1
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Zhang DJ, Yuan ZQ, Yue YX, Zhang M, Wu WJ, Yang CG, Qiu WW. Synthesis and antibacterial activities of heterocyclic ring-fused 20(S)-protopanaxadiol derivatives. Bioorg Med Chem 2024; 112:117901. [PMID: 39232465 DOI: 10.1016/j.bmc.2024.117901] [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: 07/11/2024] [Revised: 08/23/2024] [Accepted: 08/25/2024] [Indexed: 09/06/2024]
Abstract
Multidrug-resistant (MDR) bacterial infections are becoming a life-threatening issue in public health; therefore, it is urgent to develop novel antibacterial agents for treating infections caused by MDR bacteria. The 20(S)-protopanaxadiol (PPD) derivative 9 was identified as a novel antibacterial hit compound in screening of our small synthetic natural product-like (NPL) library. A series of novel PPD derivatives with heterocyclic rings fused at the C-2 and C-3 positions of the A-ring were synthesized and their antibacterial activities against Staphylococcus aureus (S. aureus) Newman strain and MDR S. aureus strains (USA300, NRS-1, NRS-70, NRS-100, NRS-108, NRS-271, XJ017, and XJ036) were evaluated. Among these compounds, quinoxaline derivative 56 (SH617) exhibited the highest activity with MICs of 0.5-4 μg/mL against the S. aureus Newman strain and the eight MDR S. aureus strains. Its antibacterial activity was comparable to that of the positive control, vancomycin. In the zebrafish, 56 revealed no obvious toxicity even at a high administered dose. In vivo, following a lethal infection induced by USA300 strains in zebrafish, 56 exhibited significantly increased survival rates in a dose-dependent manner.
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Affiliation(s)
- De-Jie Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Zi-Qi Yuan
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan-Xin Yue
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Min Zhang
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, China
| | - Wen-Juan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai 264117, China.
| | - Wen-Wei Qiu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, 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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Ruggieri F, Compagne N, Antraygues K, Eveque M, Flipo M, Willand N. Antibiotics with novel mode of action as new weapons to fight antimicrobial resistance. Eur J Med Chem 2023; 256:115413. [PMID: 37150058 DOI: 10.1016/j.ejmech.2023.115413] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/09/2023] [Accepted: 04/22/2023] [Indexed: 05/09/2023]
Abstract
Antimicrobial resistance (AMR) is a major public health issue, causing 5 million deaths per year. Without any action plan, AMR will be in a near future the leading cause of death ahead of cancer. AMR comes from the ability of bacteria to rapidly develop and share resistance mechanisms towards current antibiotics, rendering them less effective. To circumvent this issue and avoid the phenomenon of cross-resistance, new antibiotics acting on novel targets or with new modes of action are required. Today, the pipeline of potential new treatments with these characteristics includes promising compounds such as gepotidacin, zoliflodacin, ibezapolstat, MGB-BP-3, CRS-3123, afabicin and TXA-709, which are currently in clinical trials, and lefamulin, which has been recently approved by FDA and EMA. In this review, we report the chemical synthesis, mode of action, structure-activity relationships, in vitro and in vivo activities as well as clinical data of these eight small molecules listed above.
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Affiliation(s)
- Francesca Ruggieri
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Nina Compagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Kevin Antraygues
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Maxime Eveque
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France.
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4
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Chen G, Chang Z, Yuan P, Wang S, Yang Y, Liang X, Zhao D. Late-stage functionalization of 5-nitrofurans derivatives and their antibacterial activities. RSC Adv 2023; 13:3204-3209. [PMID: 36756397 PMCID: PMC9853512 DOI: 10.1039/d2ra07676d] [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: 12/02/2022] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Structure modification of drugs is a reliable way to optimize lead compounds, among which the most striking and direct method is late-stage functionalization (LSF). Here, we employed the Cu-catalyzed C-H LSF to modify 5-nitrofuran drugs. A series of modifications have been carried out including hydroxylation, methylation, azidination, cyanation, arylation, etc. Antibacterial activities of all compounds in vitro were measured. The results showed that compound 1 and compound 18 were the most active among all compounds. Meanwhile, the cell cytotoxicity assays of potent compounds 1, 3, 4, 5 & 18 and the parent drug FZD were conducted.
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Affiliation(s)
- Geshuyi Chen
- The First Clinical Medical College, Lanzhou University Lanzhou China
| | - Zhe Chang
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University Guangzhou China
| | - Pei Yuan
- The First Clinical Medical College, Lanzhou University Lanzhou China
| | - Si Wang
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University Guangzhou China
| | - Yongxiu Yang
- The First Clinical Medical College, Lanzhou University Lanzhou China .,The First Clinical Medical College, Lanzhou University. Department of Obstetrics and Gynecology, The First Hospital of Lanzhou University, Key Laboratory for Gynecologic Oncology Lanzhou 730000 Gansu Province China .,Lead Contact China
| | - Xiaolei Liang
- The First Clinical Medical College, Lanzhou University Lanzhou China .,The First Clinical Medical College, Lanzhou University. Department of Obstetrics and Gynecology, The First Hospital of Lanzhou University, Key Laboratory for Gynecologic Oncology Lanzhou 730000 Gansu Province China
| | - Depeng Zhao
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University Guangzhou China
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5
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Ma H, Qian A, Zheng Y, Meng X, Wang T, Zhang Y, Sun L, Zou F, Zhao B, Zhang S, Zhang D, Yang Y. Design, Synthesis, and Structure-Activity Relationship Studies of Bisamide Derivatives of Amphotericin B with Potent Efficacy and Low Toxicity. J Med Chem 2022; 65:8897-8913. [PMID: 35786969 DOI: 10.1021/acs.jmedchem.1c02227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amphotericin B (AMB, 1) is the most powerful antibiotic in treating potentially life-threatening invasive fungal infections (IFIs), though severe toxicity derived from self-aggregation greatly limits its clinical application. Herein, we applied a bisamidation strategy at the C16-COOH and C3'-NH2 to improve the therapeutic properties by suppressing self-aggregation. It was found that basic amino groups at the residue of C16 amide were beneficial to activity, while lipophilic fragments contributed to toxicity reduction. Additionally, N-methyl-amino acetyl and amino acetyl moieties at C3' amide could help keep the fungistatic effectiveness. The modification work culminated in the discovery of 36 (ED50 = 0.21 mg/kg), which exerted a 1.5-fold stronger antifungal efficacy than amphamide, the optimal derivative theretofore, in mice, low self-aggregation propensity, and thus low acute toxicity. With the improvement in therapeutic index and good PK profile, 36 is promising for further development as a second-generation polyene antifungal agent.
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Affiliation(s)
- Huijun Ma
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Anran Qian
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yazhou Zheng
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Xin Meng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
| | - Ting Wang
- Department of Microbiology, Sichuan Primed Bio-Tech Group Co., Ltd., Chengdu, Sichuan Province 610041, P. R. China
| | - Yinyong Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
| | - Lulu Sun
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
| | - Feng Zou
- Department of Microbiology, Sichuan Primed Bio-Tech Group Co., Ltd., Chengdu, Sichuan Province 610041, P. R. China
| | - Bomei Zhao
- Department of Microbiology, Sichuan Primed Bio-Tech Group Co., Ltd., Chengdu, Sichuan Province 610041, P. R. China
| | - Shuhua Zhang
- Department of Microbiology, Sichuan Primed Bio-Tech Group Co., Ltd., Chengdu, Sichuan Province 610041, P. R. China
| | - Dan Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yushe Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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6
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Batista VF, Pinto DCGA, Silva AMS. Recent in vivo advances of spirocyclic scaffolds for drug discovery. Expert Opin Drug Discov 2022; 17:603-618. [PMID: 35333138 DOI: 10.1080/17460441.2022.2055544] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Spirocyclic scaffolds are an exceptional tool in drug design, allowing fine-tuning of a molecule's conformational and physicochemical properties. As it expands and diversifies, so does the number of therapeutics that contain this core. Several spirocyclic drugs are already marketed, and considerably more have shown promising results. AREAS COVERED This review addresses recent in vivo studies (2017-2021) on applying spirocyclic compounds to treat various diseases, mainly grouped within neurological, infectious, and metabolic diseases and cancer. An emphasis is given on the influence of the spiro-structure on activity and consequent structure-activity study. In vivo results and their significance in the future progression towards clinical trials are also presented. EXPERT OPINION Spirocyclic compounds present an exciting opportunity as an unexplored chemical space in medicinal chemistry. However, their development is hindered by their complexity and synthesis challenges. Furthermore, a clear preference is still seen for readily available spirocyclic compounds involving amine or amide bonds. Nevertheless, these are temporary as high-throughput synthesis, and computational techniques allow fast optimization studies. In our opinion, the field of spirocyclic chemistry will continue to thrive and contribute to drug development, improving activity and selectivity on emergent ailments, such as cancer, metabolic, infectious, and neurological diseases.
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Affiliation(s)
- Vasco F Batista
- Laqv-requimte & Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Diana C G A Pinto
- Laqv-requimte & Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Artur M S Silva
- Laqv-requimte & Department of Chemistry, University of Aveiro, Aveiro, Portugal
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7
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Király SB, Bényei A, Lisztes E, Bíró T, Tóth BI, Kurtán T. Knoevenagel‐Cyclization Cascade Reactions of Substituted 5,6‐Dihydro‐2
H
‐Pyran Derivatives. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sándor Balázs Király
- Department of Organic Chemistry University of Debrecen P. O. Box 400, 4002 Debrecen Hungary
- Doctoral School of Chemistry University of Debrecen Egyetem tér 1 4032 Debrecen Hungary
| | - Attila Bényei
- Department of Physical Chemistry University of Debrecen 4032 Debrecen Egyetem square 1 Hungary
| | - Erika Lisztes
- Department of Physiology University of Debrecen < postCode/>4032 Debrecen Hungary
| | - Tamás Bíró
- Department of Immunology University of Debrecen postCode/>4032 < Debrecen Hungary
| | - Balázs István Tóth
- Department of Physiology University of Debrecen < postCode/>4032 Debrecen Hungary
| | - Tibor Kurtán
- Department of Organic Chemistry University of Debrecen P. O. Box 400, 4002 Debrecen Hungary
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8
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Bheemanaboina RRY, Wang J, Hu YY, Meng JP, Guan Z, Zhou CH. A facile reaction to access novel structural sulfonyl-hybridized imidazolyl ethanols as potential DNA-targeting antibacterial agents. Bioorg Med Chem Lett 2021; 47:128198. [PMID: 34119615 DOI: 10.1016/j.bmcl.2021.128198] [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: 02/07/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 12/20/2022]
Abstract
A novel type of sulfonyl-hybridized imidazolyl ethanols as potential DNA-targeting antibacterial agents was constructed via the unique ring-opened reaction of oxiranes by imidazoles for the first time. Some developed target hybrids showed potential antimicrobial potency against the tested microbes. Especially, imidazole derivative 5f could strongly suppressed the growth of MRSA (MIC = 4 μg/mL), which was 2-fold and 16-fold more potent than the positive control sulfathiazole and norfloxacin. This compound exhibited quite low propensity to induce bacterial resistance. Antibacterial mechanism exploration indicated that compound 5f could embed in MRSA DNA to form steady 5f-DNA complex, which possibly hinder DNA replication to exert antimicrobial behavior. Molecular docking showed that molecule 5f could bind with dihydrofolate synthetase through hydrogen bonds. These results implied that imidazole derivative 5f could be served as a promising molecule for the exploration of novel antibacterial candidates.
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Affiliation(s)
- Rammohan R Yadav Bheemanaboina
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Juan Wang
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Yuan-Yuan Hu
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Jiang-Ping Meng
- National & Local Joint Engineering Research Center of Targeted and Innovative Therapeutics, IATTI, College of Pharmacy, Chongqing University of Arts and Sciences, Chongqing 402160, China.
| | - Zhi Guan
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China.
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China.
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9
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Qin Y, Xu L, Teng Y, Wang Y, Ma P. Discovery of novel antibacterial agents: Recent developments in D-alanyl-D-alanine ligase inhibitors. Chem Biol Drug Des 2021; 98:305-322. [PMID: 34047462 DOI: 10.1111/cbdd.13899] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/09/2021] [Accepted: 05/23/2021] [Indexed: 01/14/2023]
Abstract
Bacterial infections can cause serious problems that threaten public health over a long period of time. Moreover, the continuous emergence of drug-resistant bacteria necessitates the development of novel antibacterial agents. D-alanyl-D-alanine ligase (Ddl) is an indispensable adenosine triphosphate-dependent bacterial enzyme involved in the biosynthesis of peptidoglycan precursor, which catalyzes the ligation of two D-alanine molecules into one D-alanyl-D-alanine dipeptide. This dipeptide is an essential component of the intracellular peptidoglycan precursor, uridine diphospho-N-acetylmuramic acid (UDP-MurNAc)-pentapeptide, that maintains the integrity of the bacterial cell wall by cross-linking the peptidoglycan chain, and is crucial for the survival of pathogens. Consequently, Ddl is expected to be a promising target for the development of antibacterial agents. In this review, we present a brief introduction regarding the structure and function of Ddl, as well as an overview of the various Ddl inhibitors currently being used as antibacterial agents, specifically highlighting their inhibitory activities, structure-activity relationships and mechanisms of action.
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Affiliation(s)
- Yinhui Qin
- Department of Pharmacy, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
| | - Linlin Xu
- Department of Pharmacy, Taian City Central Hospital, Taian, China
| | - Yuetai Teng
- Department of Pharmacy, Jinan Vocational College of Nursing, Jinan, China
| | - Yinhu Wang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China
| | - Peizhi Ma
- Department of Pharmacy, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
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10
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Salehpour M, Azizian J. Exploration of interaction behavior between spiro[indene-2,2'-[1,3,5]oxathiazine]-1,3-diones and DNA with the help of DFT, molecular docking, and MD simulations. J Biomol Struct Dyn 2021; 40:9194-9213. [PMID: 33998964 DOI: 10.1080/07391102.2021.1924266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A detailed computational study covering density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulations of some spirocyclic compounds interacting with a B-DNA has been performed. DFT calculations were performed using the B3LYP functional with 6-311++G(d,p) basis set and were used to identify the electrophilic and nucleophilic centers in electrostatic forces. NMR results were in agreement with previous experimental data and approved the reliability of the used method and basis set. The in silico screening results showed that spirocyclic compounds fulfill the Lipinski's rule of five and can be developed as potential oral bioavailable drug candidates. Based on molecular docking results, the binding affinities follow the 4c < 4d < 4a = 4b < 4e < 4g < 4f order and ranged from -8.6 to -9.7 kcal/mol indicating a reasonably favorable interaction between DNA and investigated compounds. The adducts were stabilized by hydrophobic and hydrogen bonding interactions. The MD simulations performed for 100 ns and the results are reported in terms of variables such as root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), center of mass (COM) separation distance between DNA and ligands, intermolecular hydrogen bonds, and radial distribution functions (RDF). The MD simulations demonstrated that compounds 4a and 4d bind into the minor groove of 1BNA and may act as potential biological probes for B-DNA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mahboobeh Salehpour
- Department of Chemistry, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Javad Azizian
- Department of Chemistry, Science and Research Branch, Islamic Azad University, Tehran, Iran
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11
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Liang XY, Battini N, Sui YF, Ansari MF, Gan LL, Zhou CH. Aloe-emodin derived azoles as a new structural type of potential antibacterial agents: design, synthesis, and evaluation of the action on membrane, DNA, and MRSA DNA isomerase. RSC Med Chem 2021; 12:602-608. [PMID: 34046631 PMCID: PMC8128066 DOI: 10.1039/d0md00429d] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/25/2021] [Indexed: 12/30/2022] Open
Abstract
As serious global drug resistance motivated the exploration of new structural drugs, we developed a type of novel structural aloe-emodin azoles as potential antibacterial agents in this work. Some target aloe-emodin azoles displayed effective activity against the tested strains, especially tetrazolyl aloe-emodin 4b showed a low MIC value of 2 μg mL-1 towards MRSA, being more efficient than the reference drug norfloxacin (MIC = 8 μg mL-1). Also, the active molecule 4b exhibited low cytotoxicity against LO2 cells with no distinct tendency to induce the concerned resistance towards MRSA. The tetrazolyl derivative 4b was preliminarily investigated for the possible mechanism; it was revealed that tetrazolyl derivative 4b could both disrupt the integrity of MRSA membrane and form 4b-DNA supramolecular complex by intercalating into DNA. Moreover, tetrazolyl aloe-emodin 4b could bind with MRSA DNA isomerase at multiple sites through hydrogen bonds in molecular simulation.
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Affiliation(s)
- Xin-Yuan Liang
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China +86 23 68254967 +86 23 68254967
| | - Narsaiah Battini
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China +86 23 68254967 +86 23 68254967
| | - Yan-Fei Sui
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China +86 23 68254967 +86 23 68254967
| | - Mohammad Fawad Ansari
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China +86 23 68254967 +86 23 68254967
| | - Lin-Ling Gan
- Chongqing Engineering Research Center of Pharmaceutical Sciences, School of Pharmacy, Chongqing Medical and Pharmaceutical College Chongqing 401331 PR China
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China +86 23 68254967 +86 23 68254967
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12
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Melot R, Zuccarello M, Cavalli D, Niggli N, Devereux M, Bürgi T, Baudoin O. Palladium(0)‐Catalyzed Enantioselective Intramolecular Arylation of Enantiotopic Secondary C−H Bonds. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Romain Melot
- University of Basel Department of Chemistry St. Johanns-Ring 19 4056 Basel Switzerland
| | - Marco Zuccarello
- University of Basel Department of Chemistry St. Johanns-Ring 19 4056 Basel Switzerland
| | - Diana Cavalli
- University of Basel Department of Chemistry St. Johanns-Ring 19 4056 Basel Switzerland
| | - Nadja Niggli
- University of Basel Department of Chemistry St. Johanns-Ring 19 4056 Basel Switzerland
| | - Michael Devereux
- University of Basel Department of Chemistry St. Johanns-Ring 19 4056 Basel Switzerland
| | - Thomas Bürgi
- University of Geneva Department of Physical Chemistry 30 Quai Ernest-Ansermet 1211 Geneva 4 Switzerland
| | - Olivier Baudoin
- University of Basel Department of Chemistry St. Johanns-Ring 19 4056 Basel Switzerland
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13
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Melot R, Zuccarello M, Cavalli D, Niggli N, Devereux M, Bürgi T, Baudoin O. Palladium(0)-Catalyzed Enantioselective Intramolecular Arylation of Enantiotopic Secondary C-H Bonds. Angew Chem Int Ed Engl 2021; 60:7245-7250. [PMID: 33325596 DOI: 10.1002/anie.202014605] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/14/2020] [Indexed: 11/10/2022]
Abstract
The enantioselective functionalization of nonactivated enantiotopic secondary C-H bonds is one of the greatest challenges in transition-metal-catalyzed C-H activation proceeding by an inner-sphere mechanism. Such reactions have remained elusive within the realm of Pd0 catalysis. Reported here is the unique reactivity profile of the IBiox ligand family in the Pd0 -catalyzed intramolecular arylation of such nonactivated secondary C-H bonds. Chiral C2 -symmetric IBiox ligands led to high enantioselectivities for a broad range of valuable indane products containing a tertiary stereocenter, as well as the arylation of secondary C-H bonds adjacent to amides. Depending on the amide substituents and upon control of reaction time, indanes containing labile tertiary stereocenters were also obtained with high enantioselectivities. Analysis of the steric maps of the IBiox ligands indicated that the level of enantioselectivity correlates with the difference between the two most occupied and the two less occupied space quadrants, and provided a blueprint for the design of even more efficient ligands.
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Affiliation(s)
- Romain Melot
- University of Basel, Department of Chemistry, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Marco Zuccarello
- University of Basel, Department of Chemistry, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Diana Cavalli
- University of Basel, Department of Chemistry, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Nadja Niggli
- University of Basel, Department of Chemistry, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Michael Devereux
- University of Basel, Department of Chemistry, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Thomas Bürgi
- University of Geneva, Department of Physical Chemistry, 30 Quai Ernest-Ansermet, 1211, Geneva 4, Switzerland
| | - Olivier Baudoin
- University of Basel, Department of Chemistry, St. Johanns-Ring 19, 4056, Basel, Switzerland
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14
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Kong Q, Yang Y. Recent advances in antibacterial agents. Bioorg Med Chem Lett 2021; 35:127799. [PMID: 33476772 DOI: 10.1016/j.bmcl.2021.127799] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance is a global challenge and the effectiveness of old antibiotics is decreasing. Discovery and development of antibacterial agents have been accelerated to replenish the arsenal of antibiotics which is limited and shrinking. In recent years, significant advances have achieved in the antibacterial area, including new compounds of known classes and new compounds with new mechanisms. This review summarizes these advances and provides perspective on future directions of antibacterial agents.
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Affiliation(s)
- Qidi Kong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing 100049, China
| | - Yushe Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing 100049, China.
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15
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Liu X, Wang C, Wang X, Ma Z, Meng L, Ding D, Liu J, Chen Y. Synthesis of Spirobarbiturate Piperidin-2-one Derivatives via Cascade Aza-Michael/Michael Cyclization Reaction. CHINESE J ORG CHEM 2021. [DOI: 10.6023/cjoc202105045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Zaitseva ER, Smirnov AY, Myasnyanko IN, Mineev KS, Sokolov AI, Volkhina TN, Mikhaylov AA, Baleeva NS, Baranov MS. Imidazol-5-ones as a substrate for [1,5]-hydride shift triggered cyclization. NEW J CHEM 2021. [DOI: 10.1039/d0nj05738j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
(2-Aminobenzylidene)-imidazolones were used as substrates for [1,5]-hydride shift triggered cyclization under promotion by TiCl4 at room temperature.
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Affiliation(s)
- Elvira R. Zaitseva
- Institute of Bioorganic Chemistry
- Russian Academy of Sciences
- Moscow
- Russia
- D. Mendeleev University of Chemical Technology of Russia
| | | | - Ivan N. Myasnyanko
- Institute of Bioorganic Chemistry
- Russian Academy of Sciences
- Moscow
- Russia
| | | | | | - Tatyana N. Volkhina
- D. Mendeleev University of Chemical Technology of Russia
- 9 Miusskaya Sq
- Moscow
- Russia
- A.N. Nesmeyanov Institute of Organoelement Compounds
| | | | | | - Mikhail S. Baranov
- Institute of Bioorganic Chemistry
- Russian Academy of Sciences
- Moscow
- Russia
- Pirogov Russian National Research Medical University
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17
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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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18
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Wang M, Gao R, Sang P, Odom T, Zheng M, Shi Y, Xu H, Cao C, Cai J. Dimeric γ-AApeptides With Potent and Selective Antibacterial Activity. Front Chem 2020; 8:441. [PMID: 32596202 PMCID: PMC7304243 DOI: 10.3389/fchem.2020.00441] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/27/2020] [Indexed: 12/30/2022] Open
Abstract
Over the past few decades, the emergence of antibiotic resistance developed by life-threatening bacteria has become increasingly prevalent. Thus, there is an urgent demand to develop novel antibiotics capable of mitigating this trend. Herein, we report a series of dimeric γ-AApeptide derivatives as potential antibiotic agents with limited toxicity and excellent selectivity against Gram-positive strains. Among them, compound 2 was identified to have the best MICs without inducing drug resistance, even after exposure to MRSA for 20 passages. Time-kill kinetics and mechanistic studies suggested that 2 could mimic host-defense peptides (HDPs) and rapidly eradicate MRSA within 2 hours through disturbing the bacteria membrane. Meanwhile, biofilm formation was successfully inhibited even at a low concentration. Taken together, these results suggested the great potential of dimeric γ-AApeptide derivatives as antibacterial agents.
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Affiliation(s)
- Minghui Wang
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Ruixuan Gao
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Peng Sang
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Timothy Odom
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Mengmeng Zheng
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Yan Shi
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Hai Xu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Chuanhai Cao
- College of Pharmacy, University of South Florida, Tampa, FL, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL, United States
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19
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Discovery of novel multi-substituted benzo-indole pyrazole schiff base derivatives with antibacterial activity targeting DNA gyrase. Bioorg Chem 2020; 99:103807. [DOI: 10.1016/j.bioorg.2020.103807] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/25/2020] [Accepted: 03/28/2020] [Indexed: 01/14/2023]
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20
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Lin S, Li H, Tao Y, Liu J, Yuan W, Chen Y, Liu Y, Liu S. In Vitro and in Vivo Evaluation of Membrane-Active Flavone Amphiphiles: Semisynthetic Kaempferol-Derived Antimicrobials against Drug-Resistant Gram-Positive Bacteria. J Med Chem 2020; 63:5797-5815. [DOI: 10.1021/acs.jmedchem.0c00053] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Shuimu Lin
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, P. R. China
| | - Hongxia Li
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, P. R. China
| | - Yiwen Tao
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, P. R. China
| | - Jiayong Liu
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, P. R. China
| | - Wenchang Yuan
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, P. R. China
| | - Yongzhi Chen
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, P. R. China
| | - Ying Liu
- Guangdong Key Laboratory of Optical Fiber Sensing and Communications, Institute of Photonics Technology, Jinan University, Guangzhou, Guangdong 510632, P. R. China
| | - Shouping Liu
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, P. R. China
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21
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Chen L, He J. DABCO-Catalyzed Michael/Alkylation Cascade Reactions Involving α-Substituted Ammonium Ylides for the Construction of Spirocyclopropyl Oxindoles: Access to the Powerful Chemical Leads against HIV-1. J Org Chem 2020; 85:5203-5219. [DOI: 10.1021/acs.joc.9b03164] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Lin Chen
- School of Chemistry and Materials Science, Guizhou Normal University, Guiyang 550001, China
| | - Jin He
- School of Chemistry and Materials Science, Guizhou Normal University, Guiyang 550001, China
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22
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Obi G, Chukwujekwu JC, van Heerden FR. Synthesis and antimicrobial activity of new prenylated 2-pyrone derivatives. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1718710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Grace Obi
- School of Chemistry and Physics, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Jude C. Chukwujekwu
- School of Chemistry and Physics, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Fanie R. van Heerden
- School of Chemistry and Physics, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
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23
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Xue W, Li X, Ma G, Zhang H, Chen Y, Kirchmair J, Xia J, Wu S. N-thiadiazole-4-hydroxy-2-quinolone-3-carboxamides bearing heteroaromatic rings as novel antibacterial agents: Design, synthesis, biological evaluation and target identification. Eur J Med Chem 2019; 188:112022. [PMID: 31901744 DOI: 10.1016/j.ejmech.2019.112022] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/22/2019] [Accepted: 12/29/2019] [Indexed: 12/12/2022]
Abstract
Due to the occurrence of antibiotic resistance, bacterial infectious diseases have become a serious threat to public health. To overcome antibiotic resistance, novel antibiotics are urgently needed. N-thiadiazole-4-hydroxy-2-quinolone-3-carboxamides are a potential new class of antibacterial agents, as one of its derivatives was identified as an antibacterial agent against S. aureus. However, no potency-directed structural optimization has been performed. In this study, we designed and synthesized 37 derivatives, and evaluated their antibacterial activity against S. aureus ATCC29213, which led to the identification of ten potent antibacterial agents with minimum inhibitory concentration (MIC) values below 1 μg/mL. Next, we performed bacterial growth inhibition assays against a panel of drug-resistant clinical isolates, including methicillin-resistant S. aureus, and cytotoxicity assays with HepG2 and HUVEC cells. One of the tested compounds named 1-ethyl-4-hydroxy-2-oxo-N-(5-(thiazol-2-yl)-1,3,4-thiadiazol-2-yl)-1,2-dihydroquinoline-3-carboxamide (g37) showed 2 to 128-times improvement compared with vancomycin in term of antibacterial potency against the tested strains (MICs: 0.25-1 μg/mL vs. 1-64 μg/mL) and an optimal selective toxicity (HepG2/MRSA, 110.6 to 221.2; HUVEC/MRSA, 77.6-155.2). Further, comprehensive evaluation indicated that g37 did not induce resistance development of MRSA over 20 passages, and it has been confirmed as a bactericidal, metabolically stable, orally active antibacterial agent. More importantly, we have identified the S. aureus DNA gyrase B as its potential target and proposed a potential binding mode by molecular docking. Taken together, the present work reports the most potent derivative of this chemical series (g37) and uncovers its potential target, which lays a solid foundation for further lead optimization facilitated by the structure-based drug design technique.
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Affiliation(s)
- Wenjie Xue
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xueyao Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Guixing Ma
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hongmin Zhang
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ya Chen
- Center for Bioinformatics (ZBH), Department of Computer Science, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany
| | - Johannes Kirchmair
- Center for Bioinformatics (ZBH), Department of Computer Science, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany; Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway; Computational Biology Unit (CBU), University of Bergen, Bergen, Norway
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
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24
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Islam MA, Pillay TS. Identification of promising anti-DNA gyrase antibacterial compounds using de novo design, molecular docking and molecular dynamics studies. J Biomol Struct Dyn 2019; 38:1798-1809. [PMID: 31084271 DOI: 10.1080/07391102.2019.1617785] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The rapidly increasing rate of antibiotic resistance is of great concern. Approximately two million deaths result annually from bacterial infections worldwide. Therefore, there is a paramount requirement to develop innovative and novel antibacterial agents with new mechanisms of action and activity against resistant bacterial strains. For this purpose, a set of benzothiazole and N-phenylpyrrolamides derivatives reported as DNA Gyrase B (GyrB) inhibitors were collected from the literature and docked inside the receptor cavity of DNA Gyrase B (PDB ID: 5L3J). The best 10 docked complexes were used to identify novel antibacterial chemical agents through a de novo design approach. Out of initial 300 chemical analogues, the best six analogues were identified using screening with a set of criteria followed by pharmacokinetic analysis. The binding interactions of the best six analogues revealed that all molecules formed a number of critical interactions with catalytic amino residues of DNA Gyrase B with high binding energy. The predicted inhibitory constant biological activity based on binding energy supported the potential of the molecules as DNA Gyrase B ligands. The RMSD, RMSF, and radius of gyration parameters obtained from the 100 ns molecular dynamics simulation study clearly demonstrated that all six analogues were efficient enough to form stable complexes with DNA Gyrase B. High negative binding energy of all ligands obtained from MM-GBSA approach undoubtedly explained the strong affinity toward the DNA Gyrase B. Therefore, the proposed de novo designed molecules can be considered as promising antibacterial chemical agents subject to experimental validation, in vitro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Ataul Islam
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Pretoria, South Africa.,School of Health Sciences, University of Kwazulu-Natal, Durban, South Africa.,Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Tahir S Pillay
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Pretoria, South Africa.,Division of Chemical Pathology, University of Cape Town, Cape Town, South Africa
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