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Zhou G, Li Y. Investigation of bacterial DNA gyrase Inhibitor classification models and structural requirements utilizing multiple machine learning methods. Mol Divers 2024:10.1007/s11030-024-10806-y. [PMID: 38372837 DOI: 10.1007/s11030-024-10806-y] [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: 11/09/2023] [Accepted: 01/04/2024] [Indexed: 02/20/2024]
Abstract
Infections from multidrug-resistant (MDR) bacteria have emerged as a paramount global health concern, and the therapeutic effectiveness of current treatments is swiftly diminishing. An urgent need exists to explore innovative strategies for countering drug-resistant bacteria. Bacterial DNA gyrase, functioning as an ATP-dependent enzyme, plays a pivotal role in the intricate processes of transcription, replication, and chromosome segregation within bacterial DNA. This renders it a prime target for the development of innovative antibacterial agents. However, the experimental identification of bacterial DNA gyrase inhibitors faces multifaceted challenges due to current methodological constraints. Recognizing its significance, this study developed 56 computational models designed for predicting bacterial DNA gyrase inhibitors. These models employed seven distinct molecular fingerprints and eight machine learning algorithms. Among these models, Model_2D, created using KlekotaRoth fingerprints and the SVM algorithm, stands out as the most robust performer (ACC = 0.86, MCC = 0.63, G-mean = 0.82). Moreover, given the limited exploration of structural fragments required for DNA Gyrase B inhibitors, crucial structural fingerprints influencing DNA Gyrase B inhibitors were identified through Bayesian classification. Subsequently, we conducted molecular docking to reveal the binding modes between these crucial structural fingerprints and the active site of DNA gyrase B. In conclusion, the present study aimed to develop the optimal classification model for bacterial DNA gyrase inhibitors, offering invaluable support to medicinal chemists creating innovative DNA gyrase inhibitors.
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Affiliation(s)
- Guozheng Zhou
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Yan Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, Liaoning, China.
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2
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Piplani P, Kumar A, Kulshreshtha A, Vohra T, Piplani V. Recent Development of DNA Gyrase Inhibitors: An Update. Mini Rev Med Chem 2024; 24:1001-1030. [PMID: 37909434 DOI: 10.2174/0113895575264264230921080718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 11/03/2023]
Abstract
Antibiotic or antimicrobial resistance is an urgent global public health threat that occurs when bacterial or fungal infections do not respond to the drug regimen designed to treat these infections. As a result, these microbes are not evaded and continue to grow. Antibiotic resistance against natural and already-known antibiotics like Ciprofloxacin and Novobiocin can be overcome by developing an agent that can act in different ways. The success of agents like Zodiflodacin and Zenoxacin in clinical trials against DNA gyrase inhibitors that act on different sites of DNA gyrase has resulted in further exploration of this target. However, due to the emergence of bacterial resistance against these targets, there is a great need to design agents that can overcome this resistance and act with greater efficacy. This review provides information on the synthetic and natural DNA gyrase inhibitors that have been developed recently and their promising potential for combating antimicrobial resistance. The review also presents information on molecules that are in clinical trials and their current status. It also analysed the SAR studies and mechanisms of action of enlisted agents.
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Affiliation(s)
- Poonam Piplani
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160017, India
| | - Ajay Kumar
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160017, India
| | - Akanksha Kulshreshtha
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160017, India
| | - Tamanna Vohra
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160017, India
| | - Vritti Piplani
- Bhojia Dental College and Hospital, Baddi, 173205, India
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3
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Vega Hissi EG, De Costa Guardamagna AB, Garro AD, Falcon CR, Anderluh M, Tomašič T, Kikelj D, Yaneff A, Davio CA, Enriz RD, Zurita AR. A Potent N-(piperidin-4-yl)-1H-pyrrole-2-carboxamide Inhibitor of Adenylyl Cyclase of G. lamblia: Biological Evaluation and Molecular Modelling Studies. ChemMedChem 2021; 16:2094-2105. [PMID: 33783977 DOI: 10.1002/cmdc.202100037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/26/2021] [Indexed: 11/06/2022]
Abstract
In this work, we report a derivative of N-(piperidin-4-yl)-1H-pyrrole-2-carboxamide as a new inhibitor for adenylyl cyclase of Giardia lamblia which was obtained from a study using structural data of the nucleotidyl cyclase 1 (gNC1) of this parasite. For such a study, we developed a model for this specific enzyme by using homology techniques, which is the first model reported for gNC1 of G. lamblia. Our studies show that the new inhibitor has a competitive mechanism of action against this enzyme. 2-Hydroxyestradiol was used as the reference compound for comparative studies. Results in this work are important from two points of view. on the one hand, an experimentally corroborated model for gNC1 of G. lamblia obtained by molecular modelling is presented; on the other hand, the new inhibitor obtained is an undoubtedly excellent starting structure for the development of new metabolic inhibitors for G. lamblia.
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Affiliation(s)
- Esteban G Vega Hissi
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, 5700, San Luis, Argentina
| | - Antonella B De Costa Guardamagna
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, 5700, San Luis, Argentina
| | - Adriana D Garro
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, 5700, San Luis, Argentina
| | - Cristian R Falcon
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, 5700, San Luis, Argentina
| | - Marko Anderluh
- Department of Medicinal Chemistry, University of Ljubljana, Faculty of Pharmacy Askerceva, cesta 7, 1000, Ljubljana, Slovenia
| | - Tihomir Tomašič
- Department of Medicinal Chemistry, University of Ljubljana, Faculty of Pharmacy Askerceva, cesta 7, 1000, Ljubljana, Slovenia
| | - Danijel Kikelj
- Department of Medicinal Chemistry, University of Ljubljana, Faculty of Pharmacy Askerceva, cesta 7, 1000, Ljubljana, Slovenia
| | - Agustín Yaneff
- Instituto de Investigaciones Farmacológicas (ININFA-UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113, AAD, Buenos Aires, Argentina
| | - Carlos A Davio
- Instituto de Investigaciones Farmacológicas (ININFA-UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113, AAD, Buenos Aires, Argentina
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, 5700, San Luis, Argentina
| | - Adolfo R Zurita
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, 5700, San Luis, Argentina
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4
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Recent advances in DNA gyrase-targeted antimicrobial agents. Eur J Med Chem 2020; 199:112326. [DOI: 10.1016/j.ejmech.2020.112326] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/16/2022]
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Jukič M, Konc J, Janežič D, Bren U. ProBiS H2O MD Approach for Identification of Conserved Water Sites in Protein Structures for Drug Design. ACS Med Chem Lett 2020; 11:877-882. [PMID: 32435399 PMCID: PMC7236268 DOI: 10.1021/acsmedchemlett.9b00651] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/19/2020] [Indexed: 01/06/2023] Open
Abstract
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The ProBiS H2O MD
approach for identification of conserved waters
and water sites of interest in macromolecular systems, which is becoming
a typical step in a structure-based drug design or macromolecular
study in general, is described. This work explores an extension of
the ProBiS H2O approach introduced by Jukič et al. Indeed,
water molecules are key players in the interaction mechanisms of macromolecules
and small molecules and play structural roles. Our earlier developed
approach, ProBiS H2O, is a simple and transparent workflow for conserved
water detection. Here we have considered generalizing the idea by
supplementing the experimental data with data derived from molecular
dynamics to facilitate work on less known systems. Newly developed
ProBiS H2O MD workflow uses trajectory data, extracts and identifies
interesting water sites, and visualizes the results. ProBiS H2O MD
can thus robustly process molecular dynamic trajectory snapshots,
perform local superpositions, collect water location data, and perform
density-based clustering to identify discrete sites with high conservation
of water molecules. This is a new approach that uses experimental
data in silico to identify interesting water sites.
Methodology is fast and water-model or molecular dynamics software
independent. Trends in the conservation of water molecules can be
followed over a variety of trajectories, and our approach has been
successfully validated using reported protein systems with experimentally
observed conserved water molecules. ProBiS H2O MD is freely available
as PyMOL plugin at http://insilab.org.
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Affiliation(s)
- Marko Jukič
- University of Maribor, Faculty of Chemistry and Chemical Engineering, Laboratory of Physical Chemistry and Chemical Thermodynamics, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagoljaška 8, SI-6000 Koper, Slovenia
| | - Janez Konc
- University of Maribor, Faculty of Chemistry and Chemical Engineering, Laboratory of Physical Chemistry and Chemical Thermodynamics, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Dušanka Janežič
- University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagoljaška 8, SI-6000 Koper, Slovenia
| | - Urban Bren
- University of Maribor, Faculty of Chemistry and Chemical Engineering, Laboratory of Physical Chemistry and Chemical Thermodynamics, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagoljaška 8, SI-6000 Koper, Slovenia
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A new calcium(II) complex of marbofloxacin showing much lower acute toxicity with retained antibacterial activity. J Inorg Biochem 2019; 203:110905. [PMID: 31707333 DOI: 10.1016/j.jinorgbio.2019.110905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/20/2019] [Accepted: 10/20/2019] [Indexed: 11/20/2022]
Abstract
Marbofloxacin (MB) is a newly developed veterinary drug with broad-spectrum antibacterial activity. In this study, a new calcium(II)-based complex of marbofloxacin, MB-Ca, was synthesized and structurally characterized by IR, ESI-MS, UV-Vis and single crystal X-ray diffraction analysis. The characterization of this complex in solution state indicated that the coordinated MB-Ca was partly retained, along with the monomeric and dimeric forms of MB. It also showed satisfactory water solubility (1.89 mg/mL), comparing with MB (2.82 mg/mL) at 35 °C. The in vitro antibacterial activity of MB-Ca was also screened towards a series of typical pathogenic bacteria, and determined by the methods of turbidimetry and disc diffusion. The results indicated it showed comparable antibacterial activity to MB. However, it exhibited higher inhibitive ability in vitro on DNA gyrase than MB alone. Furthermore, MB-Ca showed significantly lower acute toxicity (LD50, 3186 mg/kg) than MB (LD50, 1294 mg/kg) in mice, based on the in vivo acute toxicity test. The histopathological examination on the major organs of the mice by the oral administration of MB-Ca did not show obvious organic lesions, which is similar to those treated by MB. The research results suggest that MB-Ca could be further developed into a new promising metal-based veterinary drug and a better substitute of MB, showing unabated antibacterial activity along with lower toxicity.
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Masci D, Hind C, Islam MK, Toscani A, Clifford M, Coluccia A, Conforti I, Touitou M, Memdouh S, Wei X, La Regina G, Silvestri R, Sutton JM, Castagnolo D. Switching on the activity of 1,5-diaryl-pyrrole derivatives against drug-resistant ESKAPE bacteria: Structure-activity relationships and mode of action studies. Eur J Med Chem 2019; 178:500-514. [DOI: 10.1016/j.ejmech.2019.05.087] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 12/13/2022]
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Abstract
New antibacterials that modulate less explored targets are needed to fight the emerging bacterial resistance. DNA gyrase and topoisomerase IV are attractive targets in this search. These are both type II topoisomerases that can cleave both DNA strands, and can thus alter DNA topology during replication or similar processes. Currently, there are no ATP-competitive inhibitors of these two enzymes on the market, as the only aminocoumarin representative, novobiocin, was withdrawn due to safety concerns. The search for novel ATP-competitive inhibitors is a focus of ongoing industrial and academical research. This review summarizes the recent efforts in the design, synthesis and evaluation of GyrB/ParE inhibitors. The various approaches to achieve improved antibacterial activities are described, with particular reference to Gram-negative bacteria.
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Tomašič T, Barančoková M, Zidar N, Ilaš J, Tammela P, Kikelj D. Design, synthesis, and biological evaluation of 1-ethyl-3-(thiazol-2-yl)urea derivatives as Escherichia coli
DNA gyrase inhibitors. Arch Pharm (Weinheim) 2017; 351. [DOI: 10.1002/ardp.201700333] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Tihomir Tomašič
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | | | - Nace Zidar
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | - Janez Ilaš
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | - Päivi Tammela
- Division of Pharmaceutical Biosciences; Faculty of Pharmacy; University of Helsinki; Helsinki Finland
| | - Danijel Kikelj
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
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10
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Jukič M, Konc J, Gobec S, Janežič D. Identification of Conserved Water Sites in Protein Structures for Drug Design. J Chem Inf Model 2017; 57:3094-3103. [DOI: 10.1021/acs.jcim.7b00443] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Marko Jukič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI−1000, Ljubljana, Slovenia
| | - Janez Konc
- National Institute of Chemistry, Hajdrihova 19, SI−1000, Ljubljana, Slovenia
- Faculty of
Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI−6000 Koper, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI−1000, Ljubljana, Slovenia
| | - Dušanka Janežič
- Faculty of
Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI−6000 Koper, Slovenia
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