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Yuan S, Shen DD, Bai YR, Zhang M, Zhou T, Sun C, Zhou L, Wang SQ, Liu HM. Oxazolidinone: A promising scaffold for the development of antibacterial drugs. Eur J Med Chem 2023; 250:115239. [PMID: 36893700 DOI: 10.1016/j.ejmech.2023.115239] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/16/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023]
Abstract
Due to the long-term and widespread use of antibiotics in clinic, the problem of bacterial resistance is increasingly serious, and the development of new drugs to treat drug-resistant bacteria has gradually become the mainstream direction of antibiotic research. The oxazolidinone-containing drugs linezolid, tedizolid phosphate and contezolid have been approved to the market, which are effective against a variety of Gram-positive bacterium infections. Moreover, there are also many antibiotics containing oxazolidinone fragment under clinical investigation that show good pharmacokinetic and pharmacodynamic properties with unique mechanism of action against resistant bacteria. In this review, we summarized the oxazolidinone-based antibiotics already on the market or in clinical trials and the representative bioactive molecules, and mainly focused on their structural optimizations, development strategies and structure-activity relationships in hope of insight into the reasonable design for medical chemists to develop new oxazolidinone antibiotics with highly potency and fewer side effects.
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Affiliation(s)
- Shuo Yuan
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China.
| | - Dan-Dan Shen
- Department of Obstetrics and Gynecology, Zhengzhou Key Laboratory of Endometrial Disease Prevention and Treatment Zhengzhou China, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yi-Ru Bai
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China
| | - Miao Zhang
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China
| | - Tian Zhou
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China
| | - Chong Sun
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China
| | - Li Zhou
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Sai-Qi Wang
- The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer, Zhengzhou Key Laboratory of Precision Therapy of Gastrointestinal Cancer, Zhengzhou, 450008, China.
| | - Hong-Min Liu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China.
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Buckley ME, Ndukwe ARN, Nair PC, Rana S, Fairfull-Smith KE, Gandhi NS. Comparative Assessment of Docking Programs for Docking and Virtual Screening of Ribosomal Oxazolidinone Antibacterial Agents. Antibiotics (Basel) 2023; 12:463. [PMID: 36978331 PMCID: PMC10044086 DOI: 10.3390/antibiotics12030463] [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: 01/16/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Oxazolidinones are a broad-spectrum class of synthetic antibiotics that bind to the 50S ribosomal subunit of Gram-positive and Gram-negative bacteria. Many crystal structures of the ribosomes with oxazolidinone ligands have been reported in the literature, facilitating structure-based design using methods such as molecular docking. It would be of great interest to know in advance how well docking methods can reproduce the correct ligand binding modes and rank these correctly. We examined the performance of five molecular docking programs (AutoDock 4, AutoDock Vina, DOCK 6, rDock, and RLDock) for their ability to model ribosomal-ligand interactions with oxazolidinones. Eleven ribosomal crystal structures with oxazolidinones as the ligands were docked. The accuracy was evaluated by calculating the docked complexes' root-mean-square deviation (RMSD) and the program's internal scoring function. The rankings for each program based on the median RMSD between the native and predicted were DOCK 6 > AD4 > Vina > RDOCK >> RLDOCK. Results demonstrate that the top-performing program, DOCK 6, could accurately replicate the ligand binding in only four of the eleven ribosomes due to the poor electron density of said ribosomal structures. In this study, we have further benchmarked the performance of the DOCK 6 docking algorithm and scoring in improving virtual screening (VS) enrichment using the dataset of 285 oxazolidinone derivatives against oxazolidinone binding sites in the S. aureus ribosome. However, there was no clear trend between the structure and activity of the oxazolidinones in VS. Overall, the docking performance indicates that the RNA pocket's high flexibility does not allow for accurate docking prediction, highlighting the need to validate VS. protocols for ligand-RNA before future use. Later, we developed a re-scoring method incorporating absolute docking scores and molecular descriptors, and the results indicate that the descriptors greatly improve the correlation of docking scores and pMIC values. Morgan fingerprint analysis was also used, suggesting that DOCK 6 underpredicted molecules with tail modifications with acetamide, n-methylacetamide, or n-ethylacetamide and over-predicted molecule derivatives with methylamino bits. Alternatively, a ligand-based approach similar to a field template was taken, indicating that each derivative's tail groups have strong positive and negative electrostatic potential contributing to microbial activity. These results indicate that one should perform VS. campaigns of ribosomal antibiotics with care and that more comprehensive strategies, including molecular dynamics simulations and relative free energy calculations, might be necessary in conjunction with VS. and docking.
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Affiliation(s)
- McKenna E. Buckley
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Audrey R. N. Ndukwe
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD 4000, Australia
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Pramod C. Nair
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia
- Flinders Health and Medical Research Institute (FHMRI), Flinders University, Adelaide, SA 5042, Australia
- South Australian Health and Medical Research Institute (SAHMRI), University of Adelaide, Adelaide, SA 5000, Australia
- Discipline of Medicine, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Santu Rana
- Applied Artificial Intelligence Institute (A2I2), Deakin University, Geelong, VIC 3220, Australia
| | - Kathryn E. Fairfull-Smith
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD 4000, Australia
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Neha S. Gandhi
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD 4000, Australia
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Liu J, Chen C, Tu W, Liu W, Zhang Y. Analysis of the microscopic interactions between processed Polygonatum cyrtonema polysaccharides and water. J Mol Graph Model 2023; 118:108350. [PMID: 36194990 DOI: 10.1016/j.jmgm.2022.108350] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 09/12/2022] [Accepted: 09/20/2022] [Indexed: 10/14/2022]
Abstract
The dissolution and microscopic interactions of processed Polygonatum cyrtonema polysaccharides in water are extremely important because they strongly influence the process to extract these polysaccharides from water. In this paper, molecular dynamics simulation methods were used to analyse the influence of extraction temperature, concentration and molecular weight on the radial distribution function (RDF), mean square displacement (MSD), diffusion coefficient (D), radius of gyration (Rg), and microstructure of processed Polygonatum cyrtonema polysaccharides in water as well as the intrinsic viscosity (η), hydrogen bond characteristics and microscopic interactions in the solutions. The research results showed that the extraction temperature, concentration and molecular weight of the polysaccharides had important effects on the RDF, MSD, D, Rg, η, hydrogen bond characteristics and the microstructure of the polysaccharide molecules, but there were some major differences. The order of the influence of the factors affecting the dissolution of polysaccharides in water was temperature > concentration > molecular weight. Extraction temperature, material fluid ratio and molecular weight had greater influence on the fluidity and dissolution state of the polysaccharides in water. As the solute concentration and molecular weight increased, hydrogen bonds between polysaccharides and water inhibited their dissolution and diffusion. Properly increasing the temperature, reducing the concentration and selecting low molecular weight polysaccharides enhanced the dissolution and diffusion of the polysaccharides in the solution system. Molecular weight was the main factor affecting the η of the polysaccharide solutions. These results can provide theoretical guidance for the extraction or tea brewing process of Polygonatum cyrtonema polysaccharides in future work.
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Affiliation(s)
- Jun Liu
- School of Resources and Environment, Nanchang University, Nanchang, 330031, Jiangxi, China.
| | - Changzhou Chen
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, Guangxi, China
| | - Wenfeng Tu
- School of Resources and Environment, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Wei Liu
- Jiangxi Shanbaotang Food Technology Co., Ltd., Nanchang, 330044, Jiangxi, China
| | - Yanru Zhang
- School of Material Science and Engineering, Hebei University of Engineering, Handan, 056038, Hebei, China
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Oxazolidinone Antibiotics: Chemical, Biological and Analytical Aspects. Molecules 2021; 26:molecules26144280. [PMID: 34299555 PMCID: PMC8305375 DOI: 10.3390/molecules26144280] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 11/17/2022] Open
Abstract
This review covers the main aspects concerning the chemistry, the biological activity and the analytical determination of oxazolidinones, the only new class of synthetic antibiotics advanced in clinical use over the past 50 years. They are characterized by a chemical structure including the oxazolidone ring with the S configuration of substituent at C5, the acylaminomethyl group linked to C5 and the N-aryl substituent. The synthesis of oxazolidinones has gained increasing interest due to their unique mechanism of action that assures high antibiotic efficiency and low susceptibility to resistance mechanisms. Here, the main features of oxazolidinone antibiotics licensed or under development, such as Linezolid, Sutezolid, Eperezolid, Radezolid, Contezolid, Posizolid, Tedizolid, Delpazolid and TBI-223, are discussed. As they are protein synthesis inhibitors active against a wide spectrum of multidrug-resistant Gram-positive bacteria, their biological activity is carefully analyzed, together with the drug delivery systems recently developed to overcome the poor oxazolidinone water solubility. Finally, the most employed analytical techniques for oxazolidinone determination in different matrices, such as biological fluids, tissues, drugs and natural waters, are reviewed. Most are based on HPLC (High Performance Liquid Chromatography) coupled with UV-Vis or mass spectrometer detectors, but, to a lesser extent are also based on spectrofluorimetry or voltammetry.
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