1
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Sakallioglu IT, Maroli AS, Leite ADL, Marshall DD, Evans BW, Zinniel DK, Dussault PH, Barletta RG, Powers R. Multi-omics Investigation into the Mechanism of Action of an Anti-tubercular Fatty Acid Analogue. J Am Chem Soc 2022; 144:21157-21173. [PMID: 36367461 PMCID: PMC10948109 DOI: 10.1021/jacs.2c08238] [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] [Indexed: 11/13/2022]
Abstract
The mechanism of action (MoA) of a clickable fatty acid analogue 8-(2-cyclobuten-1-yl)octanoic acid (DA-CB) has been investigated for the first time. Proteomics, metabolomics, and lipidomics were combined with a network analysis to investigate the MoA of DA-CB against Mycobacterium smegmatis (Msm). The metabolomics results showed that DA-CB has a general MoA related to that of ethionamide (ETH), a mycolic acid inhibitor that targets enoyl-ACP reductase (InhA), but DA-CB likely inhibits a step downstream from InhA. Our combined multi-omics approach showed that DA-CB appears to disrupt the pathway leading to the biosynthesis of mycolic acids, an essential mycobacterial fatty acid for both Msm and Mycobacterium tuberculosis (Mtb). DA-CB decreased keto-meromycolic acid biosynthesis. This intermediate is essential in the formation of mature mycolic acid, which is a key component of the mycobacterial cell wall in a process that is catalyzed by the essential polyketide synthase Pks13 and the associated ligase FadD32. The multi-omics analysis revealed further collateral alterations in bacterial metabolism, including the overproduction of shorter carbon chain hydroxy fatty acids and branched chain fatty acids, alterations in pyrimidine metabolism, and a predominate downregulation of proteins involved in fatty acid biosynthesis. Overall, the results with DA-CB suggest the exploration of this and related compounds as a new class of tuberculosis (TB) therapeutics. Furthermore, the clickable nature of DA-CB may be leveraged to trace the cellular fate of the modified fatty acid or any derived metabolite or biosynthetic intermediate.
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Affiliation(s)
- Isin T. Sakallioglu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Amith S. Maroli
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Aline De Lima Leite
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Darrell D. Marshall
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
- Total Analysis LLC, Detroit, MI 48204-3268, United States
| | - Boone W. Evans
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Denise K. Zinniel
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0905, United States
| | - Patrick H. Dussault
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Raúl G. Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0905, United States
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588-0664, United States
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588-0664, United States
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2
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Synthesis and evaluation of inhibitors of Mycobacterium tuberculosis UGM using bioisosteric replacement. Bioorg Med Chem 2022; 69:116896. [DOI: 10.1016/j.bmc.2022.116896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/08/2022] [Accepted: 06/20/2022] [Indexed: 11/22/2022]
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3
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Bedwell E, McCarthy WJ, Coyne AG, Abell C. Development of potent inhibitors by fragment-linking strategies. Chem Biol Drug Des 2022; 100:469-486. [PMID: 35854428 DOI: 10.1111/cbdd.14120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/12/2022] [Accepted: 07/17/2022] [Indexed: 11/29/2022]
Abstract
Fragment-based drug discovery (FBDD) is a method of identifying small molecule hits that can be elaborated rationally through fragment growing, merging, and linking, to afford high affinity ligands for biological targets. Despite the promised theoretical potential of fragment linking, examples are still surprisingly sparse and remain overshadowed by the successes of fragment growing. The aim of this review is to outline a number of key examples of fragment linking strategies and discuss their strengths and limitations. Structure-based approaches including X-ray crystallography and in silico methods fragment optimisation are discussed, as well as fragment linking guided by NMR experiments. Target-guided approaches, exploiting the biological target to assemble its own inhibitors through dynamic combinatorial chemistry (DCC) and kinetic target-guided synthesis (KTGS), are identified as alternative efficient methods for fragment linking.
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Affiliation(s)
- Elizabeth Bedwell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - William J McCarthy
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
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4
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Zagiel B, Peker T, Marquant R, Cazals G, Webb G, Miclet E, Bich C, Sachon E, Moumné R. Dynamic Amino Acid Side‐Chains Grafting on Folded Peptide Backbone**. Chemistry 2022; 28:e202200454. [DOI: 10.1002/chem.202200454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Benjamin Zagiel
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
| | - Taleen Peker
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
| | - Rodrigue Marquant
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
| | - Guillaume Cazals
- UMR 5247-CNRS-UM-ENSCM Institut des Biomolécules Max Mousseron (IBMM) Université de Montpellier 34293 Montpellier France
| | - Gabrielle Webb
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
| | - Emeric Miclet
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
| | - Claudia Bich
- UMR 5247-CNRS-UM-ENSCM Institut des Biomolécules Max Mousseron (IBMM) Université de Montpellier 34293 Montpellier France
| | - Emmanuelle Sachon
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
- MS3 U platform UFR 926 UFR 927 Sorbonne Université 4 place Jussieu 75005 Paris France
| | - Roba Moumné
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
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5
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Belete TM. Recent Progress in the Development of Novel Mycobacterium Cell Wall Inhibitor to Combat Drug-Resistant Tuberculosis. Microbiol Insights 2022; 15:11786361221099878. [PMID: 35645569 PMCID: PMC9131376 DOI: 10.1177/11786361221099878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/21/2022] [Indexed: 11/16/2022] Open
Abstract
Despite decades of research in drug development against TB, it is still the leading cause of death due to infectious diseases. The long treatment duration, patient noncompliance coupled with the ability of the tuberculosis bacilli to resist the current drugs increases multidrug-resistant tuberculosis that exacerbates the situation. Identification of novel drug targets is important for the advancement of drug development against Mycobacterium tuberculosis. The development of an effective treatment course that could help us eradicates TB. Hence, we require drugs that could eliminate the bacteria and shorten the treatment duration. This review briefly describes the available data on the peptidoglycan component structural characterization, identification of the metabolic pathway, and the key enzymes involved in the peptidoglycan synthesis, like N-Acetylglucosamine-1-phosphate uridyltransferase, mur enzyme, alanine racemase as well as their inhibition. Besides, this paper also provides studies on mycolic acid and arabinogalactan synthesis and the transport mechanisms that show considerable promise as new targets to develop a new product with their inhibiter.
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Affiliation(s)
- Tafere Mulaw Belete
- Department of Pharmacology, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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6
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Caillaud K, Ladavière C. Water‐soluble (poly)acylhydrazones: Syntheses and Applications. MACROMOL CHEM PHYS 2022. [DOI: 10.1002/macp.202200064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kilian Caillaud
- Univ Lyon, CNRS, UMR 5223, Ingénierie des Matériaux Polymères Université Claude Bernard Lyon1, INSA Lyon, Université Jean Monnet Villeurbanne Cédex F‐69622 France
| | - Catherine Ladavière
- Univ Lyon, CNRS, UMR 5223, Ingénierie des Matériaux Polymères Université Claude Bernard Lyon1, INSA Lyon, Université Jean Monnet Villeurbanne Cédex F‐69622 France
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7
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Ahmed DM, Chen JM, Sanders DAR. Pyrazole and Triazole Derivatives as Mycobacterium tuberculosis UDP-Galactopyranose Inhibitors. Pharmaceuticals (Basel) 2022; 15:ph15020197. [PMID: 35215309 PMCID: PMC8874540 DOI: 10.3390/ph15020197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/30/2022] Open
Abstract
UDP-galactopyranose mutase (UGM) is an essential enzyme involved in the bacterial cell wall synthesis, and is not present in mammalian cells. Thus, UGM from Mycobacterium tuberculosis (Mtb) represents a novel and attractive drug target for developing antituberculosis agents. A pyrazole-based compound, MS208, was previously identified as a mixed inhibitor of MtbUGM which targets an allosteric site. To understand more about the structure activity relationship around the MS208 scaffold as a MtbUGM inhibitor, thirteen pyrazoles and triazole analogues were synthesized and tested against both MtbUGM and Mycobacterium tuberculosis in vitro. While the introduced structural modifications to MS208 did not improve the antituberculosis activity, most of the compounds showed MtbUGM inhibitory activity. Interestingly, the pyrazole derivative DA10 showed a competitive model for MtbUGM inhibition with improved Ki value of 51 ± 4 µM. However, the same compound did not inhibit the growth of Mycobacterium tuberculosis.
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Affiliation(s)
- Dalia M. Ahmed
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada;
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Jeffrey M. Chen
- Vaccine and Infectious Disease Organization, Saskatoon, SK S7N 5E3, Canada;
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
- Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, SK S7N 2Z4, Canada
| | - David A. R. Sanders
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada;
- Correspondence:
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8
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Wu Y, Zhao S, Hu L. Identification of potent α-amylase inhibitors via dynamic combinatorial chemistry. Bioorg Med Chem 2022; 55:116609. [PMID: 35021143 DOI: 10.1016/j.bmc.2022.116609] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/31/2021] [Accepted: 01/02/2022] [Indexed: 11/30/2022]
Abstract
In this study, we report for the first time the discovery of potent α-amylase inhibitors using principle of dynamic combinatorial chemistry. The best compound identified exhibited not only high inhibitory efficiency but also low cytotoxicity. The binding mode and possible mechanism are determined in the subsequent kinetic and molecular docking studies.
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Affiliation(s)
- Yao Wu
- School of Pharmacy, Jiangsu University, 301 Xuefu Rd., Zhenjiang, China
| | - Shuang Zhao
- School of Pharmacy, Jiangsu University, 301 Xuefu Rd., Zhenjiang, China
| | - Lei Hu
- School of Pharmacy, Jiangsu University, 301 Xuefu Rd., Zhenjiang, China.
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9
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Pecnard S, Hamze A, Pozzo JL, Alami M, Provot O. Synthesis of Oxazino[4,3-a]indoles and biological applications. Eur J Med Chem 2021; 224:113728. [PMID: 34340043 DOI: 10.1016/j.ejmech.2021.113728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/20/2021] [Accepted: 07/27/2021] [Indexed: 12/23/2022]
Abstract
This review brings together the various pathways to the oxazino[4,3-a]indole motif over the last decades. Representative examples showing the scope of these processes will illustrate the synthetic pathways and the biological activity of the synthesized oxazinoindoles will be mentioned wherever possible.
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Affiliation(s)
- Shannon Pecnard
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France
| | - Abdallah Hamze
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France
| | - Jean-Luc Pozzo
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR5255, 351 cours Libération, F-33405, Bordeaux, France
| | - Mouad Alami
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France
| | - Olivier Provot
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France.
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10
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Champciaux B, Raynaud C, Viljoen A, Chene L, Thibonnet J, Vincent SP, Kremer L, Thiery E. Synthesis and biological evaluation of 3,4-dihydro-1H-[1,4] oxazepino [6,5,4-hi] indol-1-ones and 4,6-dihydrooxepino [5,4,3-cd] indol-1(3H)-ones as Mycobacterium tuberculosis inhibitors. Bioorg Med Chem 2021; 43:116248. [PMID: 34274760 DOI: 10.1016/j.bmc.2021.116248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/13/2021] [Accepted: 05/28/2021] [Indexed: 11/16/2022]
Abstract
This study focuses on the synthesis of 1,7- and 3,4-indole-fused lactones via a simple and efficient reaction sequence. The functionalization of these "oxazepino-indole" and "oxepino-indole" tricycles is carried out by palladium catalysed CC coupling, nucleophilic substitution or 1,3-dipolar cycloaddition. The evaluation of their activity against Mycobacterium tuberculosis shows that the "oxazepino-indole" structure is a new inhibitor of M. tuberculosis growth in vitro.
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Affiliation(s)
- Bastien Champciaux
- Laboratoire Synthèse et Isolement de Molécules Bioactives (SIMBA, EA 7502), Université de Tours, Faculté de Pharmacie, Parc de Grandmont, 31 Avenue Monge, 37200 Tours, France
| | - Clément Raynaud
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS UMR 9004, Université de Montpellier, 34293 Montpellier, France
| | - Albertus Viljoen
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS UMR 9004, Université de Montpellier, 34293 Montpellier, France
| | - Loïc Chene
- Department of Chemistry, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Jérôme Thibonnet
- Laboratoire Synthèse et Isolement de Molécules Bioactives (SIMBA, EA 7502), Université de Tours, Faculté de Pharmacie, Parc de Grandmont, 31 Avenue Monge, 37200 Tours, France
| | - Stéphane P Vincent
- Department of Chemistry, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS UMR 9004, Université de Montpellier, 34293 Montpellier, France; INSERM, IRIM, 34293 Montpellier, France
| | - Emilie Thiery
- Laboratoire Synthèse et Isolement de Molécules Bioactives (SIMBA, EA 7502), Université de Tours, Faculté de Pharmacie, Parc de Grandmont, 31 Avenue Monge, 37200 Tours, France.
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11
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Fu J, Fu H, Xia Y, N'Go I, Cao J, Pan W, Vincent SP. Identification of inhibitors of UDP-galactopyranose mutase via combinatorial in situ screening. Org Biomol Chem 2021; 19:1818-1826. [PMID: 33565547 DOI: 10.1039/d1ob00138h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
An in situ screening assay for UDP-galactopyranose mutase (UGM, an essential enzyme of M. tuberculosis cell wall biosynthesis) has been developed to discover novel UGM inhibitors. The approach is based on the amide-forming reaction of an amino acid core with various cinnamic acids, followed by a direct fluorescence polarization assay to identify the best UGM binders without isolation and purification of the screened ligands. This assay allows us to perform one-pot high-throughput synthesis and screening of enzyme inhibitors in a 384-well plate format. UGM ligands were successfully identified by this technology and their inhibition levels were established from pure synthetic compounds in vitro and in a whole cell antibacterial assay. This study provides a blueprint for designing enamide structures as new UGM inhibitors and anti-mycobacterial agents.
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Affiliation(s)
- Jian Fu
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China and Department of Chemistry, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium. and The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Huixiao Fu
- Department of Chemistry, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium.
| | - Yufen Xia
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Inès N'Go
- Department of Chemistry, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium.
| | - Jun Cao
- Department of Chemistry, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium.
| | - Weidong Pan
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Stéphane P Vincent
- Department of Chemistry, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium.
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12
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Canal-Martín A, Pérez-Fernández R. Protein-Directed Dynamic Combinatorial Chemistry: An Efficient Strategy in Drug Design. ACS OMEGA 2020; 5:26307-26315. [PMID: 33110958 PMCID: PMC7581073 DOI: 10.1021/acsomega.0c03800] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/24/2020] [Indexed: 05/05/2023]
Abstract
Protein-directed dynamic combinatorial chemistry (P-D DCC) is considered a powerful strategy to identify ligands to pharmacologically relevant protein targets. The protein selects its affinity ligands in situ through a thermodynamic templated effect in which the library composition shifts to the formation of specific library members at the expense of other (nonbinding) species. The increase in concentration of the selected species is known as amplification and leads to the discovery of new hit compounds for protein targets. This Mini-Review contains an updated overview of the protein-directed DCC applications and the fundamental aspects to take into account when designing a P-D DCC experiment such as the most biocompatible reversible reactions and the methodology used to analyze the experiments.
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13
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Hartman AM, Jumde VR, Elgaher WAM, Te Poele EM, Dijkhuizen L, Hirsch AKH. Potential Dental Biofilm Inhibitors: Dynamic Combinatorial Chemistry Affords Sugar-Based Molecules that Target Bacterial Glucosyltransferase. ChemMedChem 2020; 16:113-123. [PMID: 32542998 PMCID: PMC7818428 DOI: 10.1002/cmdc.202000222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/15/2020] [Indexed: 12/21/2022]
Abstract
We applied dynamic combinatorial chemistry (DCC) to find novel ligands of the bacterial virulence factor glucosyltransferase (GTF) 180. GTFs are the major producers of extracellular polysaccharides, which are important factors in the initiation and development of cariogenic dental biofilms. Following a structure‐based strategy, we designed a series of 36 glucose‐ and maltose‐based acylhydrazones as substrate mimics. Synthesis of the required mono‐ and disaccharide‐based aldehydes set the stage for DCC experiments. Analysis of the dynamic combinatorial libraries (DCLs) by UPLC‐MS revealed major amplification of four compounds in the presence of GTF180. Moreover, we found that derivatives of the glucose‐acceptor maltose at the C1‐hydroxy group act as glucose‐donors and are cleaved by GTF180. The synthesized hits display medium to low binding affinity (KD values of 0.4–10.0 mm) according to surface plasmon resonance. In addition, they were investigated for inhibitory activity in GTF‐activity assays. The early‐stage DCC study reveals that careful design of DCLs opens up easy access to a broad class of novel compounds that can be developed further as potential inhibitors.
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Affiliation(s)
- Alwin M Hartman
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG Groningen, The Netherlands
| | - Varsha R Jumde
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG Groningen, The Netherlands
| | - Walid A M Elgaher
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Evelien M Te Poele
- Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen (The, Netherlands.,CarbExplore Research BV, Zernikepark 1, 9747 AN, Groningen (The, Netherlands
| | - Lubbert Dijkhuizen
- Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen (The, Netherlands.,CarbExplore Research BV, Zernikepark 1, 9747 AN, Groningen (The, Netherlands
| | - Anna K H Hirsch
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG Groningen, The Netherlands
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14
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Synthesis and evaluation of heterocycle structures as potential inhibitors of Mycobacterium tuberculosis UGM. Bioorg Med Chem 2020; 28:115579. [DOI: 10.1016/j.bmc.2020.115579] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/26/2020] [Accepted: 05/29/2020] [Indexed: 11/19/2022]
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15
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16
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Jiao T, Wu G, Zhang Y, Shen L, Lei Y, Wang C, Fahrenbach AC, Li H. Self‐Assembly in Water with N‐Substituted Imines. Angew Chem Int Ed Engl 2020; 59:18350-18367. [DOI: 10.1002/anie.201910739] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/09/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Tianyu Jiao
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Guangcheng Wu
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Yang Zhang
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Libo Shen
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Ye Lei
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Cai‐Yun Wang
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | | | - Hao Li
- Department of Chemistry Zhejiang University Hangzhou 310027 China
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17
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Xu J, Zhang S, Zhao S, Hu L. Identification and synthesis of an efficient multivalent E. coli heat labile toxin inhibitor __ A dynamic combinatorial chemistry approach. Bioorg Med Chem 2020; 28:115436. [DOI: 10.1016/j.bmc.2020.115436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/01/2020] [Accepted: 03/10/2020] [Indexed: 12/20/2022]
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18
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Biosynthesis of Galactan in Mycobacterium tuberculosis as a Viable TB Drug Target? Antibiotics (Basel) 2020; 9:antibiotics9010020. [PMID: 31935842 PMCID: PMC7168186 DOI: 10.3390/antibiotics9010020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/21/2022] Open
Abstract
While target-based drug design has proved successful in several therapeutic areas, this approach has not yet provided compelling outcomes in the field of antibacterial agents. This statement remains especially true for the development of novel therapeutic interventions against tuberculosis, an infectious disease that is among the top ten leading causes of death globally. Mycobacterial galactan is an important component of the protective cell wall core of the tuberculosis pathogen and it could provide a promising target for the design of new drugs. In this review, we summarize the current knowledge on galactan biosynthesis in Mycobacterium tuberculosis, including landmark findings that led to the discovery and understanding of three key enzymes in this pathway: UDP-galactose mutase, and galactofuranosyl transferases GlfT1 and GlfT2. Moreover, we recapitulate the efforts aimed at their inhibition. The predicted common transition states of the three enzymes provide the lucrative possibility of multitargeting in pharmaceutical development, a favourable property in the mitigation of drug resistance. We believe that a tight interplay between target-based computational approaches and experimental methods will result in the development of original inhibitors that could serve as the basis of a new generation of drugs against tuberculosis.
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Xu J, Zhao S, Zhang S, Pei J, Li Y, Zhang Y, He X, Hu L. Development of a multivalent acetylcholinesterase inhibitor via dynamic combinatorial chemistry. Int J Biol Macromol 2019; 150:1184-1191. [PMID: 31758986 DOI: 10.1016/j.ijbiomac.2019.10.127] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 01/13/2023]
Abstract
In this study, we report the generation of a polymer based dynamic combinatorial library (DCL) using aldehyde-functionalized linear poly(glycidol) and hydrazide derivatives as initial building blocks. In combination with tetrameric acetylcholinesterase (AChE), a certain type of amplified acylhydrazone side chain is identified and further used for the synthesis of a multivalent AChE inhibitor. The cytotoxicity and inhibition properties of the multivalent inhibitor are evaluated, and the results indicate superior bioactivity compared to the commercial reference Edrophonium chloride.
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Affiliation(s)
- Jintao Xu
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China
| | - Shuang Zhao
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China
| | - Shixin Zhang
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China
| | - Jialu Pei
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China
| | - Yanhong Li
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China
| | - Yongxin Zhang
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China
| | - Xiangyang He
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China
| | - Lei Hu
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China.
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20
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Hartman AM, Gierse RM, Hirsch AKH. Protein-Templated Dynamic Combinatorial Chemistry: Brief Overview and Experimental Protocol. European J Org Chem 2019; 2019:3581-3590. [PMID: 31680778 PMCID: PMC6813629 DOI: 10.1002/ejoc.201900327] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Indexed: 01/08/2023]
Abstract
Dynamic combinatorial chemistry (DCC) is a powerful tool to identify bioactive compounds. This efficient technique allows the target to select its own binders and circumvents the need for synthesis and biochemical evaluation of all individual derivatives. An ever-increasing number of publications report the use of DCC on biologically relevant target proteins. This minireview complements previous reviews by focusing on the experimental protocol and giving detailed examples of essential steps and factors that need to be considered, such as protein stability, buffer composition and cosolvents.
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Affiliation(s)
- Alwin M. Hartman
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Stratingh Institute for ChemistryHelmholtz Centre for Infection Research (HZI)University of GroningenNijenborgh 79747AG GroningenThe Netherlands
- Department of PharmacyMedicinal ChemistrySaarland UniversityCampus Building E8.166123SaarbrückenGermany
| | - Robin M. Gierse
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Stratingh Institute for ChemistryHelmholtz Centre for Infection Research (HZI)University of GroningenNijenborgh 79747AG GroningenThe Netherlands
- Department of PharmacyMedicinal ChemistrySaarland UniversityCampus Building E8.166123SaarbrückenGermany
| | - Anna K. H. Hirsch
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Stratingh Institute for ChemistryHelmholtz Centre for Infection Research (HZI)University of GroningenNijenborgh 79747AG GroningenThe Netherlands
- Department of PharmacyMedicinal ChemistrySaarland UniversityCampus Building E8.166123SaarbrückenGermany
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21
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Yoneyama K, Suzuki R, Kuramochi Y, Satake A. A Candidate for Multitopic Probes for Ligand Discovery in Dynamic Combinatorial Chemistry. Molecules 2019; 24:E2166. [PMID: 31181809 PMCID: PMC6600254 DOI: 10.3390/molecules24112166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 05/30/2019] [Accepted: 06/07/2019] [Indexed: 11/26/2022] Open
Abstract
Multifunctionalized materials are expected to be versatile probes to find specific interactions between a ligand and a target biomaterial. Thus, efficient methods to prepare possible combinations of the functionalities is desired. The concept of dynamic combinatorial chemistry (DCC) is ideal for the generation of any possible combination, as well as screening for target biomaterials. Here, we propose a new molecular design of multitopic probes for ligand discovery in DCC. We synthesized a new Gable Porphyrin, GP1, having prop-2-yne groups as a scaffold to introduce various functional groups. GP1 is a bis(imidazolylporphyrinatozinc) compound connected through a 1,3-phenylene moiety, and it gives macrocycles spontaneously and quantitatively by strong imidazole-to-zinc complementary coordination. Some different types of functional groups were introduced into GP1 in high yields. Formation of heterogeneous macrocycles composed of GP1 derivatives having different types of substituents was accomplished under equilibrium conditions. These results promise that enormous numbers of macrocycles having various functional groups can be provided when the kinds of GP components increase. These features are desirable for DCC, and the present system using GP1 is a potential candidate to provide a dynamic combinatorial library of multitopic probes to discover specific interactions between a ligand and a biomaterial.
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Affiliation(s)
- Keiko Yoneyama
- Graduate School of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Rina Suzuki
- Graduate School of Chemical Sciences and Technology, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Yusuke Kuramochi
- Department of Chemistry, Faculty of Science Division II, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Akiharu Satake
- Department of Chemistry, Faculty of Science Division II, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
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22
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Beatty MA, Pye AT, Shaurya A, Kim B, Selinger AJ, Hof F. Using reversible non-covalent and covalent bonds to create assemblies and equilibrating molecular networks that survive 5 molar urea. Org Biomol Chem 2019; 17:2081-2086. [PMID: 30698579 DOI: 10.1039/c8ob02909a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The limits of self-assembly and host-guest chemistry in water solutions containing competitive solutes are largely unexplored. We report here a new family of self-assembling systems that are stitched together at two levels by reversible hydrazone bonds and by non-covalent self-assembly in strongly denaturing conditions. Three different hydrazides of various charge and hydrophobicity are combined with an aldehyde-containing calixarene, and each system spontaneously forms AB hydrazones that subsequently self-assemble into four-component (AB)2 structures in water. The assemblies display varying responses to added NaCl and/or urea. The most robust assembly survives completely intact in solution up to 5 M urea. We also combine the aldehyde calixarene with two different hydrazides in the same tube to create complex, competitive dynamic libraries. We report experiments in which the composition of the dynamic equilibrating library is under the control of self-assembly, allowing the systems to choose the components that form the most stable assemblies under a variety of competitive solutions conditions. These dynamic networks of equilibrating molecules maintain remarkably similar equilibrium positions under widely varying concentrations of urea and NaCl.
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Affiliation(s)
- Meagan A Beatty
- Department of Chemistry, University of Victoria, Victoria, BC V8W 3V6 Canada.
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Frei P, Hevey R, Ernst B. Dynamic Combinatorial Chemistry: A New Methodology Comes of Age. Chemistry 2018; 25:60-73. [DOI: 10.1002/chem.201803365] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Priska Frei
- Institute of Molecular Pharmacy, PharmacenterUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Rachel Hevey
- Institute of Molecular Pharmacy, PharmacenterUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Beat Ernst
- Institute of Molecular Pharmacy, PharmacenterUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
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Bartolec B, Altay M, Otto S. Template-promoted self-replication in dynamic combinatorial libraries made from a simple building block. Chem Commun (Camb) 2018; 54:13096-13098. [PMID: 30395138 DOI: 10.1039/c8cc06253f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report dynamic combinatorial libraries made from a simple building block that is on the verge of enabling self-assembly driven self-replication. Adding a template provides a sufficient additional push yielding self-replication. Self-assembly and self-replication can emerge with building blocks that are considerably smaller than those reported thus far.
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Affiliation(s)
- B Bartolec
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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García P, Alonso VL, Serra E, Escalante AM, Furlan RLE. Discovery of a Biologically Active Bromodomain Inhibitor by Target-Directed Dynamic Combinatorial Chemistry. ACS Med Chem Lett 2018; 9:1002-1006. [PMID: 30344907 DOI: 10.1021/acsmedchemlett.8b00247] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/11/2018] [Indexed: 12/24/2022] Open
Abstract
Target-directed dynamic combinatorial chemistry (DCC) has emerged as a strategy for the identification of inhibitors of relevant therapeutic targets. In this contribution, we use this strategy for the identification of a high-affinity binder of a parasite target, the Trypanosoma cruzi bromodomain-containing protein TcBDF3. This protein is essential for viability of T. cruzi, the protozoan parasite that causes Chagas disease. A small dynamic library of acylhydrazones was prepared from aldehydes and acylhydrazides at neutral pH in the presence of aniline. The most amplified library member shows (a) high affinity for the template, (b) interesting antiparasitic activity against different parasite forms, and (c) low toxicity against Vero cells. In addition, parasites are rescued from the compound toxicity by TcBDF3 overexpression, suggesting that the toxicity of this compound is due to the TcBDF3 inhibition, i.e., the binding event that initially drives the molecular amplification is reproduced in the parasite, leading to selective toxicity.
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Affiliation(s)
- Paula García
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, S2002LRK Rosario, Argentina
| | - Victoria L. Alonso
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, S2002LRK Rosario, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, CONICET, Ocampo y Esmeralda, 2000 Rosario, Argentina
| | - Esteban Serra
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, S2002LRK Rosario, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, CONICET, Ocampo y Esmeralda, 2000 Rosario, Argentina
| | - Andrea M. Escalante
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, S2002LRK Rosario, Argentina
| | - Ricardo L. E. Furlan
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, S2002LRK Rosario, Argentina
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Antimycobacterial, Enzyme Inhibition, and Molecular Interaction Studies of Psoromic Acid in Mycobacterium tuberculosis: Efficacy and Safety Investigations. J Clin Med 2018; 7:jcm7080226. [PMID: 30127304 PMCID: PMC6111308 DOI: 10.3390/jcm7080226] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/13/2018] [Accepted: 08/17/2018] [Indexed: 01/11/2023] Open
Abstract
The current study explores the antimycobacterial efficacy of lichen-derived psoromic acid (PA) against clinical strains of Mycobacterium tuberculosis (M.tb). Additionally, the inhibitory efficacy of PA against two critical enzymes associated with M.tb, namely, UDP-galactopyranose mutase (UGM) and arylamine-N-acetyltransferase (TBNAT), as drug targets for antituberculosis therapy were determined. PA showed a profound inhibitory effect towards all the M.tb strains tested, with minimum inhibitory concentrations (MICs) ranging between 3.2 and 4.1 µM, and selectivity indices (SIs) ranging between 18.3 and 23.4. On the other hand, the standard drug isoniazid (INH) displayed comparably high MIC values (varying from 5.4 to 5.8 µM) as well as low SI values (13.0–13.9). Interestingly, PA did not exhibit any cytotoxic effects on a human liver hepatocellular carcinoma cell line even at the highest concentration tested (75 µM). PA demonstrated remarkable suppressing propensity against UGM compared to standard uridine-5'-diphosphate (UDP), with 85.8 and 99.3% of inhibition, respectively. In addition, PA also exerted phenomenal inhibitory efficacy (half maximal inhibitory concentration (IC50) value = 8.7 µM, and 77.4% inhibition) against TBNAT compared with standard INH (IC50 value = 6.2 µM and 96.3% inhibition). Furthermore, in silico analysis validated the outcomes of in vitro assays, as the molecular interactions of PA with the active sites of UGM and TBNAT were unveiled using molecular docking and structure–activity relationship studies. Concomitantly, our findings present PA as an effective and safe natural drug plausible for use in controlling tuberculosis infections.
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