 119, Haryana, India
| | - Harish Rajak
- Institute of Pharmaceutical Sciences, Guru Ghasidas University, Bilaspur-495 009, Chhattisgarh, India
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25
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Cappellacci L, Perinelli DR, Maggi F, Grifantini M, Petrelli R. Recent Progress in Histone Deacetylase Inhibitors as Anticancer Agents. Curr Med Chem 2020; 27:2449-2493. [PMID: 30332940 DOI: 10.2174/0929867325666181016163110] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/29/2018] [Accepted: 10/09/2018] [Indexed: 12/13/2022]
Abstract
Histone Deacetylase (HDAC) inhibitors are a relatively new class of anti-cancer agents that play important roles in epigenetic or non-epigenetic regulation, inducing death, apoptosis, and cell cycle arrest in cancer cells. Recently, their use has been clinically validated in cancer patients resulting in the approval by the FDA of four HDAC inhibitors, vorinostat, romidepsin, belinostat and panobinostat, used for the treatment of cutaneous/peripheral T-cell lymphoma and multiple myeloma. Many more HDAC inhibitors are at different stages of clinical development for the treatment of hematological malignancies as well as solid tumors. Also, clinical trials of several HDAC inhibitors for use as anti-cancer drugs (alone or in combination with other anti-cancer therapeutics) are ongoing. In the intensifying efforts to discover new, hopefully, more therapeutically efficacious HDAC inhibitors, molecular modelingbased rational drug design has played an important role. In this review, we summarize four major structural classes of HDAC inhibitors (hydroxamic acid derivatives, aminobenzamide, cyclic peptide and short-chain fatty acids) that are in clinical trials and different computer modeling tools available for their structural modifications as a guide to discover additional HDAC inhibitors with greater therapeutic utility.
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Affiliation(s)
- Loredana Cappellacci
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Diego R Perinelli
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Filippo Maggi
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Mario Grifantini
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Riccardo Petrelli
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
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Jalde SS, Choi HK. Recent advances in the development of β-lactamase inhibitors. J Microbiol 2020; 58:633-647. [PMID: 32720096 DOI: 10.1007/s12275-020-0285-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/02/2020] [Accepted: 07/02/2020] [Indexed: 02/07/2023]
Abstract
β-Lactam antibiotics are the most commonly prescribed antibiotics worldwide; however, antimicrobial resistance (AMR) is a global challenge. The β-lactam resistance in Gram-negative bacteria is due to the production of β-lactamases, including extended-spectrum β-lactamases, metallo-β-lactamases, and carbapenem-hydrolyzing class D β-lactamases. To restore the efficacy of BLAs, the most successful strategy is to use them in combination with β-lactamase inhibitors (BLI). Here we review the medically relevant β-lactamase families and penicillins, diazabicyclooctanes, boronic acids, and novel chemical scaffold-based BLIs, in particular approved and under clinical development.
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Affiliation(s)
- Shivakumar S Jalde
- Department of Medicinal Chemistry, Jungwon University, Goesan, 28420, Republic of Korea
| | - Hyun Kyung Choi
- Department of Medicinal Chemistry, Jungwon University, Goesan, 28420, Republic of Korea.
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Miyake Y, Itoh Y, Suzuma Y, Kodama H, Kurohara T, Yamashita Y, Narozny R, Hanatani Y, Uchida S, Suzuki T. Metalloprotein-Catalyzed Click Reaction for In Situ Generation of a Potent Inhibitor. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yuka Miyake
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yukihiro Itoh
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yoshinori Suzuma
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Hidehiko Kodama
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Takashi Kurohara
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Yasunobu Yamashita
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Remy Narozny
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Yutaro Hanatani
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Shusaku Uchida
- Graduate School of Medicine, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takayoshi Suzuki
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
- CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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Jamal S, Ahmed A, Moin ST. Evaluation of a sesquiterpene as possible drug lead against gelatinases via molecular dynamics simulations. J Biomol Struct Dyn 2020; 39:1645-1660. [PMID: 32174257 DOI: 10.1080/07391102.2020.1743363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Malignant tumors can be targeted by accounting for their metastatic capabilities. Matrix metalloproteinases (MMPs) are the key players in tumor metastasis facilitating through their proteolytic activities of angiogenesis and extracellular matrix components (ECM) degradation. MMP-2 and MMP-9 being the members of a distinguished class of MMPs more commonly known as gelatinases are the prominent enzymes which are involved in different cancer progression stages. Targeting these isoforms specifically has always been a challenging task due to highly similar structural and functional features among the other members of MMPs with well preserve active sites containing catalytic zinc atom that was the only reason that none of the MMP inhibitor has been successfully marketed for the tumor pathology up till now. Therefore, non-competitive inhibitors with different structural attributed are needed to be evaluated at the molecular level for further experiments. The present study deals with the application of molecular dynamics simulation for the investigation of an alternative pathway for the inhibition of MMP-2 and MMP-9 by a sesquiterpene isolated from Polygonum barbatum which demonstrates the characteristics binding to the S1' subsite of the enzymes followed by in vitro gene expression studies. The simulation results provide information on the possible binding profile producing inhibitory effects imposed by the inhibitor to these enzymes by acquiring different structural and dynamical features. Moreover, thermodynamic quantities based on the computationally intensive thermodynamic integration approach were also obtained in terms of inhibitor binding affinity computed for the inhibitor against MMP-2 and MMP-9 that completely augmented the experimental gene expression study.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sehrish Jamal
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Ayaz Ahmed
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Syed Tarique Moin
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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A short guide to histone deacetylases including recent progress on class II enzymes. Exp Mol Med 2020; 52:204-212. [PMID: 32071378 PMCID: PMC7062823 DOI: 10.1038/s12276-020-0382-4] [Citation(s) in RCA: 213] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/27/2019] [Indexed: 01/07/2023] Open
Abstract
The interaction between histones and DNA is important for eukaryotic gene expression. A loose interaction caused, for example, by the neutralization of a positive charge on the histone surface by acetylation, induces a less compact chromatin structure, resulting in feasible accessibility of RNA polymerase and increased gene expression. In contrast, the formation of a tight chromatin structure due to the deacetylation of histone lysine residues on the surface by histone deacetylases enforces the interaction between the histones and DNA, which minimizes the chance of RNA polymerases contacting DNA, resulting in decreased gene expression. Therefore, the balance of the acetylation of histones mediated by histone acetylases (HATs) and histone deacetylases (HDACs) is an issue of transcription that has long been studied in relation to posttranslational modification. In this review, current knowledge of HDACs is briefly described with an emphasis on recent progress in research on HDACs, especially on class IIa HDACs. Targeting specific structural and functional features of enzymes involved in regulating the interactions between DNA and the histone proteins associated with it could lead to the development of more effective cancer therapeutics. Histone deacetylases (HDACs), enzymes which remove acetyl groups from histones, make the histones wrap more tightly around the DNA so that it becomes inaccessible to the initial steps in gene expression. Drugs that target these enzymes have shown limited efficacy due to lack of specificity and off-target toxicity. Jeong-Sun Kim at Chonnam National University, Gwangju, and Suk-Youl Park at Pohang Accelerator Laboratory, Pohang University of Science and Technology, South Korea, review the latest knowledge about class II HDACs. They suggest that their unique structural features and low enzymatic activity are important features to consider when designing new, more selective HDAC inhibitors.
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Taily IM, Saha D, Banerjee P. Palladium-catalyzed regio- and stereoselective access to allyl ureas/carbamates: facile synthesis of imidazolidinones and oxazepinones. Org Biomol Chem 2020; 18:6564-6570. [PMID: 32789352 DOI: 10.1039/d0ob01514h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Typically, transition metal catalysis enforces the stereodefined outcome of a reaction. Here we disclose the palladium-catalyzed regio- and stereoselective access to allylic ureas/carbamates and their further exploitation to diverse cyclic structures under operationally simple reaction conditions. This protocol features palladium-catalyzed decarboxylative amidation of highly modular VECs with good to excellent yield, minimal waste production, wide substrate scope, and low catalyst loading. In follow-up chemistry, we demonstrated the debenzylation of vinylic imidazolidinones to N-hydroxycyclic ureas and regioselective derivatization towards the facile synthesis of halohydrins and oxiranes under mild reaction conditions in good to excellent yields.
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Affiliation(s)
- Irshad Maajid Taily
- Department of Chemistry, Indian Institute of Technology Ropar, Nangal Road, Rupnagar, Punjab-140001, India.
| | - Debarshi Saha
- Department of Chemistry, Indian Institute of Technology Ropar, Nangal Road, Rupnagar, Punjab-140001, India.
| | - Prabal Banerjee
- Department of Chemistry, Indian Institute of Technology Ropar, Nangal Road, Rupnagar, Punjab-140001, India.
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Taily IM, Saha D, Banerjee P. [3+3] Annulation via Ring Opening/Cyclization of Donor-Acceptor Cyclopropanes with (Un)symmetrical Ureas: A Quick Access to Highly Functionalized Tetrahydropyrimidinones. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901400] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Irshad Maajid Taily
- Department of Chemistry; Indian Institute of Technology Ropar; Nangal Road 140001 Rupnagar Punjab India
| | - Debarshi Saha
- Department of Chemistry; Indian Institute of Technology Ropar; Nangal Road 140001 Rupnagar Punjab India
| | - Prabal Banerjee
- Department of Chemistry; Indian Institute of Technology Ropar; Nangal Road 140001 Rupnagar Punjab India
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Burkett DJ, Wyatt BN, Mews M, Bautista A, Engel R, Dockendorff C, Donaldson WA, St Maurice M. Evaluation of α-hydroxycinnamic acids as pyruvate carboxylase inhibitors. Bioorg Med Chem 2019; 27:4041-4047. [PMID: 31351848 DOI: 10.1016/j.bmc.2019.07.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/10/2019] [Accepted: 07/14/2019] [Indexed: 10/26/2022]
Abstract
Through a structure-based drug design project (SBDD), potent small molecule inhibitors of pyruvate carboxylase (PC) have been discovered. A series of α-keto acids (7) and α-hydroxycinnamic acids (8) were prepared and evaluated for inhibition of PC in two assays. The two most potent inhibitors were 3,3'-(1,4-phenylene)bis[2-hydroxy-2-propenoic acid] (8u) and 2-hydroxy-3-(quinoline-2-yl)propenoic acid (8v) with IC50 values of 3.0 ± 1.0 μM and 4.3 ± 1.5 μM respectively. Compound 8v is a competitive inhibitor with respect to pyruvate (Ki = 0.74 μM) and a mixed-type inhibitor with respect to ATP, indicating that it targets the unique carboxyltransferase (CT) domain of PC. Furthermore, compound 8v does not significantly inhibit human carbonic anhydrase II, matrix metalloproteinase-2, malate dehydrogenase or lactate dehydrogenase.
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Affiliation(s)
- Daniel J Burkett
- Department of Chemistry, Marquette University, P. O. Box 1881, Milwaukee, WI 53201-1881, USA
| | - Brittney N Wyatt
- Department of Biological Sciences, Marquette University, P. O. Box 1881, Milwaukee, WI 53201-1881, USA
| | - Mallory Mews
- Department of Biological Sciences, Marquette University, P. O. Box 1881, Milwaukee, WI 53201-1881, USA
| | - Anson Bautista
- Department of Chemistry, Marquette University, P. O. Box 1881, Milwaukee, WI 53201-1881, USA
| | - Ryan Engel
- Department of Chemistry, Marquette University, P. O. Box 1881, Milwaukee, WI 53201-1881, USA
| | - Chris Dockendorff
- Department of Chemistry, Marquette University, P. O. Box 1881, Milwaukee, WI 53201-1881, USA
| | - William A Donaldson
- Department of Chemistry, Marquette University, P. O. Box 1881, Milwaukee, WI 53201-1881, USA.
| | - Martin St Maurice
- Department of Biological Sciences, Marquette University, P. O. Box 1881, Milwaukee, WI 53201-1881, USA.
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Segat GC, Moreira CG, Santos EC, Heller M, Schwanke RC, Aksenov AV, Aksenov NA, Aksenov DA, Kornienko A, Marcon R, Calixto JB. A new series of acetohydroxamates shows in vitro and in vivo anticancer activity against melanoma. Invest New Drugs 2019; 38:977-989. [DOI: 10.1007/s10637-019-00849-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 08/21/2019] [Indexed: 11/30/2022]
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Ganesan A. Epigenetic drug discovery: a success story for cofactor interference. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0069. [PMID: 29685973 DOI: 10.1098/rstb.2017.0069] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2017] [Indexed: 02/06/2023] Open
Abstract
Within the past two decades, seven epigenetic drugs have received regulatory approval and numerous other candidates are currently in clinical trials. Among the epigenetic targets are the writer and eraser enzymes that are, respectively, responsible for the reversible introduction and removal of structural modifications in the nucleosome. This review discusses the progress achieved in the design and development of inhibitors against the key writer and eraser pairs: DNA methyltransferases and Tet demethylases; lysine/arginine methyltransferases and lysine demethylases; and histone acetyltransferases and histone deacetylases. A common theme for the successful inhibition of these enzymes in a potent and selective manner is the targeting of the cofactors present in the active site, namely zinc and iron cations, S-adenosylmethione, nicotinamide adenine dinucleotide, flavin adenine dinucleotide and acetyl Coenzyme A.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- A Ganesan
- School of Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK .,Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg, 79104 Freiburg im Breisgau, Germany
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35
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Bagchi RA, Weeks KL. Histone deacetylases in cardiovascular and metabolic diseases. J Mol Cell Cardiol 2019; 130:151-159. [PMID: 30978343 DOI: 10.1016/j.yjmcc.2019.04.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/29/2019] [Accepted: 04/06/2019] [Indexed: 12/13/2022]
Abstract
Histone deacetylases (HDACs) regulate gene transcription by catalyzing the removal of acetyl groups from key lysine residues in nucleosomal histones and via the recruitment of other epigenetic regulators to DNA promoter/enhancer regions. Over the past two decades, HDACs have been implicated in multiple processes pertinent to cardiovascular and metabolic diseases, including cardiac hypertrophy and remodeling, fibrosis, calcium handling, inflammation and energy metabolism. The development of small molecule HDAC inhibitors and genetically modified loss- and gain-of-function mouse models has allowed interrogation of the roles of specific HDAC isoforms in these processes. Isoform-selective HDAC inhibitors may prove to be powerful therapeutic agents for the treatment of cardiovascular diseases, obesity and diabetes.
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Affiliation(s)
- Rushita A Bagchi
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America
| | - Kate L Weeks
- Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Department of Diabetes, Central Clinical School, Monash University, Clayton, VIC 3800, Australia.
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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Credille CV, Dick BL, Morrison CN, Stokes RW, Adamek RN, Wu NC, Wilson IA, Cohen SM. Structure-Activity Relationships in Metal-Binding Pharmacophores for Influenza Endonuclease. J Med Chem 2018; 61:10206-10217. [PMID: 30351002 DOI: 10.1021/acs.jmedchem.8b01363] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Metalloenzymes represent an important target space for drug discovery. A limitation to the early development of metalloenzyme inhibitors has been the lack of established structure-activity relationships (SARs) for molecules that bind the metal ion cofactor(s) of a metalloenzyme. Herein, we employed a bioinorganic perspective to develop an SAR for inhibition of the metalloenzyme influenza RNA polymerase PAN endonuclease. The identified trends highlight the importance of the electronics of the metal-binding pharmacophore (MBP), in addition to MBP sterics, for achieving improved inhibition and selectivity. By optimization of the MBPs for PAN endonuclease, a class of highly active and selective fragments was developed that displays IC50 values <50 nM. This SAR led to structurally distinct molecules that also displayed IC50 values of ∼10 nM, illustrating the utility of a metal-centric development campaign in generating highly active and selective metalloenzyme inhibitors.
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Affiliation(s)
- Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Ryjul W Stokes
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Nicholas C Wu
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , La Jolla , California 92037 , United States.,The Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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Adamek RN, Credille CV, Dick BL, Cohen SM. Isosteres of hydroxypyridinethione as drug-like pharmacophores for metalloenzyme inhibition. J Biol Inorg Chem 2018; 23:1129-1138. [PMID: 30003339 DOI: 10.1007/s00775-018-1593-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 06/28/2018] [Indexed: 12/18/2022]
Abstract
Hydroxypyridinethiones (HOPTOs) are strong ligands for metal ions and potentially useful pharmacophores for inhibiting metalloenzymes relevant to human disease. However, HOPTOs have been sparingly used in drug discovery efforts due, in part, to concerns that this scaffold will act as a promiscuous, non-selective metalloenzyme inhibitor, as well as possess poor pharmacokinetics (PK), which may undermine drug candidates containing this functional group. To advance HOPTOs as a useful pharmacophore for metalloenzyme inhibitors, a library of 22 HOPTO isostere compounds has been synthesized and investigated. This library demonstrates that it is possible to maintain the core metal-binding pharmacophore (MBP) while generating diversity in structure, electronics, and PK properties. This HOPTO library has been screened against a set of four different metalloenzymes, demonstrating that while the same metal-binding donor atoms are maintained, there is a wide range of activity between metalloenzyme targets. Overall, this work shows that HOPTO isosteres are useful MBPs and valuable scaffolds for metalloenzyme inhibitors.
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Affiliation(s)
- Rebecca N Adamek
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Cy V Credille
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, CA, 92093, USA.
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42
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Chen Y, Lai B, Zhang Z, Cohen SM. The effect of metalloprotein inhibitors on cellular metal ion content and distribution. Metallomics 2017; 9:250-257. [PMID: 28168254 DOI: 10.1039/c6mt00267f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
With metalloproteins garnering increased interest as therapeutic targets, designing target-specific metalloprotein inhibitors (MPi) is of substantial importance. However, in many respects, the development and evaluation of MPi lags behind that of conventional small molecule therapeutics. Core concerns around MPi, such as target selectivity and potential disruption of metal ion homeostasis linger. Herein, we used a suite of analytical methods, including energy-dispersive X-ray spectroscopy (EDX), inductively coupled plasma atomic emission spectroscopy (ICP-OES), and synchrotron X-ray fluorescence microscopy (SXRF) to investigate the effect of several MPi on cellular metal ion distribution and homeostasis. The results reveal that at therapeutically relevant concentrations, the tested MPi have no significant effects on cellular metal ion content or distribution. In addition, the affinity of the metal-binding pharmacophore (MBP) utilized by the MPi does not have a substantial influence on the effect of the MPi on cellular metal distribution. These studies provide an important, original data set indicating that metal ion homeostasis is not notably perturbed by MPi, which should encourage the development of and aid in designing new MPi, guide MBP selection, and clarify the effect of MPi on the 'metallome'.
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Affiliation(s)
- Yao Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, China. and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.
| | - Barry Lai
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zhenjie Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, China. and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.
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Bang CG, Jensen JF, O’Hanlon Cohrt E, Olsen LB, Siyum SG, Mortensen KT, Skovgaard T, Berthelsen J, Yang L, Givskov M, Qvortrup K, Nielsen TE. A Linker for the Solid-Phase Synthesis of Hydroxamic Acids and Identification of HDAC6 Inhibitors. ACS COMBINATORIAL SCIENCE 2017; 19:657-669. [PMID: 28746804 DOI: 10.1021/acscombsci.7b00068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We herein present broadly useful, readily available and nonintegral hydroxylamine linkers for the routine solid-phase synthesis of hydroxamic acids. The developed protocols enable the efficient synthesis and release of a wide range of hydroxamic acids from various resins, relying on high control and flexibility with respect to reagents and synthetic processes. A trityl-based hydroxylamine linker was used to synthesize a library of peptide hydroxamic acids. The inhibitory effects of the compounds were examined for seven HDAC enzyme subtypes using a chemiluminescence-based assay.
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Affiliation(s)
- Claus G. Bang
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Jakob F. Jensen
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Emil O’Hanlon Cohrt
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Lasse B. Olsen
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Saba G. Siyum
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Kim T. Mortensen
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Tine Skovgaard
- The
Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jens Berthelsen
- The
Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Liang Yang
- Singapore
Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Michael Givskov
- The
Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Singapore
Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Katrine Qvortrup
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Thomas E. Nielsen
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
- The
Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Singapore
Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
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44
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Chen AY, Thomas PW, Stewart AC, Bergstrom A, Cheng Z, Miller C, Bethel CR, Marshall SH, Credille CV, Riley CL, Page RC, Bonomo RA, Crowder MW, Tierney DL, Fast W, Cohen SM. Dipicolinic Acid Derivatives as Inhibitors of New Delhi Metallo-β-lactamase-1. J Med Chem 2017; 60:7267-7283. [PMID: 28809565 PMCID: PMC5599375 DOI: 10.1021/acs.jmedchem.7b00407] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The efficacy of β-lactam antibiotics is threatened by the emergence and global spread of metallo-β-lactamase (MBL) mediated resistance, specifically New Delhi metallo-β-lactamase-1 (NDM-1). By utilization of fragment-based drug discovery (FBDD), a new class of inhibitors for NDM-1 and two related β-lactamases, IMP-1 and VIM-2, was identified. On the basis of 2,6-dipicolinic acid (DPA), several libraries were synthesized for structure-activity relationship (SAR) analysis. Inhibitor 36 (IC50 = 80 nM) was identified to be highly selective for MBLs when compared to other Zn(II) metalloenzymes. While DPA displayed a propensity to chelate metal ions from NDM-1, 36 formed a stable NDM-1:Zn(II):inhibitor ternary complex, as demonstrated by 1H NMR, electron paramagnetic resonance (EPR) spectroscopy, equilibrium dialysis, intrinsic tryptophan fluorescence emission, and UV-vis spectroscopy. When coadministered with 36 (at concentrations nontoxic to mammalian cells), the minimum inhibitory concentrations (MICs) of imipenem against clinical isolates of Eschericia coli and Klebsiella pneumoniae harboring NDM-1 were reduced to susceptible levels.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Pei W Thomas
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas , Austin, Texas 78712, United States
| | - Alesha C Stewart
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas , Austin, Texas 78712, United States
| | - Alexander Bergstrom
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Callie Miller
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Christopher R Bethel
- Research Services, Louis Stokes Cleveland Department of Veterans Affairs Medical Center , Cleveland, Ohio 44106, United States
| | - Steven H Marshall
- Research Services, Louis Stokes Cleveland Department of Veterans Affairs Medical Center , Cleveland, Ohio 44106, United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Christopher L Riley
- Department of Molecular Biosciences, University of Texas , Austin, Texas 78712, United States
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Robert A Bonomo
- Research Services, Louis Stokes Cleveland Department of Veterans Affairs Medical Center , Cleveland, Ohio 44106, United States
- Department of Medicine, Department of Molecular Biology and Microbiology, Department of Biochemistry, and Department of Pharmacology, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - David L Tierney
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Walter Fast
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas , Austin, Texas 78712, United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
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45
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Gabr MT, El-Gohary NS, El-Bendary ER, El-Kerdawy MM, Ni N. Microwave-assisted synthesis and antitumor evaluation of a new series of thiazolylcoumarin derivatives. EXCLI JOURNAL 2017; 16:1114-1131. [PMID: 29285008 PMCID: PMC5735336 DOI: 10.17179/excli2017-208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/31/2017] [Indexed: 12/22/2022]
Abstract
A new series of thiazolylcoumarin derivatives was synthesized. The designed strategy embraced a molecular hybridization approach which involves the combination of the thiazole and coumarin pharmacophores together. The new hybrid compounds were tested for in vitro antitumor efficacy over cervical (Hela) and kidney fibroblast (COS-7) cancer cells. Compounds 5f, 5h, 5m and 5r displayed promising efficacy toward Hela cell line. In addition, 5h and 5r were found to be the most active candidates toward COS-7 cell line. The four active analogs, 5f, 5h, 5m and 5r were screened for in vivo antitumor activity over EAC cells in mice, as well as in vitro cytotoxicity toward W138 normal cells. Results illustrated that 5r has the highest in vivo activity, and that the four analogs are less cytotoxic than 5-FU toward W138 normal cells. In this study, 3D pharmacophore analysis was performed to investigate the matching pharmacophoric features of the synthesized compounds with trichostatin A. In silico studies showed that the investigated compounds meet the optimal needs for good oral absorption with no expected toxicity hazards.
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Affiliation(s)
- Moustafa T Gabr
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.,Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
| | - Nadia S El-Gohary
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Eman R El-Bendary
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed M El-Kerdawy
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Nanting Ni
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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46
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Bourguet E, Ozdarska K, Moroy G, Jeanblanc J, Naassila M. Class I HDAC Inhibitors: Potential New Epigenetic Therapeutics for Alcohol Use Disorder (AUD). J Med Chem 2017; 61:1745-1766. [PMID: 28771357 DOI: 10.1021/acs.jmedchem.7b00115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Alcohol use disorder (AUD) represents a serious public health issue, and discovery of new therapies is a pressing necessity. Alcohol exposure has been widely demonstrated to modulate epigenetic mechanisms, such as histone acetylation/deacetylation balance, in part via histone deacetylase (HDAC) inhibition. Epigenetic factors have been suggested to play a key role in AUD. To date, 18 different mammalian HDAC isoforms have been identified, and these have been divided into four classes. Since recent studies have suggested that both epigenetic mechanisms underlying AUD and the efficacy of HDAC inhibitors (HDACIs) in different animal models of AUD may involve class I HDACs, we herein report the development of class I HDACIs, including information regarding their structure, potency, and selectivity. More effort is required to improve the selectivity, pharmacokinetics, and toxicity profiles of HDACIs to achieve a better understanding of their efficacy in reducing addictive behavior.
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Affiliation(s)
- Erika Bourguet
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, UFR Pharmacie , Université de Reims Champagne-Ardenne , 51 rue Cognacq-Jay , 51096 Reims Cedex , France.,Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé) , 51095 Reims Cedex , France
| | - Katarzyna Ozdarska
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, UFR Pharmacie , Université de Reims Champagne-Ardenne , 51 rue Cognacq-Jay , 51096 Reims Cedex , France.,Department of Bioanalysis and Drugs Analysis , Medical University of Warsaw , S. Banacha 1 , 02-097 Warsaw , Poland
| | - Gautier Moroy
- Sorbonne Paris Cité, Molécules Thérapeutiques In Silico (MTi), INSERM UMR-S 973 , Université Paris Diderot , 35 rue Hélène Brion , 75013 Paris , France
| | - Jérôme Jeanblanc
- INSERM ERi 24, Groupe de Recherche sur l'Alcool et les Pharmacodépendances (GRAP) , Université de Picardie Jules Verne, C.U.R.S. (Centre Universitaire de Recherche en Santé) , Chemin du Thil , 80000 Amiens , France.,Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé) , 51095 Reims Cedex , France
| | - Mickaël Naassila
- INSERM ERi 24, Groupe de Recherche sur l'Alcool et les Pharmacodépendances (GRAP) , Université de Picardie Jules Verne, C.U.R.S. (Centre Universitaire de Recherche en Santé) , Chemin du Thil , 80000 Amiens , France.,Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé) , 51095 Reims Cedex , France
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47
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Cohen SM. A Bioinorganic Approach to Fragment-Based Drug Discovery Targeting Metalloenzymes. Acc Chem Res 2017; 50:2007-2016. [PMID: 28715203 DOI: 10.1021/acs.accounts.7b00242] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Metal-dependent enzymes (i.e., metalloenzymes) make up a large fraction of all enzymes and are critically important in a wide range of biological processes, including DNA modification, protein homeostasis, antibiotic resistance, and many others. Consequently, metalloenzymes represent a vast and largely untapped space for drug development. The discovery of effective therapeutics that target metalloenzymes lies squarely at the interface of bioinorganic and medicinal chemistry and requires expertise, methods, and strategies from both fields to mount an effective campaign. In this Account, our research program that brings together the principles and methods of bioinorganic and medicinal chemistry are described, in an effort to bridge the gap between these fields and address an important class of medicinal targets. Fragment-based drug discovery (FBDD) is an important drug discovery approach that is particularly well suited for metalloenzyme inhibitor development. FBDD uses relatively small but diverse chemical structures that allow for the assembly of privileged molecular collections that focus on a specific feature of the target enzyme. For metalloenzyme inhibition, the specific feature is rather obvious, namely, a metal-dependent active site. Surprisingly, prior to our work, the exploration of diverse molecular fragments for binding the metal active sites of metalloenzymes was largely unexplored. By assembling a modest library of metal-binding pharmacophores (MBPs), we have been able to find lead hits for many metalloenzymes and, from these hits, develop inhibitors that act via novel mechanisms of action. A specific case study on the use of this strategy to identify a first-in-class inhibitor of zinc-dependent Rpn11 (a component of the proteasome) is highlighted. The application of FBDD for the development of metalloenzyme inhibitors has raised several other compelling questions, such as how the metalloenzyme active site influences the coordination chemistry of bound fragments, how one can identify the best fragments for a given metalloenzyme, and many others. Among the most significant, and concerning, questions for metalloenzyme inhibition are those that reside around issues of specificity and whether metalloenzyme inhibitors can be as selective and specific as other small molecule inhibitors (i.e., compounds that inhibit enzymes that do not utilize a metal at their active site). This also leads to the question of whether metalloenzyme inhibitors might interfere more broadly with the metallome. Efforts to address these and related questions are discussed, with the expectation that our findings will illuminate some of these topics, alleviate some of these concerns, and encourage greater interest in this important, undervalued class of drug targets.
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Affiliation(s)
- Seth M. Cohen
- Department of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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48
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Lomonosova E, Daw J, Garimallaprabhakaran AK, Agyemang NB, Ashani Y, Murelli RP, Tavis JE. Efficacy and cytotoxicity in cell culture of novel α-hydroxytropolone inhibitors of hepatitis B virus ribonuclease H. Antiviral Res 2017. [PMID: 28633989 DOI: 10.1016/j.antiviral.2017.06.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chronic Hepatitis B virus (HBV) infection is a major worldwide public health problem. Current direct-acting anti-HBV drugs target the HBV DNA polymerase activity, but the equally essential viral ribonuclease H (RNaseH) activity is unexploited as a drug target. Previously, we reported that α-hydroxytropolone compounds can inhibit the HBV RNaseH and block viral replication. Subsequently, we found that our biochemical RNaseH assay underreports efficacy of the α-hydroxytropolones against HBV replication. Therefore, we conducted a structure-activity analysis of 59 troponoids against HBV replication in cell culture. These studies revealed that antiviral efficacy is diminished by larger substitutions on the tropolone ring, identified key components in the substitutions needed for high efficacy, and revealed that cytotoxicity correlates with increased lipophilicity of the α-hydroxytropolones. These data provide key guidance for further optimization of the α-hydroxytropolone scaffold as novel HBV RNaseH inhibitors.
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Affiliation(s)
- Elena Lomonosova
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, USA; Saint Louis University Liver Center, Saint Louis, MO, USA
| | - Jil Daw
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, USA
| | | | - Nana B Agyemang
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, NY, USA
| | - Yashkumar Ashani
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, NY, USA
| | - Ryan P Murelli
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, NY, USA; PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - John E Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, USA; Saint Louis University Liver Center, Saint Louis, MO, USA.
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49
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Chechetka SA, Yu Y, Zhen X, Pramanik M, Pu K, Miyako E. Light-driven liquid metal nanotransformers for biomedical theranostics. Nat Commun 2017; 8:15432. [PMID: 28561016 PMCID: PMC5460022 DOI: 10.1038/ncomms15432] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/29/2017] [Indexed: 02/07/2023] Open
Abstract
Room temperature liquid metals (LMs) represent a class of emerging multifunctional
materials with attractive novel properties. Here, we show that photopolymerized LMs
present a unique nanoscale capsule structure characterized by high water
dispersibility and low toxicity. We also demonstrate that the LM nanocapsule
generates heat and reactive oxygen species under biologically neutral near-infrared
(NIR) laser irradiation. Concomitantly, NIR laser exposure induces a transformation
in LM shape, destruction of the nanocapsules, contactless controlled release of the
loaded drugs, optical manipulations of a microfluidic blood vessel model and
spatiotemporal targeted marking for X-ray-enhanced imaging in biological organs and
a living mouse. By exploiting the physicochemical properties of LMs, we achieve
effective cancer cell elimination and control of intercellular calcium ion flux. In
addition, LMs display a photoacoustic effect in living animals during NIR laser
treatment, making this system a powerful tool for bioimaging. Liquid metals are excellent candidate materials for biomedicine, owing to their
intriguing optical properties and chemical stability. Here, the authors design
multifunctional theranostic liquid metal nanocapsules that, upon irradiation, generate
heat and reactive oxygen species and change shape to release drugs.
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Affiliation(s)
- Svetlana A Chechetka
- Department of Materials and Chemistry, Nanomaterials Research Institute (NMRI), National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Yue Yu
- Department of Materials and Chemistry, Nanomaterials Research Institute (NMRI), National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Xu Zhen
- School of Chemical and Biomedical Engineering, Nanyang Technological University (NTU), Singapore 637457, Singapore
| | - Manojit Pramanik
- School of Chemical and Biomedical Engineering, Nanyang Technological University (NTU), Singapore 637457, Singapore
| | - Kanyi Pu
- School of Chemical and Biomedical Engineering, Nanyang Technological University (NTU), Singapore 637457, Singapore
| | - Eijiro Miyako
- Department of Materials and Chemistry, Nanomaterials Research Institute (NMRI), National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
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50
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Teruya K, Rankin GM, Chrysanthopoulos PK, Tonissen KF, Poulsen S. Characterisation of Photoaffinity‐Based Chemical Probes by Fluorescence Imaging and Native‐State Mass Spectrometry. Chembiochem 2017; 18:739-754. [DOI: 10.1002/cbic.201600598] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Kanae Teruya
- Griffith Institute for Drug Discovery Griffith University Don Young Road Nathan Queensland 4111 Australia
- School of Natural Sciences Griffith University Nathan Queensland 4111 Australia
| | - Gregory M. Rankin
- Griffith Institute for Drug Discovery Griffith University Don Young Road Nathan Queensland 4111 Australia
| | | | - Kathryn F. Tonissen
- Griffith Institute for Drug Discovery Griffith University Don Young Road Nathan Queensland 4111 Australia
- School of Natural Sciences Griffith University Nathan Queensland 4111 Australia
| | - Sally‐Ann Poulsen
- Griffith Institute for Drug Discovery Griffith University Don Young Road Nathan Queensland 4111 Australia
- School of Natural Sciences Griffith University Nathan Queensland 4111 Australia
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