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Sun L, Yu Q, Peng F, Sun C, Wang D, Pu L, Xiong F, Tian Y, Peng C, Zhou Q. The antibacterial activity of berberine against Cutibacterium acnes: its therapeutic potential in inflammatory acne. Front Microbiol 2024; 14:1276383. [PMID: 38249466 PMCID: PMC10797013 DOI: 10.3389/fmicb.2023.1276383] [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: 08/11/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Cutibacterium acnes (C. acnes) is a major pathogen implicated in the evolution of acne inflammation. Inhibition of C. acnes-induced inflammation is a prospective acne therapy strategy. Berberine (BBR), a safe and effective natural ingredient, has been proven to exhibit powerful antimicrobial and anti-inflammatory properties. However, the antimicrobial effect of BBR against C. acnes and its role in C. acnes-mediated inflammatory acne have not been explored. The objective of this investigation was to assess the antibacterial activity of BBR against C. acnes and its inhibitory effect on the inflammatory response. The results of in vitro experiments showed that BBR exhibited significant inhibition zones against four C. acnes strains, with the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) in the range of 6.25-12.5 μg/mL and 12.5-25 μg/mL, respectively. On the bacterial growth curve, the BBR-treated C. acnes exhibited obvious growth inhibition. Transmission electron microscopy (TEM) images indicated that BBR treatment resulted in significant morphological changes in C. acnes. High-content imaging analysis further confirmed that BBR could effectively inhibit the proliferation of C. acnes. The disruption of cell wall and cell membrane structure by BBR treatment was preliminary confirmed according to the leakage of cellular contents such as potassium (K+), magnesium (Mg2+), and alkaline phosphatase (AKP). Furthermore, we found that BBR could reduce the transcript levels of genes associated with peptidoglycan synthesis (murC, murD, mraY, and murG). Meanwhile, we investigated the modulatory ability of BBR on C. acnes-induced skin inflammation in mice. The results showed that BBR effectively reduced the number of C. acnes colonized in mice's ears, thereby alleviating ear swelling and erythema and significantly decreasing ear thickness and weight. In addition, BBR significantly decreased the levels of pro-inflammatory cytokines IL-6, IL-1β, and TNF-α in auricular tissues. These results suggest that BBR has the potential to treat inflammatory acne induced by C. acnes.
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Affiliation(s)
- Luyao Sun
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qian Yu
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Fu Peng
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, China
| | - Chen Sun
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Daibo Wang
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lin Pu
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Fang Xiong
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuncai Tian
- Shanghai Zhizhenzhichen Technologies Co., Ltd., Shanghai, China
| | - Cheng Peng
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qinmei Zhou
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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2
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Hervin V, Roy V, Agrofoglio LA. Antibiotics and Antibiotic Resistance-Mur Ligases as an Antibacterial Target. Molecules 2023; 28:8076. [PMID: 38138566 PMCID: PMC10745416 DOI: 10.3390/molecules28248076] [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: 07/29/2023] [Revised: 11/09/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The emergence of Multidrug Resistance (MDR) strains of bacteria has accelerated the search for new antibacterials. The specific bacterial peptidoglycan biosynthetic pathway represents opportunities for the development of novel antibacterial agents. Among the enzymes involved, Mur ligases, described herein, and especially the amide ligases MurC-F are key targets for the discovery of multi-inhibitors, as they share common active sites and structural features.
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Affiliation(s)
| | - Vincent Roy
- ICOA UMR CNRS 7311, Université d’Orléans et CNRS, Rue de Chartres, 45067 Orléans, France;
| | - Luigi A. Agrofoglio
- ICOA UMR CNRS 7311, Université d’Orléans et CNRS, Rue de Chartres, 45067 Orléans, France;
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3
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Azam MA, Jupudi S. MurD inhibitors as antibacterial agents: a review. CHEMICAL PAPERS 2020. [DOI: 10.1007/s11696-020-01057-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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4
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Bogdanov AV, Iskhakova KR, Voloshina AD, Sapunova AS, Kulik NV, Terekhova NV, Arsenyev MV, Ziyatdinova GK, Bukharov SV. Ammonium-Charged Sterically Hindered Phenols with Antioxidant and Selective Anti-Gram-Positive Bacterial Activity. Chem Biodivers 2020; 17:e2000147. [PMID: 32349191 DOI: 10.1002/cbdv.202000147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 03/27/2020] [Indexed: 11/10/2022]
Abstract
The increase in the resistance of pathogens, in particular Staphylococcus aureus, to the action of antibiotics necessitates the search for new readily available and non-toxic drugs. In solving this problem, phenolic acylhydrazones have high potential. In this communication, the synthesis of quaternary ammonium compounds containing a differently substituted phenolic moiety has been performed. An initial study of antimicrobial activity showed that these compounds are highly selective against S. aureus and B. cereus. The highest activity (MIC 2.0 μm) was shown by hydrazones containing a catechol fragment. These compounds are more than 3-fold more active against S. aureus and 3-10-fold more active against B. cereus than norfloxacin. Low hemolytic and high antioxidant activities of all new compounds were also established.
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Affiliation(s)
- Andrei V Bogdanov
- A.E.Arbuzov Institute of Organic and Physical Chemistry, FRC, Kazan Scientific Center of RAS, 8 Arbuzov Str., Kazan, 420088, Russian Federation
| | - Kamilla R Iskhakova
- Kazan National Research Technological University, 68 K. Marx Str., Kazan, 420015, Russian Federation
| | - Alexandra D Voloshina
- A.E.Arbuzov Institute of Organic and Physical Chemistry, FRC, Kazan Scientific Center of RAS, 8 Arbuzov Str., Kazan, 420088, Russian Federation
| | - Anastasia S Sapunova
- A.E.Arbuzov Institute of Organic and Physical Chemistry, FRC, Kazan Scientific Center of RAS, 8 Arbuzov Str., Kazan, 420088, Russian Federation
| | - Natalia V Kulik
- A.E.Arbuzov Institute of Organic and Physical Chemistry, FRC, Kazan Scientific Center of RAS, 8 Arbuzov Str., Kazan, 420088, Russian Federation
| | - Natalia V Terekhova
- A.E.Arbuzov Institute of Organic and Physical Chemistry, FRC, Kazan Scientific Center of RAS, 8 Arbuzov Str., Kazan, 420088, Russian Federation
| | - Maxim V Arsenyev
- G. A. Razuvaev Institute of Organometallic Chemistry, RAS, 49 Tropinin Str., Nizhny, Novgorod, 603950, Russian Federation
| | - Guzel K Ziyatdinova
- Kazan Federal University, 18 Kremlevskaya Str., Kazan, 420008, Russian Federation
| | - Sergey V Bukharov
- Kazan National Research Technological University, 68 K. Marx Str., Kazan, 420015, Russian Federation
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5
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Shan L, Wenling Q, Mauro P, Stefano B. Antibacterial Agents Targeting the Bacterial Cell Wall. Curr Med Chem 2020; 27:2902-2926. [PMID: 32003656 DOI: 10.2174/0929867327666200128103653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 11/22/2022]
Abstract
The introduction of antibiotics to treat bacterial infections either by killing or blocking their growth has been accompanied by the studies of mechanism that allows the drugs to kill the bacteria or to stop their proliferation. In such a scenario, the emergence of antibacterial agents active on the bacterial cell wall has been of fundamental importance in the fight against bacterial agents responsible for severe diseases. As a matter of fact, the cell wall, which plays many roles during the lifecycle, is an essential constituent of most bacteria. This overview focuses on the intracellular steps of peptidoglycan biosynthesis and the research of new antibacterial agents based on the enzymes involved in these early steps of the formation of cell membrane components.
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Affiliation(s)
- Li Shan
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, China
| | - Qin Wenling
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, China
| | - Panunzio Mauro
- Isof-CNR Chemistry Department, Via Selmi, 2, 40126 Bologna, Italy
| | - Biondi Stefano
- BioVersys AG, C/o Technologiepark Basel, Hochbergerstrasse 60c, CH- 4057 Basel, Switzerland
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Helal AM, Sayed AM, Omara M, Elsebaei MM, Mayhoub AS. Peptidoglycan pathways: there are still more! RSC Adv 2019; 9:28171-28185. [PMID: 35530449 PMCID: PMC9071014 DOI: 10.1039/c9ra04518j] [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: 06/16/2019] [Accepted: 08/22/2019] [Indexed: 11/21/2022] Open
Abstract
The discovery of 3rd and 4th generations of currently existing classes of antibiotics has not hindered bacterial resistance, which is escalating at an alarming global level. This review follows WHO recommendations through implementing new criteria for newly discovered antibiotics. These recommendations focus on abandoning old scaffolds and hitting new targets. In light of these recommendations, this review discusses seven bacterial proteins that no commercial antibiotics have targeted yet, alongside their reported chemical scaffolds.
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Affiliation(s)
- Ahmed M Helal
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Ahmed M Sayed
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Mariam Omara
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Mohamed M Elsebaei
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Abdelrahman S Mayhoub
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
- University of Science and Technology, Zewail City of Science and Technology Giza Egypt
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7
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Identification of Ideal Multi-targeting Bioactive Compounds Against Mur Ligases of Enterobacter aerogenes and Its Binding Mechanism in Comparison with Chemical Inhibitors. Interdiscip Sci 2017; 11:135-144. [PMID: 29086207 DOI: 10.1007/s12539-017-0261-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 08/02/2017] [Accepted: 09/11/2017] [Indexed: 10/18/2022]
Abstract
Enterobacter aerogenes have been reported as important opportunistic and multi-resistant bacterial pathogens for humans during the last three decades in hospital wards. The emergence of drug-resistant E. aerogenes demands the need for developing new drugs. Peptidoglycan is an important component of the cell wall of bacteria and the peptidoglycan biochemical pathway is considered as the best source of antibacterial targets. Within this pathway, four Mur ligases MurC, MurD, MurE, and MurF are responsible for the successive additions of L-alanine and suitable targets for developing novel antibacterial drugs. As an inference from this fact, we modeled the three-dimensional structure of above Mur ligases using best template structures available in PDB and analyzed its common binding features. Structural refinement and energy minimization of the predicted Mur ligases models is also being done using molecular dynamics studies. The models of Mur ligases were further investigated for in silico docking studies using bioactive plant compounds from the literature. Interestingly, these results indicate that four plant compounds Isojuripidine, Atroviolacegenin, Porrigenin B, and Nummularogenin showing better docking results in terms of binding energy and number of hydrogen bonds. All these four compounds are spirostan-based compounds with differences in side chains and the amino acid such as ASN, LYS, THR, HIS, ARG (polar) and PHE, GLY, VAL, ALA, MET (non-polar) playing active role in binding site of all four Mur ligases. Overall, in the predicted model, the four plant compounds with its binding features could pave way to design novel multi-targeted antibacterial plant-based bioactive compounds specific to Mur ligases for the treatment of Enterobacter infections.
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Pansare DN, Shelke RN, Shinde DB. A Facial Synthesis and Anticancer Activity of (Z)-2-((5-(4-nitrobenzylidene)-4-oxo-4,5-dihydrothiazol-2-yl)amino)-substituted Acid. J Heterocycl Chem 2017. [DOI: 10.1002/jhet.2919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Dattatraya N. Pansare
- Department of Chemical Technology; Dr. Babasaheb Ambedkar Marathwada University; Aurangabad 431 004 MS India
| | - Rohini N. Shelke
- Department of Chemistry; Deogiri College; Station Road Aurangabad 431 005 MS India
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A facile synthesis of novel series ( Z )-2-((4-oxo-5-(thiophen-2-ylmethylene)-4,5-dihydrothiazol-2-yl)amino) substituted acid. JOURNAL OF SAUDI CHEMICAL SOCIETY 2017. [DOI: 10.1016/j.jscs.2015.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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10
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Gorantla V, Gundla R, Jadav SS, Anugu SR, Chimakurthy J, Nidasanametla SK, Korupolu R. Molecular hybrid design, synthesis and biological evaluation of N-phenyl sulfonamide linked N-acyl hydrazone derivatives functioning as COX-2 inhibitors: new anti-inflammatory, anti-oxidant and anti-bacterial agents. NEW J CHEM 2017. [DOI: 10.1039/c7nj03332j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design, synthesis and biological evaluation of the anti-inflammatory activities of novel N-phenyl sulfonamide linked N-acylhydrazones (NPS–NAH) have been reported.
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Affiliation(s)
- Vasubabu Gorantla
- Department of Engineering Chemistry
- Andhra University College of Engineering (A)
- Vishakhapatnam
- India
- GVK Biosciences Private Limited
| | - Rambabu Gundla
- Department of Chemistry
- School of Technology
- GITAM University
- Hyderabad (TS)
- India
| | | | | | | | | | - Raghubabu Korupolu
- Department of Engineering Chemistry
- Andhra University College of Engineering (A)
- Vishakhapatnam
- India
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11
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Sreenivasulu R, Sujitha P, Jadav SS, Ahsan MJ, Kumar CG, Raju RR. Synthesis, antitumor evaluation, and molecular docking studies of indole–indazolyl hydrazide–hydrazone derivatives. MONATSHEFTE FUR CHEMIE 2016. [DOI: 10.1007/s00706-016-1750-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Šink R, Kotnik M, Zega A, Barreteau H, Gobec S, Blanot D, Dessen A, Contreras-Martel C. Crystallographic Study of Peptidoglycan Biosynthesis Enzyme MurD: Domain Movement Revisited. PLoS One 2016; 11:e0152075. [PMID: 27031227 PMCID: PMC4816537 DOI: 10.1371/journal.pone.0152075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 03/08/2016] [Indexed: 11/30/2022] Open
Abstract
The biosynthetic pathway of peptidoglycan, an essential component of bacterial cell wall, is a well-recognized target for antibiotic development. Peptidoglycan precursors are synthesized in the bacterial cytosol by various enzymes including the ATP-hydrolyzing Mur ligases, which catalyze the stepwise addition of amino acids to a UDP-MurNAc precursor to yield UDP-MurNAc-pentapeptide. MurD catalyzes the addition of D-glutamic acid to UDP-MurNAc-L-Ala in the presence of ATP; structural and biochemical studies have suggested the binding of the substrates with an ordered kinetic mechanism in which ligand binding inevitably closes the active site. In this work, we challenge this assumption by reporting the crystal structures of intermediate forms of MurD either in the absence of ligands or in the presence of small molecules. A detailed analysis provides insight into the events that lead to the closure of MurD and reveals that minor structural modifications contribute to major overall conformation alterations. These novel insights will be instrumental in the development of new potential antibiotics designed to target the peptidoglycan biosynthetic pathway.
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Affiliation(s)
- Roman Šink
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia
| | - Miha Kotnik
- Lek Pharmaceuticals d. d., Verovškova 57, Ljubljana, Slovenia
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia
| | - Hélène Barreteau
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Stanislav Gobec
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia
| | - Didier Blanot
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Andréa Dessen
- Univ. Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo, Brazil
| | - Carlos Contreras-Martel
- Univ. Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- * E-mail:
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Caneva C, Alfei S, De Maria M, Ibba C, Delogu I, Spallarossa A, Loddo R. Synthesis and biological evaluation of (acyl)hydrazones and thiosemicarbazones obtained via in situ condensation of iminium salts with nitrogen-containing nucleophiles. Mol Divers 2015; 19:669-84. [PMID: 26077842 DOI: 10.1007/s11030-015-9597-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 04/02/2015] [Indexed: 11/25/2022]
Abstract
An unprecedented, highly convergent, high-yielding, one-pot synthesis of (acyl)hydrazones and thiosemicarbazones was carried out by the in situ condensation of isolable iminium chlorides of imidazolidin-2-(thio)one, tetrahydropyrimidin-2-thione and indole derivatives with nitrogen nucleophiles in the presence of a base. The developed reaction procedure is largely advantageous. It is highly parallelizable, no intermediates need to be isolated and minimal sample handling is required during the purification steps. Some relevant reaction parameters including reaction temperature and p[Formula: see text] of the base are discussed. NMR analysis was carried out to assess the stereochemistry of the obtained compounds. The stereochemical outcome of the reaction was found to be affected by the nature of the nitrogen-containing nucleophile being the majority of the derivatives isolated as single geometric isomers. The cytotoxicity and antiviral activities of the prepared compounds have been preliminary assessed. In cell-based screenings some of the derivatives proved to be cytotoxic at low micromolar concentrations and interesting anti-Reo-1 properties have been detected.
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Affiliation(s)
- Chiara Caneva
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto XV 3, 16132, Genova, Italy
| | - Silvana Alfei
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto XV 3, 16132, Genova, Italy
| | - Monica De Maria
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich-Alexander University, Schuhstraße 19, 91052, Erlangen, Germany
| | - Cristina Ibba
- Dipartimento di Scienze Biomediche, Sezione di Microbiologia e Virologia, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, s.p.8, Km 0.700, 09042, Monserrato, Cagliari, Italy
| | - Ilenia Delogu
- Dipartimento di Scienze Biomediche, Sezione di Microbiologia e Virologia, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, s.p.8, Km 0.700, 09042, Monserrato, Cagliari, Italy
| | - Andrea Spallarossa
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto XV 3, 16132, Genova, Italy.
| | - Roberta Loddo
- Dipartimento di Scienze Biomediche, Sezione di Microbiologia e Virologia, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, s.p.8, Km 0.700, 09042, Monserrato, Cagliari, Italy.
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14
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Kouidmi I, Levesque RC, Paradis-Bleau C. The biology of Mur ligases as an antibacterial target. Mol Microbiol 2014; 94:242-53. [DOI: 10.1111/mmi.12758] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2014] [Indexed: 01/19/2023]
Affiliation(s)
- Imène Kouidmi
- Department of Microbiology, Infectiology and Immunology; Université de Montreal; Montreal Quebec Canada
| | - Roger C. Levesque
- Institut de biologie intégrative et des systèmes; Université Laval; Montreal Quebec Canada
| | - Catherine Paradis-Bleau
- Department of Microbiology, Infectiology and Immunology; Université de Montreal; Montreal Quebec Canada
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15
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Perdih A, Hrast M, Barreteau H, Gobec S, Wolber G, Solmajer T. Inhibitor design strategy based on an enzyme structural flexibility: a case of bacterial MurD ligase. J Chem Inf Model 2014; 54:1451-66. [PMID: 24724969 DOI: 10.1021/ci500104m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Increasing bacterial resistance to available antibiotics stimulated the discovery of novel efficacious antibacterial agents. The biosynthesis of the bacterial peptidoglycan, where the MurD enzyme is involved in the intracellular phase of the UDP-MurNAc-pentapeptide formation, represents a collection of highly selective targets for novel antibacterial drug design. In our previous computational studies, the C-terminal domain motion of the MurD ligase was investigated using Targeted Molecular Dynamic (TMD) simulation and the Off-Path Simulation (OPS) technique. In this study, we present a drug design strategy using multiple protein structures for the identification of novel MurD ligase inhibitors. Our main focus was the ATP-binding site of the MurD enzyme. In the first stage, three MurD protein conformations were selected based on the obtained OPS/TMD data as the initial criterion. Subsequently, a two-stage virtual screening approach was utilized combining derived structure-based pharmacophores with molecular docking calculations. Selected compounds were then assayed in the established enzyme binding assays, and compound 3 from the aminothiazole class was discovered to act as a dual MurC/MurD inhibitor in the micomolar range. A steady-state kinetic study was performed on the MurD enzyme to provide further information about the mechanistic aspects of its inhibition. In the final stage, all used conformations of the MurD enzyme with compound 3 were simulated in classical molecular dynamics (MD) simulations providing atomistic insights of the experimental results. Overall, the study depicts several challenges that need to be addressed when trying to hit a flexible moving target such as the presently studied bacterial MurD enzyme and show the possibilities of how computational tools can be proficiently used at all stages of the drug discovery process.
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Affiliation(s)
- Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
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16
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Hrast M, Sosič I, Sink R, Gobec S. Inhibitors of the peptidoglycan biosynthesis enzymes MurA-F. Bioorg Chem 2014; 55:2-15. [PMID: 24755374 DOI: 10.1016/j.bioorg.2014.03.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 03/23/2014] [Accepted: 03/24/2014] [Indexed: 01/12/2023]
Abstract
The widespread emergence of resistant bacterial strains is becoming a serious threat to public health. This thus signifies the need for the development of new antibacterial agents with novel mechanisms of action. Continuous efforts in the design of novel antibacterials remain one of the biggest challenges in drug development. In this respect, the Mur enzymes, MurA-F, that are involved in the formation of UDP-N-acetylmuramyl-pentapeptide can be genuinely considered as promising antibacterial targets. This review provides an in-depth insight into the recent developments in the field of inhibitors of the MurA-F enzymes. Special attention is also given to compounds that act as multiple inhibitors of two, three or more of the Mur enzymes. Moreover, the reasons for the lack of preclinically successful inhibitors and the challenges to overcome these hurdles in the next years are also debated.
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Affiliation(s)
- Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Roman Sink
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia.
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Synthesis and antibacterial evaluation of New N-acylhydrazone derivatives from dehydroabietic acid. Molecules 2012; 17:4634-50. [PMID: 22522394 PMCID: PMC6269020 DOI: 10.3390/molecules17044634] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 04/01/2012] [Accepted: 04/05/2012] [Indexed: 11/16/2022] Open
Abstract
A series of new N-acylhydrazone derivatives were synthesized in good yields through the reactions of dehydroabietic acid hydrazide with a variety of substituted arylaldehydes. The structures of the synthesized compounds were confirmed by IR, 1H- and 13C-NMR, ESI-MS, elemental analysis and single crystal X-ray diffraction. From the crystal structure of compound 4l, the C=N double bonds of these N-acylhydrazones showed (E)-configuration, while the NMR data of compounds 4a-q indicated the existence of two rotamers for each compound in solution. The target compounds were evaluated for their antibacterial activities against four microbial strains. The result suggested that several compounds exhibited pronounced antibacterial activities. Particularly, compound 4p exhibited good antibacterial activity against Staphylococcus aureus and Bacillus subtilis comparable to positive control. The possible antibacterial metabolism and the strategy for further optimization of this compound were also discussed.
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Homology modeling and docking analyses of M. leprae Mur ligases reveals the common binding residues for structure based drug designing to eradicate leprosy. J Mol Model 2011; 18:2659-72. [PMID: 22102165 DOI: 10.1007/s00894-011-1285-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 10/17/2011] [Indexed: 10/15/2022]
Abstract
Multi drug resistance capacity for Mycobacterium leprae (MDR-Mle) demands the profound need for developing new anti-leprosy drugs. Since most of the drugs target a single enzyme, mutation in the active site renders the antibiotic ineffective. However, structural and mechanistic information on essential bacterial enzymes in a pathway could lead to the development of antibiotics that targets multiple enzymes. Peptidoglycan is an important component of the cell wall of M. leprae. The biosynthesis of bacterial peptidoglycan represents important targets for the development of new antibacterial drugs. Biosynthesis of peptidoglycan is a multi-step process that involves four key Mur ligase enzymes: MurC (EC:6.3.2.8), MurD (EC:6.3.2.9), MurE (EC:6.3.2.13) and MurF (EC:6.3.2.10). Hence in our work, we modeled the three-dimensional structure of the above Mur ligases using homology modeling method and analyzed its common binding features. The residues playing an important role in the catalytic activity of each of the Mur enzymes were predicted by docking these Mur ligases with their substrates and ATP. The conserved sequence motifs significant for ATP binding were predicted as the probable residues for structure based drug designing. Overall, the study was successful in listing significant and common binding residues of Mur enzymes in peptidoglycan pathway for multi targeted therapy.
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Tomašić T, Zidar N, Šink R, Kovač A, Blanot D, Contreras-Martel C, Dessen A, Müller-Premru M, Zega A, Gobec S, Kikelj D, Peterlin Mašič L. Structure-Based Design of a New Series of d-Glutamic Acid Based Inhibitors of Bacterial UDP-N-acetylmuramoyl-l-alanine:d-glutamate Ligase (MurD). J Med Chem 2011; 54:4600-10. [DOI: 10.1021/jm2002525] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tihomir Tomašić
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Roman Šink
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Andreja Kovač
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Didier Blanot
- Enveloppes Bactériennes et Antibiotiques, IBBMC, UMR 8619 CNRS, Université Paris-Sud, 91405 Orsay, France
| | | | | | - Manica Müller-Premru
- Medical Faculty, Institute of Microbiology and Immunology, University of Ljubljana, 1105 Ljubljana, Slovenia
| | - Anamarija Zega
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
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Second-generation sulfonamide inhibitors of D-glutamic acid-adding enzyme: activity optimisation with conformationally rigid analogues of D-glutamic acid. Eur J Med Chem 2011; 46:2880-94. [PMID: 21524830 DOI: 10.1016/j.ejmech.2011.04.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 03/24/2011] [Accepted: 04/03/2011] [Indexed: 01/06/2023]
Abstract
D-Glutamic acid-adding enzyme (MurD) catalyses the essential addition of d-glutamic acid to the cytoplasmic peptidoglycan precursor UDP-N-acetylmuramoyl-l-alanine, and as such it represents an important antibacterial drug-discovery target enzyme. Based on a series of naphthalene-N-sulfonyl-d-Glu derivatives synthesised recently, we synthesised two series of new, optimised sulfonamide inhibitors of MurD that incorporate rigidified mimetics of d-Glu. The compounds that contained either constrained d-Glu or related rigid d-Glu mimetics showed significantly better inhibitory activities than the parent compounds, thereby confirming the advantage of molecular rigidisation in the design of MurD inhibitors. The binding modes of the best inhibitors were examined with high-resolution NMR spectroscopy and X-ray crystallography. We have solved a new crystal structure of the complex of MurD with an inhibitor bearing a 4-aminocyclohexane-1,3-dicarboxyl moiety. These data provide an additional step towards the development of sulfonamide inhibitors with potential antibacterial activities.
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21
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A metabolomic view of Staphylococcus aureus and its ser/thr kinase and phosphatase deletion mutants: involvement in cell wall biosynthesis. ACTA ACUST UNITED AC 2011; 17:820-30. [PMID: 20797611 DOI: 10.1016/j.chembiol.2010.06.012] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 06/24/2010] [Accepted: 06/28/2010] [Indexed: 01/23/2023]
Abstract
Little is known about intracellular metabolite pools in pathogens such as Staphylococcus aureus. We have studied a particular metabolome by means of the presented LC-MS method. By investigating the central carbon metabolism which includes most of the energy transfer molecules like nucleotides, sugar mono- and biphosphates, and cofactors, a conclusion about phenotypes and stress answers in microorganisms is possible. Quantitative metabolite levels of S. aureus grown in complex lysogeny broth and in minimal medium were compared in the wild-type S. aureus strain 8325 and the isogenic eukaryotic-like protein serine/threonine kinase (DeltapknB) and phosphatase (Deltastp) deletion mutants. Detection of several remarkable differences, e.g., in nucleotide metabolism and especially cell wall precursor metabolites, indicates a previously unreported importance of serine/threonine kinase/phosphatase on peptidoglycan and wall teichoic acid biosynthesis. These findings may lead to new insights into the regulation of staphylococcal cell wall metabolism.
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22
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Gautam A, Vyas R, Tewari R. Peptidoglycan biosynthesis machinery: a rich source of drug targets. Crit Rev Biotechnol 2010; 31:295-336. [PMID: 21091161 DOI: 10.3109/07388551.2010.525498] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The range of antibiotic therapy for the control of bacterial infections is becoming increasingly limited because of the rapid rise in multidrug resistance in clinical bacterial isolates. A few diseases, such as tuberculosis, which were once thought to be under control, have re-emerged as serious health threats. These problems have resulted in intensified research to look for new inhibitors for bacterial pathogens. Of late, the peptidoglycan (PG) layer, the most important component of the bacterial cell wall has been the subject of drug targeting because, first, it is essential for the survivability of eubacteria and secondly, it is absent in humans. The last decade has seen tremendous inputs in deciphering the 3-D structures of the PG biosynthetic enzymes. Many inhibitors against these enzymes have been developed using virtual and high throughput screening techniques. This review discusses the mechanistic and structural properties of the PG biosynthetic enzymes and inhibitors developed in the last decade.
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Affiliation(s)
- Ankur Gautam
- Department of Biotechnology, Panjab University, Chandigarh, India
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23
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Andrade MM, Barros MT. Fast synthesis of N-acylhydrazones employing a microwave assisted neat protocol. ACTA ACUST UNITED AC 2010; 12:245-7. [PMID: 20050700 DOI: 10.1021/cc9001444] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A variety of N-acylhydrazones were synthesized under microwave irradiation within 2.5-10 min, starting from benzo, salicyloyl, and isonicotinic hydrazides. The protocol developed employs microwave irradiation in the absence of solvents and catalysts, leading to high yields. The results are reproducible in a 500 mg to 5 g scale.
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Affiliation(s)
- Marta M Andrade
- REQUIMTE, CQFB, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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Tomasić T, Zidar N, Kovac A, Turk S, Simcic M, Blanot D, Müller-Premru M, Filipic M, Grdadolnik SG, Zega A, Anderluh M, Gobec S, Kikelj D, Peterlin Masic L. 5-Benzylidenethiazolidin-4-ones as multitarget inhibitors of bacterial Mur ligases. ChemMedChem 2010; 5:286-95. [PMID: 20024979 DOI: 10.1002/cmdc.200900449] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mur ligases participate in the intracellular path of bacterial peptidoglycan biosynthesis and constitute attractive, although so far underexploited, targets for antibacterial drug discovery. A series of hydroxy-substituted 5-benzylidenethiazolidin-4-ones were synthesized and tested as inhibitors of Mur ligases. The most potent compound 5 a was active against MurD-F with IC(50) values between 2 and 6 microm, making it a promising multitarget inhibitor of Mur ligases. Antibacterial activity against different strains, inhibitory activity against protein kinases, mutagenicity and genotoxicity of 5 a were also investigated, and kinetic and NMR studies were conducted.
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Affiliation(s)
- Tihomir Tomasić
- University of Ljubljana, Faculty of Pharmacy, Askerceva 7, 1000 Ljubljana, Slovenia
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Perdih A, Kovac A, Wolber G, Blanot D, Gobec S, Solmajer T. Discovery of novel benzene 1,3-dicarboxylic acid inhibitors of bacterial MurD and MurE ligases by structure-based virtual screening approach. Bioorg Med Chem Lett 2009; 19:2668-73. [PMID: 19369074 DOI: 10.1016/j.bmcl.2009.03.141] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 03/25/2009] [Accepted: 03/27/2009] [Indexed: 01/17/2023]
Abstract
The peptidoglycan biosynthetic pathway provides an array of potential targets for antibacterial drug design, attractive especially with respect to selective toxicity. Within this pathway, the members of the Mur ligase family are considered as promising emerging targets for novel antibacterial drug design. Based on the available MurD crystal structures co-crystallised with N-sulfonyl glutamic acid inhibitors, a virtual screening campaign was performed, combining three-dimensional structure-based pharmacophores and molecular docking calculations. A novel class of glutamic acid surrogates-benzene 1,3-dicarboxylic acid derivatives-were identified and compounds 14 and 16 found to possess dual MurD and MurE inhibitory activity.
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Affiliation(s)
- Andrej Perdih
- National Institute of Chemistry, Hajdrihova, Ljubljana, Slovenia
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