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Jin X, Ding N, Guo HY, Hu Q. Macrocyclic-based strategy in drug design: From lab to the clinic. Eur J Med Chem 2024; 277:116733. [PMID: 39098132 DOI: 10.1016/j.ejmech.2024.116733] [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: 07/05/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
Macrocyclic compounds have emerged as potent tools in the field of drug design, offering unique advantages for enhancing molecular recognition, improving pharmacokinetic properties, and expanding the chemical space accessible to medicinal chemists. This review delves into the evolutionary trajectory of macrocyclic-based strategies, tracing their journey from laboratory innovations to clinical applications. Beginning with an exploration of the defining structural features of macrocycles and their impact on drug-like characteristics, this discussion progresses to highlight key design principles that have facilitated the development of diverse macrocyclic drug candidates. Through a series of illustrative representative case studies from approved macrocyclic drugs and candidates spanning various therapeutic areas, particular emphasis is placed on their efficacy in targeting challenging protein-protein interactions, enzymes, and receptors. Additionally, this review thoroughly examines how macrocycles effectively address critical issues such as metabolic stability, oral bioavailability and selectivity. Valuable insights into optimization strategies employed during both approved and clinical phases underscore successful translation of promising leads into efficacious therapies while providing valuable perspectives on harnessing the full potential of macrocycles in drug discovery and development endeavors.
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Affiliation(s)
- Xin Jin
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ning Ding
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Hong-Yu Guo
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qing Hu
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China.
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2
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Ma CX, Liu WT, Li XM, Ding J, Liu SM, Xue F, Li Y, Liang JH. Design, synthesis and structure-activity relationships of novel non-ketolides: 9-Oxime clarithromycin featured with seven-to thirteen-atom-length diamine linkers at 3-OH. Eur J Med Chem 2024; 276:116630. [PMID: 38972081 DOI: 10.1016/j.ejmech.2024.116630] [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: 04/25/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/09/2024]
Abstract
We report here on the structure-activity relationships of hybrids combining 3-descladinosyl clarithromycin with quinolones linked by extended diamine connectors. Several hybrids, exemplified by 23Bc, 23Be, 23Bf, 26Be, and 30Bc, not only restored potency against inducibly resistant pathogens but also exhibited significantly enhanced activities against constitutively resistant strains of Staphylococcus pneumoniae and Staphylococcus pyogenes, which express high-level resistance independent of clarithromycin or erythromycin induction. Additionally, the novel hybrids showed susceptibility against Gram-negative Haemophilus influenzae. Notably, hybrid 23Be demonstrated dual modes of action by inhibiting both protein synthesis and DNA replication in vitro and in vivo. Given these promising characteristics, 23Be emerges as a potential candidate for the treatment of community-acquired bacterial pneumonia.
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Affiliation(s)
- Cong-Xuan Ma
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Wen-Tian Liu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Xue-Meng Li
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Jing Ding
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Si-Meng Liu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Feng Xue
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, 100034, China
| | - Yun Li
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, 100034, China.
| | - Jian-Hua Liang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China.
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3
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Zhang N, Liu WT, Cui XY, Liu SM, Ma CX, Liang JH. Design and structure-activity relationships of ether-linked alkylides: Hybrids of 3-O-descladinosyl macrolides and quinolone motifs. Bioorg Chem 2024; 151:107712. [PMID: 39146761 DOI: 10.1016/j.bioorg.2024.107712] [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: 07/19/2024] [Revised: 08/07/2024] [Accepted: 08/09/2024] [Indexed: 08/17/2024]
Abstract
Ketolides (3-keto) such as TE-802 and acylides (3-O-acyl) like TEA0929 are ineffective against constitutively resistant pathogens harboring erythromycin ribosomal methylation (erm) genes. Following our previous work on alkylides (3-O-alkyl), we explored the structure-activity relationships of hybrids combining (R/S) 3-descladinosyl erythromycin with 6/7-quinolone motifs, featuring extended ether-linked spacers, with a focus on their efficacy against pathogens bearing constitutive erm gene resistance. Optimized compounds 17a and 31f not only reinstated efficacy against inducibly resistant pathogens but also demonstrated significantly augmented activities against constitutively resistant strains of Streptococcus pneumoniae and Streptococcus pyogenes, which are typically refractory to existing C-3 modified macrolides. Notably, hybrid 31f (coded ZN-51) represented a pioneering class of agents distinguished by its dual modes of action, with ribosomes as the primary target and topoisomerases as the secondary target. As a novel chemotype of macrolide-quinolone hybrids, alkylide 31f is a valuable addition to our armamentarium against macrolide-resistant bacteria.
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Affiliation(s)
- Na Zhang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Wen-Tian Liu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Xin-Yi Cui
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Si-Meng Liu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Cong-Xuan Ma
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Jian-Hua Liang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China.
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Aleksandrova EV, Ma CX, Klepacki D, Alizadeh F, Vázquez-Laslop N, Liang JH, Polikanov YS, Mankin AS. Macrolones target bacterial ribosomes and DNA gyrase and can evade resistance mechanisms. Nat Chem Biol 2024:10.1038/s41589-024-01685-3. [PMID: 39039256 DOI: 10.1038/s41589-024-01685-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/19/2024] [Indexed: 07/24/2024]
Abstract
Growing resistance toward ribosome-targeting macrolide antibiotics has limited their clinical utility and urged the search for superior compounds. Macrolones are synthetic macrolide derivatives with a quinolone side chain, structurally similar to DNA topoisomerase-targeting fluoroquinolones. While macrolones show enhanced activity, their modes of action have remained unknown. Here, we present the first structures of ribosome-bound macrolones, showing that the macrolide part occupies the macrolide-binding site in the ribosomal exit tunnel, whereas the quinolone moiety establishes new interactions with the tunnel. Macrolones efficiently inhibit both the ribosome and DNA topoisomerase in vitro. However, in the cell, they target either the ribosome or DNA gyrase or concurrently both of them. In contrast to macrolide or fluoroquinolone antibiotics alone, dual-targeting macrolones are less prone to select resistant bacteria carrying target-site mutations or to activate inducible macrolide resistance genes. Furthermore, because some macrolones engage Erm-modified ribosomes, they retain activity even against strains with constitutive erm resistance genes.
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Affiliation(s)
- Elena V Aleksandrova
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Cong-Xuan Ma
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Faezeh Alizadeh
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Jian-Hua Liang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA.
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
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5
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Nakao T, Kosai K, Akamatsu N, Ota K, Mitsumoto-Kaseida F, Hasegawa H, Izumikawa K, Mukae H, Yanagihara K. Molecular and phenotypic characterization of Streptococcus pneumoniae isolates in a Japanese tertiary care hospital. Front Cell Infect Microbiol 2024; 14:1391879. [PMID: 39104851 PMCID: PMC11298800 DOI: 10.3389/fcimb.2024.1391879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/18/2024] [Indexed: 08/07/2024] Open
Abstract
This study aimed to investigate the bacterial characteristics of pneumococcal isolates obtained from a tertiary care hospital in Japan. We analyzed the antimicrobial susceptibility, possession of macrolide resistance genes, pneumococcal serogroup/serotype, and sequence type (ST) of pneumococcal isolates from patients aged 15 years or older between 2011 and 2020 at Nagasaki University Hospital. Of the 73 isolates analyzed, 86.3% showed resistance to macrolides, and 28.8%, 46.6%, and 11.0% harbored mefA, ermB, and both, respectively. Of the isolates possessing ermB, 97.6% showed high levels of macrolide resistance [minimal inhibitory concentration (MIC) range, > 16 µg/mL]. Solithromycin (MIC range, 0.03-0.25 µg/mL), regardless of the presence of macrolide resistance genes, and lascufloxacin (MIC range, 0.06-0.5 µg/mL) showed potent in vitro activity against pneumococci. Serotype 19A was the most prevalent (six isolates), followed by serotypes 10A, 15A, and 15B/C (five isolates each). Four serotypes (11A, 19A, 22F, and 23B) and five STs (36, 99, 433, 558, and 3111) were significantly correlated with the presence of macrolide resistance genes. All four isolates with serotype 11A/ST99 and three isolates with serotype 19A/ST3111 harbored both mefA and ermB. No macrolide resistance genes were detected in either of the two isolates with serotype 22F/ST433, while all ten isolates with serogroup 15 (serotypes 15A and 15B/C, five isolates each) possessed ermB alone. Our study revealed the bacterial characteristics of the pneumococcal isolates obtained from our hospital. In vitro activity of solithromycin and lascufloxacin against these isolates was confirmed.
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Affiliation(s)
- Takumi Nakao
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kosuke Kosai
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Norihiko Akamatsu
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Kenji Ota
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Fujiko Mitsumoto-Kaseida
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroo Hasegawa
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Koichi Izumikawa
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
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Ma CX, Li Y, Liu WT, Li Y, Zhao F, Lian XT, Ding J, Liu SM, Liu XP, Fan BZ, Liu LY, Xue F, Li J, Zhang JR, Xue Z, Pei XT, Lin JZ, Liang JH. Synthetic macrolides overcoming MLS BK-resistant pathogens. Cell Discov 2024; 10:75. [PMID: 38992047 PMCID: PMC11239830 DOI: 10.1038/s41421-024-00702-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/26/2024] [Indexed: 07/13/2024] Open
Abstract
Conventional macrolide-lincosamide-streptogramin B-ketolide (MLSBK) antibiotics are unable to counter the growing challenge of antibiotic resistance that is conferred by the constitutive methylation of rRNA base A2058 or its G2058 mutation, while the presence of unmodified A2058 is crucial for high selectivity of traditional MLSBK in targeting pathogens over human cells. The absence of effective modes of action reinforces the prevailing belief that constitutively antibiotic-resistant Staphylococcus aureus remains impervious to existing macrolides including telithromycin. Here, we report the design and synthesis of a novel series of macrolides, featuring the strategic fusion of ketolide and quinolone moieties. Our effort led to the discovery of two potent compounds, MCX-219 and MCX-190, demonstrating enhanced antibacterial efficacy against a broad spectrum of formidable pathogens, including A2058-methylated Staphylococcus aureus, Streptococcus pneumoniae, Streptococcus pyogenes, and notably, the clinical Mycoplasma pneumoniae isolates harboring A2058G mutations which are implicated in the recent pneumonia outbreak in China. Mechanistic studies reveal that the modified quinolone moiety of MCX-190 establishes a distinctive secondary binding site within the nascent peptide exit tunnel. Structure-activity relationship analysis underscores the importance of this secondary binding, maintained by a sandwich-like π-π stacking interaction and a water-magnesium bridge, for effective engagement with A2058-methylated ribosomes rather than topoisomerases targeted by quinolone antibiotics. Our findings not only highlight MCX-219 and MCX-190 as promising candidates for next-generation MLSBK antibiotics to combat antibiotic resistance, but also pave the way for the future rational design of the class of MLSBK antibiotics, offering a strategic framework to overcome the challenges posed by escalating antibiotic resistance.
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Affiliation(s)
- Cong-Xuan Ma
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Ye Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for mRNA Translational Research, Fudan University, Shanghai, China
| | - Wen-Tian Liu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Yun Li
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Fei Zhao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
| | - Xiao-Tian Lian
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Jing Ding
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Si-Meng Liu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Xie-Peng Liu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Bing-Zhi Fan
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Li-Yong Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
| | - Feng Xue
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Jian Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for mRNA Translational Research, Fudan University, Shanghai, China
| | - Jue-Ru Zhang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Zhao Xue
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for mRNA Translational Research, Fudan University, Shanghai, China
| | - Xiao-Tong Pei
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for mRNA Translational Research, Fudan University, Shanghai, China
| | - Jin-Zhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China.
- Center for mRNA Translational Research, Fudan University, Shanghai, China.
| | - Jian-Hua Liang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.
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Kurono Y, Kudo F, Watanabe A, Yamatake T, Shimada S, Suzuki K. Efficacy, safety, and tissue penetration of solithromycin in Japanese patients with otorhinolaryngological infections. Auris Nasus Larynx 2024; 51:379-390. [PMID: 38065757 DOI: 10.1016/j.anl.2023.11.008] [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: 08/29/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 01/18/2024]
Abstract
OBJECTIVE To assess the efficacy, safety, and tissue penetration of solithromycin for the treatment of otorhinolaryngological infections, we conducted three studies: a tissue penetration study with patients scheduled to undergo otorhinolaryngological tissue removal, an open-label study comprising patients with otitis media, pharyngitis, laryngitis, and tonsillitis, and a non-inferiority study compared with high-dose cefcapene-pivoxil (CFPN-PI). METHODS Tissue penetration study; 17 patients with chronic rhinosinusitis, chronic otitis media, chronic tonsillitis, or palatine tonsillar hypertrophy, who required resection or removal of their tissue, were enrolled. Solithromycin was administered orally, and otorhinolaryngological tissues were collected 3.5-6 h after drug administration; blood was collected within 15 min before and after drug administration. The collected tissues and blood concentrations were measured at a central laboratory. Open-label study; 55 patients who were diagnosed with acute otitis media, laryngopharyngitis, or tonsillitis were enrolled. Solithromycin was administered orally 800 mg on Day 1, while on days 2-7, 400 mg of the drug was administered once daily. The primary endpoint is the clinical response at Test-of-Cure (TOC: 5-10 days after completion) Non-inferiority study; 283 patients with acute rhinosinusitis or acute exacerbation of chronic rhinosinusitis were randomized into either the solithromycin group or CFPN-PI group. Solithromycin was administered 800 mg once daily on Day 1 and 400 mg once daily while on Days 2-7 in solithromycin group, and CFPN-PI was administered 150 mg three times a day while on Days 1-7 in CFPN-PI group. The primary endpoint is the clinical response at TOC. RESULTS In the tissue penetration study, the tissue concentration ratios (tissue concentration/plasma concentration) of solithromycin were 4.19 in the sinonasal mucosa, 1.33 in the middle ear mucosa, and 6.12 in the palatine tonsil tissue. In the open-label study, the efficacy rates at the TOC were 97.0 % for acute otitis media, 100 % for laryngopharyngitis, and 81.8 % for tonsillitis. In the non-inferiority study comprising patients with rhinosinusitis, the efficacy rate at the TOC was 87.7 % for solithromycin and 89.7 % for CFPN-PI. The difference in the efficacy rate (95 % confidence interval) was -2.0 % (-9.4 % to 5.4 %), verifying the non-inferiority of solithromycin to CFPN-PI. The most common adverse events in patients administered solithromycin were diarrhea (20.7 %), nausea and nasopharyngitis (3.6 %,), pharyngitis and elevated hepatic function test results (3.1 %), and abnormal hepatic function (2.1 %). CONCLUSION Based on the findings, it is suggested that solithromycin is useful for the treatment of otorhinolaryngological infections.
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Affiliation(s)
| | | | - Akira Watanabe
- Research Division for Development of Anti-Infective Agents, Tohoku Bunka Gakuen University, Japan
| | - Takahiro Yamatake
- Project Management Department, FUJIFILM Toyama chemical Co., Ltd., Chuo-ku, Tokyo 104-0031, Japan
| | - Satoshi Shimada
- Project Management Department, FUJIFILM Toyama chemical Co., Ltd., Chuo-ku, Tokyo 104-0031, Japan.
| | - Kenji Suzuki
- Department of Otorhinolaryngology, Yonaha Okanoue Hospital, Japan
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Bian C, Zhang J, Zheng X, Qiao M, Li Y, Chen X, Si S. Synthesis and structure-activity relationships of novel 14-membered 2-fluoro ketolides with structural modification at the C11 position. Eur J Med Chem 2024; 267:116181. [PMID: 38354519 DOI: 10.1016/j.ejmech.2024.116181] [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: 10/20/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/16/2024]
Abstract
A series of novel C11 substituted 14-membered 2-fluoro ketolides were synthesized and evaluated for their antibacterial activity against erythromycin-resistant and erythromycin-susceptible clinical isolates and strains from ATCC. The overall antibacterial spectra of the semi-synthetic antibiotics are similar to that of telithromycin (TEL) and most of them exhibited excellent activity against Gram-positive bacteria (S. epidermidis, S. pneumoniae, S. aureus) and several Gram-negative bacteria (M. catarrhalis, H. influenza). Compounds 11c, 11g, 11h, 11q, 12a, 12b, 12d and 12e displayed 4-16 fold more potency than TEL against all the tested erythromycin-resistant S. epidermidis strains and S. pneumonia SPN19-8 and SPN19-8. Compounds 11b, 11c, 11e, 11g, 11h, 11q, 12a, 12b and 12c showed at least 8 fold potency than TEL against erythromycin-resistant M. catarrhalis BCA19-5 and BCA19-6. Molecular docking suggested compound 12d oriented the macrolide ring and side chain similarly to solithromycin (SOL). Noticeably an additional hydrogen bond was observed between the Lys90 residue of ribosome protein L22 and the carbamate group at the C11 position, which might provide a rational explanation for the enhanced antibacterial activity of target compounds. Therefore this research would offer a new perspective for further structural optimization of the C11 side chain. Based on the results of antibacterial activity, cytotoxicity and structural diversity, 5 compounds (11a, 11b, 11h, 12d and 12i) were selected for the stability testing of human liver microsomes and compound 11a exhibited preferable metabolic stability.
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Affiliation(s)
- Cong Bian
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China
| | - Jing Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China
| | - Xiao Zheng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China
| | - Mengqian Qiao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China
| | - Yan Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China.
| | - Xiaofang Chen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China.
| | - Shuyi Si
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China.
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9
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Gingras H, Peillard-Fiorente F, Godin C, Patron K, Leprohon P, Ouellette M. New Resistance Mutations Linked to Decreased Susceptibility to Solithromycin in Streptococcus pneumoniae Revealed by Chemogenomic Screens. Antimicrob Agents Chemother 2023; 67:e0039523. [PMID: 37409958 PMCID: PMC10433811 DOI: 10.1128/aac.00395-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/18/2023] [Indexed: 07/07/2023] Open
Abstract
Two strains of Streptococcus pneumoniae, one expressing the methyltransferase Erm(B) and the other negative for erm(B), were selected for solithromycin resistance in vitro either with direct drug selection or with chemical mutagenesis followed by drug selection. We obtained a series of mutants that we characterized by next-generation sequencing. We found mutations in various ribosomal proteins (L3, L4, L22, L32, and S4) and in the 23S rRNA. We also found mutations in subunits of the phosphate transporter, in the DEAD box helicase CshB, and in the erm(B)L leader peptide. All mutations were shown to decrease solithromycin susceptibility when transformed into sensitive isolates. Some of the genes derived from our in vitro screens were found to be mutated also in clinical isolates with decreased susceptibility to solithromycin. While many mutations were in coding sequences, some were found in regulatory regions. These included novel phenotypic mutations in the intergenic regions of the macrolide resistance locus mef(E)/mel and in the vicinity of the ribosome binding site of erm(B). Our screens highlighted that macrolide-resistant S. pneumoniae can easily acquire resistance to solithromycin, and they revealed many new phenotypic mutations.
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Affiliation(s)
- Hélène Gingras
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Flora Peillard-Fiorente
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Chantal Godin
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Kevin Patron
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
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Chen CW, Leimer N, Syroegin EA, Dunand C, Bulman ZP, Lewis K, Polikanov YS, Svetlov MS. Structural insights into the mechanism of overcoming Erm-mediated resistance by macrolides acting together with hygromycin-A. Nat Commun 2023; 14:4196. [PMID: 37452045 PMCID: PMC10349075 DOI: 10.1038/s41467-023-39653-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
The ever-growing rise of antibiotic resistance among bacterial pathogens is one of the top healthcare threats today. Although combination antibiotic therapies represent a potential approach to more efficiently combat infections caused by susceptible and drug-resistant bacteria, only a few known drug pairs exhibit synergy/cooperativity in killing bacteria. Here, we discover that well-known ribosomal antibiotics, hygromycin A (HygA) and macrolides, which target peptidyl transferase center and peptide exit tunnel, respectively, can act cooperatively against susceptible and drug-resistant bacteria. Remarkably, HygA slows down macrolide dissociation from the ribosome by 60-fold and enhances the otherwise weak antimicrobial activity of the newest-generation macrolide drugs known as ketolides against macrolide-resistant bacteria. By determining a set of high-resolution X-ray crystal structures of drug-sensitive wild-type and macrolide-resistant Erm-methylated 70S ribosomes in complex with three HygA-macrolide pairs, we provide a structural rationale for the binding cooperativity of these drugs and also uncover the molecular mechanism of overcoming Erm-type resistance by macrolides acting together with hygromycin A. Altogether our structural, biochemical, and microbiological findings lay the foundation for the subsequent development of synergistic antibiotic tandems with improved bactericidal properties against drug-resistant pathogens, including those expressing erm genes.
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Affiliation(s)
- Chih-Wei Chen
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Nadja Leimer
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Egor A Syroegin
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Clémence Dunand
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Zackery P Bulman
- Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Kim Lewis
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
| | - Maxim S Svetlov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
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11
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Jeremia L, Deprez BE, Dey D, Conn GL, Wuest WM. Ribosome-targeting antibiotics and resistance via ribosomal RNA methylation. RSC Med Chem 2023; 14:624-643. [PMID: 37122541 PMCID: PMC10131624 DOI: 10.1039/d2md00459c] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/17/2023] [Indexed: 03/05/2023] Open
Abstract
The rise of multidrug-resistant bacterial infections is a cause of global concern. There is an urgent need to both revitalize antibacterial agents that are ineffective due to resistance while concurrently developing new antibiotics with novel targets and mechanisms of action. Pathogen associated resistance-conferring ribosomal RNA (rRNA) methyltransferases are a growing threat that, as a group, collectively render a total of seven clinically-relevant ribosome-targeting antibiotic classes ineffective. Increasing frequency of identification and their growing prevalence relative to other resistance mechanisms suggests that these resistance determinants are rapidly spreading among human pathogens and could contribute significantly to the increased likelihood of a post-antibiotic era. Herein, with a view toward stimulating future studies to counter the effects of these rRNA methyltransferases, we summarize their prevalence, the fitness cost(s) to bacteria of their acquisition and expression, and current efforts toward targeting clinically relevant enzymes of this class.
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Affiliation(s)
- Learnmore Jeremia
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Benjamin E Deprez
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - William M Wuest
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
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12
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Lian X, Liu W, Fan B, Yu M, Liang J. Design, Synthesis and Biological Evaluation of Conjugates of 3- O-Descladinose-azithromycin and Nucleobases against rRNA A2058G- or A2059G-Mutated Strains. Molecules 2023; 28:molecules28031327. [PMID: 36770992 PMCID: PMC9920417 DOI: 10.3390/molecules28031327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/22/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Structurally unrelated antibiotics MLSB (macrolide-lincosamide-streptogramin B) compromised with clinically resistant pathogens because of the cross-resistance resulting from the structural modification of rRNA A2058. The structure-activity relationships of a novel 3-O-descladinose azithromycin chemotype conjugating with nucleobases were fully explored with the aid of engineered E. coli SQ110DTC and SQ110LPTD. The conjugates of macrolides with nucleobases, especially adenine, displayed antibacterial superiority over telithromycin, azithromycin and clindamycin against rRNA A2058/2059-mutated engineered E. coli strains at the cost of lowering permeability and increasing vulnerability to efflux proteins against clinical isolates.
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Affiliation(s)
- Xiaotian Lian
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
- Yangtze Delta Region Academy, Beijing Institute of Technology, Jiaxing 314019, China
| | - Wentian Liu
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Bingzhi Fan
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Mingjia Yu
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
- Correspondence: (M.Y.); (J.L.)
| | - Jianhua Liang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
- Yangtze Delta Region Academy, Beijing Institute of Technology, Jiaxing 314019, China
- Correspondence: (M.Y.); (J.L.)
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13
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Bernal FA, Hammann P, Kloss F. Natural products in antibiotic development: is the success story over? Curr Opin Biotechnol 2022; 78:102783. [PMID: 36088735 DOI: 10.1016/j.copbio.2022.102783] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/14/2022] [Accepted: 08/02/2022] [Indexed: 12/14/2022]
Abstract
Natural product (NP)-based antibiotics have been exploited for more than eighty years and continue saving uncountable lives every year. However, antimicrobial R&D is inadequate to counteract antimicrobial resistance. The majority of marketed antibiotics are inspired by NP classes that were discovered more than 50 years ago. With the advent of advanced genomic approaches, cultivation methods, and modern analytical techniques, NP discovery holds promise that there are way more powerful antibiotic scaffolds to be discovered. However, the currently lean antibiotic R&D pipeline shows a clear trend away from NP-based programs and innovative compounds are also rare in early stages. Within this review, we give an overview of the current NP antibiotic development pipeline, elaborate constraints the field is facing, and suggest measures to streamline NP-based antibiotic discovery. It is unlikely that NPs have lost significance, but reinforcement of discovery will require more targeted efforts and support to revitalize this established source.
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Affiliation(s)
- Freddy A Bernal
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Peter Hammann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) and Department of Pharmacy Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Florian Kloss
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany.
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14
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Khairullina ZZ, Makarov GI, Tereshchenkov AG, Buev VS, Lukianov DA, Polshakov VI, Tashlitsky VN, Osterman IA, Sumbatyan NV. Conjugates of Desmycosin with Fragments of Antimicrobial Peptide Oncocin: Synthesis, Antibacterial Activity, Interaction with Ribosome. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:871-889. [PMID: 36180983 DOI: 10.1134/s0006297922090024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 06/16/2023]
Abstract
Design and synthesis of conjugates consisting of the macrolide antibiotic desmycosin and fragments of the antibacterial peptide oncocin were performed in attempt to develop new antimicrobial compounds. New compounds were shown to bind to the E. coli 70S ribosomes, to inhibit bacterial protein synthesis in vitro, as well as to suppress bacterial growth. The conjugates of N-terminal hexa- and tripeptide fragments of oncocin and 3,2',4''-triacetyldesmycosin were found to be active against some strains of macrolide-resistant bacteria. By simulating molecular dynamics of the complexes of these compounds with the wild-type bacterial ribosomes and with ribosomes, containing A2059G 23S RNA mutation, the specific structural features of their interactions were revealed.
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Affiliation(s)
| | | | - Andrey G Tereshchenkov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Vitaly S Buev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Dmitrii A Lukianov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vadim N Tashlitsky
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ilya A Osterman
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Natalia V Sumbatyan
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
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15
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Liu XP, Lv W, Zhao F, Ding J, Zhang JR, Xue F, Zhang JZ, Liu LY, Cushman M, Li Y, Liang JH. Design and synthesis of novel macrolones bridged with linkers from 11,12-positions of macrolides. Bioorg Med Chem Lett 2022; 68:128761. [PMID: 35483593 DOI: 10.1016/j.bmcl.2022.128761] [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: 11/28/2021] [Revised: 04/11/2022] [Accepted: 04/21/2022] [Indexed: 11/02/2022]
Abstract
Resistance to telithromycin and off-target effects associated with the metabolic instability present serious and challenging problems for the development of novel macrolides. Herein, studies of hybrids of macrolides and quinolones (termed macrolones) bridged with linkers from 11,12-cyclic carbamate of macrolides revealed different structure-activity relationships from the previously reported macrolones bridged with linkers derived from 6-, 9- and 4''-positions of macrolides. The optimized macrolone 34 g with a longer and rigid sidechain than telithromycin had improved metabolic stability compared to telithromycin (t1/2: 110 vs 32 min), whose future has been heavily clouded by metabolic issues. Moreover, 34 g was 38-fold more potent than telithromycin against A2058/2059-mutated Mycoplasma pneumoniae (8 vs 315 μM), which may be attributed to a novel mode of action between the carboxylic acid of quinolone moiety and the bacterial ribosome. This work increases the prospect for discovery of novel and safe antibacterial agents to combat serious human infectious diseases.
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Affiliation(s)
- Xie-Peng Liu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Wei Lv
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, United States
| | - Fei Zhao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - Jing Ding
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Jue-Ru Zhang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Feng Xue
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing 100034, China
| | - Jian-Zhong Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - Li-Yong Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, United States
| | - Yun Li
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing 100034, China.
| | - Jian-Hua Liang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China; Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing 314019, China.
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16
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Kaur R, Rani P, Atanasov AG, Alzahrani Q, Gupta R, Kapoor B, Gulati M, Chawla P. Discovery and Development of Antibacterial Agents: Fortuitous and Designed. Mini Rev Med Chem 2021; 22:984-1029. [PMID: 34939541 DOI: 10.2174/1570193x19666211221150119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022]
Abstract
Today, antibacterial drug resistance has turned into a significant public health issue. Repeated intake, suboptimal and/or unnecessary use of antibiotics, and, additionally, the transfer of resistance genes are the critical elements that make microorganisms resistant to conventional antibiotics. A substantial number of antibacterials that were successfully utilized earlier for prophylaxis and therapeutic purposes have been rendered inadequate due to this phenomenon. Therefore, the exploration of new molecules has become a continuous endeavour. Many such molecules are at various stages of investigation. A surprisingly high number of new molecules are currently in the stage of phase 3 clinical trials. A few new agents have been commercialized in the last decade. These include solithromycin, plazomicin, lefamulin, omadacycline, eravacycline, delafloxacin, zabofloxacin, finafloxacin, nemonoxacin, gepotidacin, zoliflodacin, cefiderocol, BAL30072, avycaz, zerbaxa, vabomere, relebactam, tedizolid, cadazolid, sutezolid, triclosan and afabiacin. This article aims to review the investigational and recently approved antibacterials with a focus on their structure, mechanisms of action/resistance, and spectrum of activity. Delving deep, their success or otherwise in various phases of clinical trials is also discussed while attributing the same to various causal factors.
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Affiliation(s)
- Ravleen Kaur
- Department of Health Sciences, Cape Breton University, Sydney, Nova Scotia. Canada
| | - Pooja Rani
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara. India
| | - Atanas G Atanasov
- Ludwig Boltzmann Institute of Digital Health and Patient Safety, Medical University of Vienna, Vienna. Austria
| | - Qushmua Alzahrani
- Department of Pharmacy/Nursing/Medicine Health and Environment, University of the Region of Joinville (UNIVILLE) volunteer researcher, Joinville. Brazil
| | - Reena Gupta
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara . India
| | - Bhupinder Kapoor
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara . India
| | - Monica Gulati
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara . India
| | - Pooja Chawla
- Department of Pharmaceutical Chemistry and Analysis, ISF College of Pharmacy, Ghal Kalan Moga, Punjab 142001. India
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17
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Pellegrino S, Terrosu S, Yusupova G, Yusupov M. Inhibition of the Eukaryotic 80S Ribosome as a Potential Anticancer Therapy: A Structural Perspective. Cancers (Basel) 2021; 13:cancers13174392. [PMID: 34503202 PMCID: PMC8430933 DOI: 10.3390/cancers13174392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 01/16/2023] Open
Abstract
Simple Summary Unravelling the molecular basis of ribosomal inhibition by small molecules is crucial to characterise the function of potential anticancer drugs. After approval of the ribosome inhibitor homoharringtonine for treatment of CML, it became clear that acting on the rate of protein synthesis can be a valuable way to prevent indefinite growth of cancers. The present review discusses the state-of-the-art structural knowledge of the binding modes of inhibitors targeting the cytosolic ribosome, with the ambition of providing not only an overview of what has been achieved so far, but to stimulate further investigations to yield more potent and specific anticancer drugs. Abstract Protein biosynthesis is a vital process for all kingdoms of life. The ribosome is the massive ribonucleoprotein machinery that reads the genetic code, in the form of messenger RNA (mRNA), to produce proteins. The mechanism of translation is tightly regulated to ensure that cell growth is well sustained. Because of the central role fulfilled by the ribosome, it is not surprising that halting its function can be detrimental and incompatible with life. In bacteria, the ribosome is a major target of inhibitors, as demonstrated by the high number of small molecules identified to bind to it. In eukaryotes, the design of ribosome inhibitors may be used as a therapy to treat cancer cells, which exhibit higher proliferation rates compared to healthy ones. Exciting experimental achievements gathered during the last few years confirmed that the ribosome indeed represents a relevant platform for the development of anticancer drugs. We provide herein an overview of the latest structural data that helped to unveil the molecular bases of inhibition of the eukaryotic ribosome triggered by small molecules.
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Affiliation(s)
- Simone Pellegrino
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
- Correspondence: (S.P.); (M.Y.)
| | - Salvatore Terrosu
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404 Illkirch, France; (S.T.); (G.Y.)
| | - Gulnara Yusupova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404 Illkirch, France; (S.T.); (G.Y.)
| | - Marat Yusupov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404 Illkirch, France; (S.T.); (G.Y.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
- Correspondence: (S.P.); (M.Y.)
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18
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Daher SS, Lee M, Jin X, Teijaro CN, Wheeler SE, Jacobson MA, Buttaro B, Andrade RB. Synthesis, Biological Evaluation, and Computational Analysis of Biaryl Side-Chain Analogs of Solithromycin. ChemMedChem 2021; 16:3368-3373. [PMID: 34355515 DOI: 10.1002/cmdc.202100435] [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: 06/16/2021] [Revised: 07/31/2021] [Indexed: 12/26/2022]
Abstract
There is an urgent need for new antibiotics to mitigate the existential threat posed by antibiotic resistance. Within the ketolide class, solithromycin has emerged as one of the most promising candidates for further development. Crystallographic studies of bacterial ribosomes and ribosomal subunits complexed with solithromycin have shed light on the nature of molecular interactions (π-stacking and H-bonding) between from the biaryl side-chain of the drug and key residues in the 50S ribosomal subunit. We have designed and synthesized a library of solithromycin analogs to study their structure-activity relationships (SAR) in tandem with new computational studies. The biological activity of each analog was evaluated in terms of ribosomal affinity (Kd determined by fluorescence polarization), as well as minimum inhibitory concentration assays (MICs). Density functional theory (DFT) studies of a simple binding site model identify key H-bonding interactions that modulate the potency of solithromycin analogs.
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Affiliation(s)
- Samer S Daher
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA 19122, USA
| | - Miseon Lee
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA 19122, USA
| | - Xiao Jin
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA 19122, USA
| | - Christiana N Teijaro
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA 19122, USA
| | - Steven E Wheeler
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, GA 30602, USA
| | - Marlene A Jacobson
- Moulder Center for Drug Discovery Research, School of Pharmacy, Temple University, 3307 N. Broad Street, Philadelphia, PA 19140, USA
| | - Bettina Buttaro
- Department of Microbiology and Immunology, School of Medicine, Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Rodrigo B Andrade
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA 19122, USA
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19
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Qin Y, Song D, Teng Y, Liu X, Zhang P, Zhang N, Zhang N, Chen W, Ma S. Design, synthesis and structure-activity relationships of novel N11-, C12- and C13-substituted 15-membered homo-aza-clarithromycin derivatives against various resistant bacteria. Bioorg Chem 2021; 113:104992. [PMID: 34051415 DOI: 10.1016/j.bioorg.2021.104992] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/12/2021] [Accepted: 05/11/2021] [Indexed: 12/01/2022]
Abstract
Bacterial infections are still the main significant problem of public health in the world, and their elimination will greatly rely on the discovery of antibacterial drugs. In the processes of our searching for novel macrolide derivatives with excellent activity against sensitive and resistant bacteria, three series of novel N11-, C12- and C13-substituted 15-membered homo-aza-clarithromycin derivatives were designed and synthesized as Series A, B and C by creatively opening the lactone ring of clarithromycin (CAM), introducing various 4-substituted phenyl-1H-1,2,3-triazole side chains at the N11, C12 or C13 position of CAM and macrolactonization. The results from their in vitro antibacterial activity demonstrated that compounds 20c, 20d and 20f displayed not only the most potent activity against S. aureus ATCC25923 with the MIC values of 0.5, 0.5 and 0.5 µg/mL, but also greatly improved activity against B. subtilis ATCC9372 with the MIC values of less than or equal to 0.25, 0.25 and 0.25 µg/mL, respectively. In particular, compound 11g exhibited the strongest antibacterial effectiveness against all the tested resistant bacterial strains and had well balanced activity with the MIC values of 4-8 µg/mL. Further study on minimum bactericidal concentration and kinetics confirmed that compound 11g possessed a bacteriostatic effect on bacterial proliferation. Moreover, the results of molecular docking revealed an potential additional binding force between compound 11g and U790 in addition to the normal binding force of macrolide skeleton, which may explain why this compound performed the most potent activity against resistant bacteria. The results of cytotoxic assay indicated that compounds 20c, 20d and 20f were non-toxic to human breast cancer MCF-7 cells at its effective antibacterial concentration.
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Affiliation(s)
- Yinhui Qin
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Di Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Yuetai Teng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Xingbang Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Panpan Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Nan Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Na Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Weijin Chen
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China.
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20
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Context-specific action of macrolide antibiotics on the eukaryotic ribosome. Nat Commun 2021; 12:2803. [PMID: 33990576 PMCID: PMC8121947 DOI: 10.1038/s41467-021-23068-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/14/2021] [Indexed: 01/09/2023] Open
Abstract
Macrolide antibiotics bind in the nascent peptide exit tunnel of the bacterial ribosome and prevent polymerization of specific amino acid sequences, selectively inhibiting translation of a subset of proteins. Because preventing translation of individual proteins could be beneficial for the treatment of human diseases, we asked whether macrolides, if bound to the eukaryotic ribosome, would retain their context- and protein-specific action. By introducing a single mutation in rRNA, we rendered yeast Saccharomyces cerevisiae cells sensitive to macrolides. Cryo-EM structural analysis showed that the macrolide telithromycin binds in the tunnel of the engineered eukaryotic ribosome. Genome-wide analysis of cellular translation and biochemical studies demonstrated that the drug inhibits eukaryotic translation by preferentially stalling ribosomes at distinct sequence motifs. Context-specific action markedly depends on the macrolide structure. Eliminating macrolide-arrest motifs from a protein renders its translation macrolide-tolerant. Our data illuminate the prospects of adapting macrolides for protein-selective translation inhibition in eukaryotic cells.
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21
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Scherzi T, D'Ambrosio EA, Daher SS, Grimes CL, Dunman PM, Andrade RB. Staphylococcus aureus resistance to albocycline can be achieved by mutations that alter cellular NAD/PH pools. Bioorg Med Chem 2021; 32:115995. [PMID: 33477021 PMCID: PMC7891091 DOI: 10.1016/j.bmc.2021.115995] [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: 10/28/2020] [Accepted: 12/31/2020] [Indexed: 11/21/2022]
Abstract
Small molecule target identification is a critical step in modern antibacterial drug discovery, particularly against multi-drug resistant pathogens. Albocycline (ALB) is a macrolactone natural product with potent activity against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant S. aureus (VRSA) whose mechanism of action has been elusive to date. Herein, we report biochemical and genomic studies that reveal ALB does not target bacterial peptidoglycan biosynthesis or the ribosome; rather, it appears to modulate NADPH ratios and upregulate redox sensing in the cell consistent with previous studies at Upjohn. Owing to the complexity inherent in biological pathways, further genomic assays are needed to identify the true molecular target(s) of albocycline.
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Affiliation(s)
- Tyler Scherzi
- Department of Microbiology and Immunology, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, United States
| | - Elizabeth A D'Ambrosio
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Samer S Daher
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Paul M Dunman
- Department of Microbiology and Immunology, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, United States
| | - Rodrigo B Andrade
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States.
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22
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Zhang L, He J, Bai L, Ruan S, Yang T, Luo Y. Ribosome-targeting antibacterial agents: Advances, challenges, and opportunities. Med Res Rev 2021; 41:1855-1889. [PMID: 33501747 DOI: 10.1002/med.21780] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/08/2020] [Accepted: 12/19/2020] [Indexed: 02/05/2023]
Abstract
Ribosomes, which synthesize proteins, are critical organelles for the survival and growth of bacteria. About 60% of approved antibiotics discovered so far combat pathogenic bacteria by targeting ribosomes. However, several issues, such as drug resistance and toxicity, have impeded the clinical use of ribosome-targeting antibiotics. Moreover, the complexity of the bacteria ribosome structure has retarded the discovery of new ribosome-targeting agents that are considered as the key to the drug-resistance and toxicity. To deal with these challenges, efforts such as medicinal chemistry optimization, combination treatment, and new drug delivery system have been developed. But not enough, the development of structural biology and new screening methods bring powerful tools, such as cryo-electron microscopy technology, advanced computer-aided drug design, and cell-free in vitro transcription/translation systems, for the discovery of novel ribosome-targeting antibiotics. Thus, in this paper, we overview the research on different aspects of bacterial ribosomes, especially focus on discussing the challenges in the discovery of ribosome-targeting antibacterial drugs and advances made to address issues such as drug-resistance and selectivity, which, we believe, provide perspectives for the discovery of novel antibiotics.
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Affiliation(s)
- Laiying Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Jun He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Lang Bai
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Shihua Ruan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China.,Laboratory of Human Diseases and Immunotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China.,Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
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23
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Qin Y, Ma S. Recent Advances in the Development of Macrolide Antibiotics as Antimicrobial Agents. Mini Rev Med Chem 2020; 20:601-625. [PMID: 31868146 DOI: 10.2174/1389557520666191223160942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/28/2018] [Accepted: 08/15/2019] [Indexed: 11/22/2022]
Abstract
The chemical modification of natural products has been a major method in the discovery and synthesis of new macrolide antibiotics (MA) to treat a variety of infectious diseases. However, a lot of MA obtained in the above methods are no longer effective, because the bacteria quickly develop their resistance to these new macrolides, which has become a great threat to successful treatment of infectious diseases, such as infections of the respiratory system and urinary system. In this paper, total synthetic methods for MA that include erythromycin A (ERY), azithromycin (AZM), the clinical candidate solithromycin (CEM-101), as well as 14-membered and 15-membered azaketolides have been systematically reviewed on the basis of the literature reported previously. The total synthetic methods we describe here helps to accelerate the discovery of newer MA to deal with the serious problem of bacterial resistance.
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Affiliation(s)
- Yinhui Qin
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
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24
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Boyce JH, Dang B, Ary B, Edmondson Q, Craik CS, DeGrado WF, Seiple IB. Platform to Discover Protease-Activated Antibiotics and Application to Siderophore-Antibiotic Conjugates. J Am Chem Soc 2020; 142:21310-21321. [PMID: 33301681 DOI: 10.1021/jacs.0c06987] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Here we present a platform for discovery of protease-activated prodrugs and apply it to antibiotics that target Gram-negative bacteria. Because cleavable linkers for prodrugs had not been developed for bacterial proteases, we used substrate phage to discover substrates for proteases found in the bacterial periplasm. Rather than focusing on a single protease, we used a periplasmic extract of E. coli to find sequences with the greatest susceptibility to the endogenous mixture of periplasmic proteases. Using a fluorescence assay, candidate sequences were evaluated to identify substrates that release native amine-containing payloads. We next designed conjugates consisting of (1) an N-terminal siderophore to facilitate uptake, (2) a protease-cleavable linker, and (3) an amine-containing antibiotic. Using this strategy, we converted daptomycin-which by itself is active only against Gram-positive bacteria-into an antibiotic capable of targeting Gram-negative Acinetobacter species. We similarly demonstrated siderophore-facilitated delivery of oxazolidinone and macrolide antibiotics into a number of Gram-negative species. These results illustrate this platform's utility for development of protease-activated prodrugs, including Trojan horse antibiotics.
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Affiliation(s)
- Jonathan H Boyce
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States.,Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Bobo Dang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China.,Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Beatrice Ary
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Quinn Edmondson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States.,Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Ian B Seiple
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States.,Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
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25
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Lewis DA. New treatment options for Neisseria gonorrhoeae in the era of emerging antimicrobial resistance. Sex Health 2020; 16:449-456. [PMID: 31292063 DOI: 10.1071/sh19034] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/16/2019] [Indexed: 12/27/2022]
Abstract
Neisseria gonorrhoeae, the causative agent of gonorrhoea, has rapidly evolved from an exquisitely susceptible pathogen into a 'superbug' with the capacity to exhibit an extensively drug resistant (XDR) phenotype. The threat of untreatable gonorrhoea now looms on the horizon while the arsenal of effective antimicrobial agents diminishes with time. Ceftriaxone remains the mainstay of first-line therapy as a single agent or as the backbone of a dual therapy regimen. The implementation of new assays to facilitate 'precision' treatment, based on the prediction of N. gonorrhoeae susceptibility to old anti-gonococcal drugs, may enable sparing use of ceftriaxone in those countries that can afford this technology. A few existing drugs, such as ertapenem, can be repositioned to help manage multi-drug resistant and XDR gonorrhoea. Recent clinical trials involving solithromycin and delafloxacin have generated disappointing results in that both agents failed to show non-inferiority to conventional ceftriaxone-based regimens. At present, zoliflodacin and gepotidacin appear to be the most promising antimicrobial agents in clinical development. Both drugs performed well in eradicating urogenital gonorrhoea in recent Phase 2 trials; however, treatment failures were reported at the oropharyngeal site, which is an important site of infection in men who have sex with men and sex workers. Given this observation, it is unlikely that either of these new agents could be promoted for monotherapy of gonorrhoea. The pre-clinical pipeline remains relatively empty of agents likely to progress to clinical development for gonorrhoea treatment and increased investment into gonorrhoea-specific drug discovery is recommended.
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Affiliation(s)
- David A Lewis
- Western Sydney Sexual Health Centre, Western Sydney Local Health District, 162 Marsden Street, Parramatta, NSW 2150, Australia
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26
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Synthetic group A streptogramin antibiotics that overcome Vat resistance. Nature 2020; 586:145-150. [PMID: 32968273 PMCID: PMC7546582 DOI: 10.1038/s41586-020-2761-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/19/2020] [Indexed: 11/08/2022]
Abstract
Natural products serve as chemical blueprints for the majority of antibiotics in our clinical arsenal. The evolutionary process by which these molecules arise is inherently accompanied by the co-evolution of resistance mechanisms that shorten the clinical lifetime of any given class1. Virginiamycin acetyltransferases (Vats) are resistance proteins that provide protection against streptogramins2, potent Gram-positive antibiotics that inhibit the bacterial ribosome3. Due to the challenge of selectively modifying the chemically complex, 23-membered macrocyclic scaffold of group A streptogramins, analogs that overcome Vat resistance have not been previously accessed2. Here we report the design, synthesis, and antibacterial evaluation of group A streptogramin antibiotics with unprecedented structural variability. Using cryo-electron microscopy and forcefield-based refinement, we characterize the binding of eight analogs to the bacterial ribosome at high resolution, revealing new binding interactions that extend into the peptidyl tRNA binding site and towards synergistic binders that occupy the nascent peptide exit tunnel (NPET). One of these analogs has excellent activity against several streptogramin-resistant strains of S. aureus, exhibits decreased acetylation rates in vitro, and is effective at lowering bacterial load in a mouse model of infection. Our results demonstrate that the combination of rational design and modular chemical synthesis can revitalize classes of antibiotics that are limited by naturally arising resistance mechanisms.
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27
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Barman TK, Kumar M, Chaira T, Gangadharan R, Singhal S, Rao M, Mathur T, Bhateja P, Pandya M, Ramadass V, Chakrabarti A, Das B, Upadhyay DJ, Raj VS. Potential of the fluoroketolide RBx 14255 against Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae in an experimental murine meningitis model. J Antimicrob Chemother 2020; 74:1962-1970. [PMID: 31049578 DOI: 10.1093/jac/dkz119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 02/19/2019] [Accepted: 02/27/2019] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND RBx 14255 is a fluoroketolide in pre-clinical evaluation with potent activity against MDR Gram-positive pathogens. OBJECTIVES To investigate the efficacy of RBx 14255 against bacterial meningitis caused by Streptococcus pneumoniae, Neisseria meningitidis or Haemophilus influenzae in an experimental murine meningitis model. METHODS In vitro activity of RBx 14255 was evaluated against clinical isolates of S. pneumoniae, N. meningitidis and H. influenzae. The in vivo efficacy of RBx 14255 was evaluated against bacterial meningitis, induced with S. pneumoniae 3579 erm(B), S. pneumoniae MA 80 erm(B), N. meningitidis 1852 and H. influenzae B1414 in a murine meningitis model. RESULTS RBx 14255 showed strong in vitro bactericidal potential against S. pneumoniae, N. meningitidis and H. influenzae with MIC ranges of 0.004-0.1, 0.03-0.5 and 1-4 mg/L, respectively. In a murine meningitis model, a 50 mg/kg dose of RBx 14255, q12h, resulted in significant reduction of bacterial counts in the brain compared with the pretreatment control. The concentration of RBx 14255 in brain tissue correlated well with the efficacy in this mouse model. CONCLUSIONS RBx 14255 showed superior bactericidal activity in time-kill assays in vitro and in vivo in an experimental murine meningitis model. RBx 14255 could be a promising candidate for future drug development against bacterial meningitis.
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Affiliation(s)
- Tarani Kanta Barman
- Department of Microbiology, Daiichi Sankyo India Pharma Private Limited, Gurgaon, Haryana, India.,New Drug Discovery Research, Ranbaxy Research Laboratories, R & D III, Gurgaon, India
| | - Manoj Kumar
- Department of Microbiology, Daiichi Sankyo India Pharma Private Limited, Gurgaon, Haryana, India.,New Drug Discovery Research, Ranbaxy Research Laboratories, R & D III, Gurgaon, India
| | - Tridib Chaira
- New Drug Discovery Research, Ranbaxy Research Laboratories, R & D III, Gurgaon, India.,Department of Drug Metabolism and Pharmacokinetics, Daiichi Sankyo India Pharma Private Limited, Gurgaon, Haryana, India.,Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Sonepat, Haryana, India
| | - Ramkumar Gangadharan
- Department of Microbiology, Daiichi Sankyo India Pharma Private Limited, Gurgaon, Haryana, India.,New Drug Discovery Research, Ranbaxy Research Laboratories, R & D III, Gurgaon, India.,Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Sonepat, Haryana, India
| | - Smita Singhal
- Department of Microbiology, Daiichi Sankyo India Pharma Private Limited, Gurgaon, Haryana, India.,New Drug Discovery Research, Ranbaxy Research Laboratories, R & D III, Gurgaon, India
| | - Madhvi Rao
- Department of Microbiology, Daiichi Sankyo India Pharma Private Limited, Gurgaon, Haryana, India.,New Drug Discovery Research, Ranbaxy Research Laboratories, R & D III, Gurgaon, India
| | - Tarun Mathur
- Department of Microbiology, Daiichi Sankyo India Pharma Private Limited, Gurgaon, Haryana, India.,New Drug Discovery Research, Ranbaxy Research Laboratories, R & D III, Gurgaon, India
| | - Pragya Bhateja
- Department of Microbiology, Daiichi Sankyo India Pharma Private Limited, Gurgaon, Haryana, India.,New Drug Discovery Research, Ranbaxy Research Laboratories, R & D III, Gurgaon, India
| | - Manisha Pandya
- Department of Microbiology, Daiichi Sankyo India Pharma Private Limited, Gurgaon, Haryana, India.,New Drug Discovery Research, Ranbaxy Research Laboratories, R & D III, Gurgaon, India
| | - Venkataramanan Ramadass
- New Drug Discovery Research, Ranbaxy Research Laboratories, R & D III, Gurgaon, India.,Department of Medicinal Chemistry, Daiichi Sankyo India Pharma Private Limited, Gurgaon, Haryana, India
| | - Anjan Chakrabarti
- New Drug Discovery Research, Ranbaxy Research Laboratories, R & D III, Gurgaon, India
| | - Biswajit Das
- New Drug Discovery Research, Ranbaxy Research Laboratories, R & D III, Gurgaon, India.,Department of Medicinal Chemistry, Daiichi Sankyo India Pharma Private Limited, Gurgaon, Haryana, India
| | - Dilip J Upadhyay
- Department of Microbiology, Daiichi Sankyo India Pharma Private Limited, Gurgaon, Haryana, India.,New Drug Discovery Research, Ranbaxy Research Laboratories, R & D III, Gurgaon, India
| | - V Samuel Raj
- Department of Microbiology, Daiichi Sankyo India Pharma Private Limited, Gurgaon, Haryana, India.,New Drug Discovery Research, Ranbaxy Research Laboratories, R & D III, Gurgaon, India.,Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Sonepat, Haryana, India
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28
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A long-distance rRNA base pair impacts the ability of macrolide antibiotics to kill bacteria. Proc Natl Acad Sci U S A 2020; 117:1971-1975. [PMID: 31932436 PMCID: PMC6995004 DOI: 10.1073/pnas.1918948117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bactericidal activity of macrolide antibiotics correlates with the presence of an extended alkyl-aryl side chain, which accounts for their slow departure rate from the ribosome. Here, we found that the base pair between 23S ribosomal RNA (rRNA) nucleotides 752 and 2609 located in the macrolide binding site is important for the ribosome functionality and for establishing the unique interactions with the extended side chain of macrolide antibiotics. Disruption of the 752-2609 base pair accelerates the departure of extended macrolides from the ribosome and reduces their cidality. Our results demonstrate that not only the chemical features of the antibiotic, but also the structure of the target site contribute to the ability of the inhibitor to kill bacteria. While most of the ribosome-targeting antibiotics are bacteriostatic, some members of the macrolide class demonstrate considerable bactericidal activity. We previously showed that an extended alkyl-aryl side chain is the key structural element determining the macrolides’ slow dissociation from the ribosome and likely accounts for the antibiotics’ cidality. In the nontranslating Escherichia coli ribosome, the extended side chain of macrolides interacts with 23S ribosomal RNA (rRNA) nucleotides A752 and U2609, that were proposed to form a base pair. However, the existence of this base pair in the translating ribosome, its possible functional role, and its impact on the binding and cidality of the antibiotic remain unknown. By engineering E. coli cells carrying individual and compensatory mutations at the 752 and 2609 rRNA positions, we show that integrity of the base pair helps to modulate the ribosomal response to regulatory nascent peptides, determines the slow dissociation rate of the extended macrolides from the ribosome, and increases their bactericidal effect. Our findings demonstrate that the ability of antibiotics to kill bacterial cells relies not only on the chemical nature of the inhibitor, but also on structural features of the target.
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29
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Fernandes P, Pereira D, Watkins PB, Bertrand D. Differentiating the Pharmacodynamics and Toxicology of Macrolide and Ketolide Antibiotics. J Med Chem 2019; 63:6462-6473. [PMID: 31644280 DOI: 10.1021/acs.jmedchem.9b01159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This is a review of the macrolide and ketolide field focusing on differentiating the pharmacodynamics and especially the toxicology of the macrolides and ketolides. We emphasize the diversity in pharmacodynamics and toxicity of the macrolides and ketolides, resulting from even small structural changes, which makes it important to consider the various different compounds separately, not necessarily as a class. The ketolide, telithromycin, was developed because of rising bacterial macrolide resistance but was withdrawn postapproval after visual disturbances, syncope, myasthenia gravis, and hepatotoxicity were noted. These diverse adverse effects could be attributed to inhibition of nicotinic acetylcholine receptors. Solithromycin, a later generation ketolide, was effective in treating bacterial pneumonia, but it was not approved by the U.S. Food and Drug Administration owing, in part, to its structural similarity to telithromycin. This Miniperspective describes that structurally similar macrolides/ketolides have clearly mechanistically distinct effects. Understanding these effects could help in developing and securing regulatory approval of a new macrolide/ketolide that is active against macrolide-resistant pathogenic bacteria.
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Affiliation(s)
| | - David Pereira
- Ponce De Leon Health, Fernandina Beach, Florida 32034, United States
| | - Paul B Watkins
- Schools of Pharmacy, Medicine and Public Health, Institute for Drug Safety Sciences, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Daniel Bertrand
- HiQScreen SÃrl, 6, Route de Compois, Vesenaz, 1222 Geneva, Switzerland
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30
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Liapikou A, Cilloniz C, Palomeque A, Torres T. Emerging antibiotics for community-acquired pneumonia. Expert Opin Emerg Drugs 2019; 24:221-231. [PMID: 31657962 DOI: 10.1080/14728214.2019.1685494] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Introduction: Community-acquired pneumonia is the most common infection leading to hospitalization and death in all age groups, especially in elderly populations. Increasing antibiotic resistance among the common bacterial pathogens associated with community-acquired pneumonia, especially Streptococcus pneumoniae and staphylococci, has made its empirical treatment increasingly problematic, highlighting the need for effective antibiotic therapy.Areas covered: We searched PubMed and ClinicalTrials.gov for English-language reports of phase III clinical trials conducted between 2000 and 2019 concerning the antibiotic treatment of community-acquired pneumonia. We provide a summary of the latest approved drugs for this indication and highlight emerging drugs with a potential indication.Expert opinion: Ceftaroline (a new cephalosporine) and omadacycline (a cycline alternative), either parenterally or orally, are the only two new antibiotics to have been approved by the FDA for the treatment of community-acquired pneumonia in the last five years. Among the antimicrobials in development, Lefamulin (the first pleuromutilin), is currently in phase III development. Among the known antibiotic classes, solithromycin (a macrolide), nemonoxacin (a quinolone), and delafloxacin and zabofloxacin (both fluoroquinolones), have been studied in phase II and III in clinical trials. The availability of these new antibiotics may offer opportunities to improve the empirical treatment for community-acquired pneumonia.
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Affiliation(s)
| | - Catia Cilloniz
- Respiratory Institute, CIBERES- IDIBAPS C, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Andrea Palomeque
- Respiratory Institute, CIBERES- IDIBAPS C, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Toni Torres
- Respiratory Institute, CIBERES- IDIBAPS C, Hospital Clinic de Barcelona, Barcelona, Spain
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31
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Pellegrino S, Meyer M, Könst ZA, Holm M, Voora VK, Kashinskaya D, Zanette C, Mobley DL, Yusupova G, Vanderwal CD, Blanchard SC, Yusupov M. Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome. Nucleic Acids Res 2019; 47:3223-3232. [PMID: 30759226 PMCID: PMC6451132 DOI: 10.1093/nar/gkz053] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/16/2019] [Accepted: 02/08/2019] [Indexed: 11/21/2022] Open
Abstract
Natural products that target the eukaryotic ribosome are promising therapeutics to treat a variety of cancers. It is therefore essential to determine their molecular mechanism of action to fully understand their mode of interaction with the target and to inform the development of new synthetic compounds with improved potency and reduced cytotoxicity. Toward this goal, we have previously established a short synthesis pathway that grants access to multiple congeners of the lissoclimide family. Here we present the X-ray co-crystal structure at 3.1 Å resolution of C45, a potent congener with two A-ring chlorine-bearing stereogenic centers with ‘unnatural’ configurations, with the yeast 80S ribosome, intermolecular interaction energies of the C45/ribosome complex, and single-molecule FRET data quantifying the impact of C45 on both human and yeast ribosomes. Together, these data provide new insights into the role of unusual non-covalent halogen bonding interactions involved in the binding of this synthetic compound to the 80S ribosome.
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Affiliation(s)
- Simone Pellegrino
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404 Illkirch, France
| | - Mélanie Meyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404 Illkirch, France
| | - Zef A Könst
- Department of Chemistry, University of California, 1102 Natural Sciences II, Irvine, CA 92697-2025, USA
| | - Mikael Holm
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Vamsee K Voora
- Department of Chemistry, University of California, 1102 Natural Sciences II, Irvine, CA 92697-2025, USA
| | - Daniya Kashinskaya
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404 Illkirch, France.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
| | - Camila Zanette
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 91010-92697, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 91010-92697, USA
| | - Gulnara Yusupova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404 Illkirch, France
| | - Chris D Vanderwal
- Department of Chemistry, University of California, 1102 Natural Sciences II, Irvine, CA 92697-2025, USA
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,Tri-Institutional PhD Training Program in Chemical Biology, Weill Cornell Medicine, Rockefeller University, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Marat Yusupov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404 Illkirch, France.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
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32
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Design, synthesis and antibacterial evaluation of novel 15-membered 11a-azahomoclarithromycin derivatives with the 1, 2, 3-triazole side chain. Eur J Med Chem 2019; 180:321-339. [DOI: 10.1016/j.ejmech.2019.07.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/17/2019] [Accepted: 07/07/2019] [Indexed: 11/23/2022]
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Chen MY, McNulty A, Avery A, Whiley D, Tabrizi SN, Hardy D, Das AF, Nenninger A, Fairley CK, Hocking JS, Bradshaw CS, Donovan B, Howden BP, Oldach D. Solithromycin versus ceftriaxone plus azithromycin for the treatment of uncomplicated genital gonorrhoea (SOLITAIRE-U): a randomised phase 3 non-inferiority trial. THE LANCET. INFECTIOUS DISEASES 2019; 19:833-842. [PMID: 31196813 DOI: 10.1016/s1473-3099(19)30116-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/31/2019] [Accepted: 02/07/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND Antibiotic-resistant gonorrhoea represents a global public health threat, and new therapies are needed. We aimed to compare the efficacy and safety of solithromycin, a fourth generation macrolide, with ceftriaxone plus azithromycin for the treatment of gonorrhoea. METHODS We did an open-label, multicentre, non-inferiority trial of patients aged 15 years or older with uncomplicated untreated genital gonorrhoea at two sites in Australia and one site in the USA. Patients were randomly assigned (1:1) to receive single dose oral solithromycin 1000 mg or intramuscular ceftriaxone 500 mg plus oral azithromycin 1000 mg. Neisseria gonorrhoeae cultures were obtained at baseline and test of cure (day 7 ± 2). The primary outcome was the proportion of patients with eradication of genital N gonorrhoeae based on culture at test of cure, assessed in the microbiological intention-to-treat (mITT) population, which included all randomly assigned patients who received any dose of study drug and had a positive genital culture for N gonorrhoeae at baseline. Non-inferiority of solithromycin was to be concluded if the lower limit of the 95% CI for the between-group differences was greater than -10%. Safety was analysed in all patients who received any dose of study drug. This trial is registered with ClinicalTrials.gov, number NCT02210325. FINDINGS Between Sept 3, 2014, and Aug 27, 2015, 262 patients were randomly assigned and 261 received treatment (130 in the solithromycin group and 131 in the ceftriaxone plus azithromycin group). In the mITT population, 99 (80%) of 123 patients in the solithromycin group and 109 (84%) of 129 patients in the ceftriaxone plus azithromycin group had N gonorrhoeae eradication at test of cure (difference -4·0%, 95% CI -13·6 to 5·5), thus solithromycin did not meet the criterion for non-inferiority at the prespecified -10% margin. The frequency of adverse events was higher in the solithromycin group than the ceftriaxone plus azithromycin group (69 [53%] of 130 patients vs 45 [34%] of 131 patients), the most common of which were diarrhoea (31 [24%] of 130 patients vs 20 [15%] of 131 patients), and nausea (27 [21%] of 130 patients vs 15 [11%] of 131 patients). INTERPRETATION Solithromycin as a single 1000 mg dose is not a suitable alternative to ceftriaxone plus azithromycin as first-line treatment for gonorrhoea. If insufficient duration of solithromycin exposure at the infection site in a subset of individuals was the reason for treatment failures, this might be adequately addressed with dose adjustment. However, any further trials with longer dosing need to consider the potential risk of gastrointestinal effects and liver enzyme elevations. FUNDING Cempra Pharmaceuticals.
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Affiliation(s)
- Marcus Y Chen
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia; Central Clinical School, Monash University, Melbourne, VIC, Australia.
| | - Anna McNulty
- Sydney Sexual Health Centre, Sydney Hospital, Sydney, NSW, Australia; School of Public Health and Community Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Ann Avery
- MetroHealth Medical Center, Cleveland, OH, USA; School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - David Whiley
- Queensland Children's Medical Research Institute, University of Queensland, Brisbane, QLD, Australia
| | - Sepehr N Tabrizi
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC, Australia
| | - Dwight Hardy
- University of Rochester Medical Center, Rochester, NY, USA
| | | | | | - Christopher K Fairley
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia; Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Jane S Hocking
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Catriona S Bradshaw
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia; Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Basil Donovan
- Sydney Sexual Health Centre, Sydney Hospital, Sydney, NSW, Australia; Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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Nguyen HL, An PH, Thai NQ, Linh HQ, Li MS. Erythromycin, Cethromycin and Solithromycin display similar binding affinities to the E. coli's ribosome: A molecular simulation study. J Mol Graph Model 2019; 91:80-90. [PMID: 31200217 DOI: 10.1016/j.jmgm.2019.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/09/2019] [Accepted: 06/02/2019] [Indexed: 01/06/2023]
Abstract
Macrolide antibiotics bind to the exit tunnel of the ribosome and inhibit protein synthesis blocking its translocation. Thus, antibiotics including the known macrolide Erythromycin (ERY) are active against bacteria. However, at present, some bacteria show resistance to drugs, which requires the development of new powerful antibacterial agents. One possible way is to use the ERY structure, but change its side chains, while the size of the lactone ring can remain unchanged or change. In this work we consider Cethromycin (CET) and Solithromycin (SOL), which are ketolides with quinolylallyl group at C6 and aminophenyl at C11, respectively (both of them have the same lactone ring as ERY). Experiments have shown that these ketolides have improved efficacy against pathogens, but their binding affinity to the E. coli's ribosome is almost identical. To clarify this issue, we have studied in detail the binding mechanisms of ERY, CET and SOL using the docking and molecular dynamic simulations. In agreement with the experiments, we showed that these compounds have similar binding affinities. Desosamine and lactone ring groups play a critical role in the binding of ERY to the ribosome. In CET and SOL, the contribution of keto and alkylaryl groups is balanced by cyclic carbamate. We have demonstrated that increased fluctuations in the ribosomal residues at the binding site led to an increase in the entropic term in the free binding energy of ERY compared to SOL and CET. The alkyl-aryl arm of both ketolides strongly interacts with A752 and U2609. In addition, the presence of macrolides in the exit tunnel can alter the conformation of U2585, which is located in the peptidyl transferase center, through non-bonded interaction. Therefore, the side chain of ketolides affects not only the binding site but also other residues possibly leading to a strong effect on the protein synthesis process. We predict that to combat bacterial mutations, it is necessary either to design a bulk and charged group as a cladinose, or to use several groups with different signs of charges. This prediction can be used for the development of new efficient antibiotics.
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Affiliation(s)
- Hoang Linh Nguyen
- Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh, Hiep Ward, District 12, Ho Chi Minh City, Viet Nam; Biomedical Engineering Department, University of Technology - VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Viet Nam
| | - Pham Hong An
- Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh, Hiep Ward, District 12, Ho Chi Minh City, Viet Nam; Department of Theoretical Physics, VNUHCM-University of Science, Ho Chi Minh City, Viet Nam
| | - Nguyen Quoc Thai
- Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh, Hiep Ward, District 12, Ho Chi Minh City, Viet Nam; Biomedical Engineering Department, University of Technology - VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Viet Nam; Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Viet Nam
| | - Huynh Quang Linh
- Biomedical Engineering Department, University of Technology - VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Viet Nam
| | - Mai Suan Li
- Institute of Physics, Polish Acad Sci, Al. Lotnikow 32/46, 02-668, Warsaw, Poland.
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Li XM, Lv W, Guo SY, Li YX, Fan BZ, Cushman M, Kong FS, Zhang J, Liang JH. Synthesis and structure-bactericidal activity relationships of non-ketolides: 9-Oxime clarithromycin 11,12-cyclic carbonate featured with three-to eight-atom-length spacers at 3-OH. Eur J Med Chem 2019; 171:235-254. [DOI: 10.1016/j.ejmech.2019.03.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 11/16/2022]
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Structure of Dirithromycin Bound to the Bacterial Ribosome Suggests New Ways for Rational Improvement of Macrolides. Antimicrob Agents Chemother 2019; 63:AAC.02266-18. [PMID: 30936109 DOI: 10.1128/aac.02266-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/19/2019] [Indexed: 11/20/2022] Open
Abstract
Although macrolides are known as excellent antibacterials, their medical use has been significantly limited due to the spread of bacterial drug resistance. Therefore, it is necessary to develop new potent macrolides to combat the emergence of drug-resistant pathogens. One of the key steps in rational drug design is the identification of chemical groups that mediate binding of the drug to its target and their subsequent derivatization to strengthen drug-target interactions. In the case of macrolides, a few groups are known to be important for drug binding to the ribosome, such as desosamine. Search for new chemical moieties that improve the interactions of a macrolide with the 70S ribosome might be of crucial importance for the invention of new macrolides. For this purpose, here we studied a classic macrolide, dirithromycin, which has an extended (2-methoxyethoxy)-methyl side chain attached to the C-9/C-11 atoms of the macrolactone ring that can account for strong binding of dirithromycin to the 70S ribosome. By solving the crystal structure of the 70S ribosome in complex with dirithromycin, we found that its side chain interacts with the wall of the nascent peptide exit tunnel in an idiosyncratic fashion: its side chain forms a lone pair-π stacking interaction with the aromatic imidazole ring of the His69 residue in ribosomal protein uL4. To our knowledge, the ability of this side chain to form a contact in the macrolide binding pocket has not been reported previously and potentially can open new avenues for further exploration by medicinal chemists developing next-generation macrolide antibiotics active against resistant pathogens.
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Wen J, Chen F, Zhao M, Wang X. Solithromycin monotherapy for treatment of community-acquired bacterial pneumonia: A meta-analysis of randomised controlled trials. Int J Clin Pract 2019; 73:e13333. [PMID: 30810253 DOI: 10.1111/ijcp.13333] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 01/09/2019] [Accepted: 02/24/2019] [Indexed: 12/01/2022] Open
Abstract
OBJECTIVES Solithromycin is a new monotherapy option for community-acquired bacterial pneumonia (CABP) patients. However, the efficacy and safety of solithromycin monotherapy for the treatment of CABP remains controversial. The aim of this meta-analysis was to evaluate the role that solithromycin played in the treatment of CABP. METHODS We systematically retrieved randomised controlled trials (RCTs) compared solithromycin with other antibiotics in the treatment of CABP, which were published on PubMed, ScienceDirect, Cochrane libary and the Clinical Trials.gov before July 2018. Ultimately, a meta-analysis of all RCTs eligible for inclusion criteria was performed. RESULTS Three RCTs, comprising 1855 patients, were included in the meta-analysis. There were no statistically significant differences between patients given solithromycin and those given other antibiotics with regard to early clinical response (ECR) [1855 patients, odds ratio (OR) = 1.00, 95% confidence interval (CI) 0.80 to 1.24, P = 0.99] and clinical success rates at short-term follow-up (SFU) (1855 patients, OR = 0.78, 95% CI 0.60 to 1.01, P = 0.06) in the intention-to-treat (ITT) population, as were the ECR (787 patients, OR = 0.90, 95% CI 0.64 to 1.27, P = 0.55) and clinical success rates at SFU (358 patients, OR = 0.73, 95% CI 0.41 to 1.31, P = 0.30) in microbiological intention-to-treat population (mITT). Similarly, with regard to the occurrence of treatment-emergent adverse events (TEAEs), drug-related adverse events (AEs), serious AEs, serious drug-related AEs and mortality, no statistically significant difference between patients given solithromycin and those given other antibiotics was observed. CONCLUSION In the treatment of CABP, solithromycin monotherapy is an effective and safe antibiotic regimen. Other advantages (ie anti-inflammatory effect, potent activity against expected pathogens of CABP and convenient clinical use) of solithromycin may make it a more fascinating option compared with the currently used regimens.
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Affiliation(s)
- Junlin Wen
- Department of Pain Management, The First Affliated Hospital, Jinan University, Guangzhou, China
| | - Feng Chen
- Department of Pharmacy, Yuebei People's Hospital, Shaoguan, China
| | - Mengxin Zhao
- Department of Pain Management, The First Affliated Hospital, Jinan University, Guangzhou, China
| | - Xiaoping Wang
- Department of Pain Management, The First Affliated Hospital, Jinan University, Guangzhou, China
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Cannone Z, Shaqra AM, Lorenc C, Henowitz L, Keshipeddy S, Robinson VL, Zweifach A, Wright D, Peczuh MW. Post-Glycosylation Diversification (PGD): An Approach for Assembling Collections of Glycosylated Small Molecules. ACS COMBINATORIAL SCIENCE 2019; 21:192-197. [PMID: 30607941 DOI: 10.1021/acscombsci.8b00139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Many small molecule natural products with antibiotic and antiproliferative activity are adorned with a carbohydrate residue as part of their molecular structure. The carbohydrate moiety can act to mediate key interactions with the target, attenuate physicochemical properties, or both. Facile incorporation of a carbohydrate group on de novo small molecules would enable these valuable properties to be leveraged in the evaluation of focused compound libraries. While there is no universal way to incorporate a sugar on small molecule libraries, techniques such as glycorandomization and neoglycorandomization have made signification headway toward this goal. Here, we report a new approach for the synthesis of glycosylated small molecule libraries. It puts the glycosylation early in the synthesis of library compounds. Functionalized aglycones subsequently participate in chemoselective diversification reactions distal to the carbohydrate. As a proof-of-concept, we prepared several desosaminyl glycosides from only a few starting glycosides, using click cycloadditions, acylations, and Suzuki couplings as diversification reactions. New compounds were then characterized for their inhibition of bacterial protein translation, bacterial growth, and in a T-cell activation assay.
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Affiliation(s)
- Zachary Cannone
- Department of Chemistry, University of Connecticut, 55 N. Eagleville Road, U3060, Storrs, Connecticut 06269, United States
| | - Ala M. Shaqra
- Department of Molecular & Cellular Biology, University of Connecticut, 91 N. Eagleville Road, U3125, Storrs, Connecticut 06269, United States
| | - Chris Lorenc
- Department of Chemistry, University of Connecticut, 55 N. Eagleville Road, U3060, Storrs, Connecticut 06269, United States
| | - Liza Henowitz
- Department of Molecular & Cellular Biology, University of Connecticut, 91 N. Eagleville Road, U3125, Storrs, Connecticut 06269, United States
| | - Santosh Keshipeddy
- Department of Pharmaceutical Sciences, School of Pharmacy, 69 N.
Eagleville Road U3092, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Victoria L. Robinson
- Department of Molecular & Cellular Biology, University of Connecticut, 91 N. Eagleville Road, U3125, Storrs, Connecticut 06269, United States
| | - Adam Zweifach
- Department of Molecular & Cellular Biology, University of Connecticut, 91 N. Eagleville Road, U3125, Storrs, Connecticut 06269, United States
| | - Dennis Wright
- Department of Chemistry, University of Connecticut, 55 N. Eagleville Road, U3060, Storrs, Connecticut 06269, United States
- Department of Pharmaceutical Sciences, School of Pharmacy, 69 N.
Eagleville Road U3092, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Mark W. Peczuh
- Department of Chemistry, University of Connecticut, 55 N. Eagleville Road, U3060, Storrs, Connecticut 06269, United States
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Ma CX, Lv W, Li YX, Fan BZ, Han X, Kong FS, Tian JC, Cushman M, Liang JH. Design, synthesis and structure-activity relationships of novel macrolones: Hybrids of 2-fluoro 9-oxime ketolides and carbamoyl quinolones with highly improved activity against resistant pathogens. Eur J Med Chem 2019; 169:1-20. [PMID: 30852383 DOI: 10.1016/j.ejmech.2019.02.073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 11/19/2022]
Abstract
Constitutively erythromycin-resistant apathogens are more difficult to address than inducibly resistant and efflux-resistant strains. Three series of the 4th generation 2-fluoro 9-oxime erythromycin ketolides were synthesized and evaluated. Incorporation of substituted heteroaryl groups (a - m), in contrast to previously reported the unsubstituted heteroaryl groups, proved to the beneficial for enhancement of the activities of the 9-propgargyl ketolide 8 series and the 9-allyl ketolide 14 series. But these aryl groups (a - m) cannot supply the resulting compounds 8 and 14, unlike corresponding the 6-allyl ketolide 20 series, with activity against constitutively resistant Streptococcus pneumoniae. However, hybrids of macrolides and quinolones (8, 14 and 20, Ar = n - t) exhibited not only high activities against susceptible, inducibly erm-mediated resistant, and efflux-mediated resistant strains, but also significantly improved potencies against constitutively resistant Streptococcus pneumoniae and Streptococcus pyogenes. The capacity was highlighted by introduction of newly designed carbamoyl quinolones (q, r, s and t) rather than commonly seen carboxy quinolones (o and p) as the pharmacophores. Structure-activity relationships and molecular modelling indicated that 8r, 14r and 20q may have different binding sites compared to current erythromycins. Moreover, 8r, 14r and 20q have 2.5-3.6 times prolonged half-life and 2.3- to 2.6-fold longer mean residence time in vivo over telithromycin. These findings pave the way for rational design of novel non-telithromycin macrolides that target new binding sites within bacterial ribosomes.
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Affiliation(s)
- Cong-Xuan Ma
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Wei Lv
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 47907, USA
| | - Ya-Xin Li
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Bing-Zhi Fan
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Xu Han
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Fan-Sheng Kong
- Beijing Increasepharm Safety & Efficacy Co. Ltd, Beijing, 102206, China
| | - Jing-Chao Tian
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 47907, USA
| | - Jian-Hua Liang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China; School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
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Unemo M, Golparian D, Eyre DW. Antimicrobial Resistance in Neisseria gonorrhoeae and Treatment of Gonorrhea. Methods Mol Biol 2019; 1997:37-58. [PMID: 31119616 DOI: 10.1007/978-1-4939-9496-0_3] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Gonorrhea and antimicrobial resistance (AMR) in Neisseria gonorrhoeae are major public health concerns globally. Dual antimicrobial therapy (mainly ceftriaxone 250-500 mg × 1 plus azithromycin 1-2 g × 1) is currently recommended in many countries. These dual therapies have high cure rates, have likely been involved in decreasing the level of cephalosporin resistance internationally, and inhibit the spread of AMR gonococcal strains. However, ceftriaxone-resistant strains are currently spreading internationally, predominately associated with travel to Asia. Furthermore, the first global treatment failure with recommended dual therapy was reported in 2016 and the first isolates with combined ceftriaxone resistance and high-level azithromycin resistance were reported in 2018 in the UK and Australia. New antimicrobials for treatment of gonorrhea are essential and, of the few antimicrobials in clinical development, zoliflodacin particularly appears promising. Holistic actions are imperative. These include an enhanced advocacy; prevention, early diagnosis, contact tracing, treatment, test-of-cure, and additional measures for effective management of anogenital and pharyngeal gonorrhea; antimicrobial stewardship; surveillance of infection, AMR and treatment failures; and intensified research, for example, regarding rapid molecular point-of-care detection of gonococci and AMR, novel AMR determinants, new antimicrobials, and an effective gonococcal vaccine, which is the only sustainable solution for management and control of gonorrhea.
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Affiliation(s)
- Magnus Unemo
- National Reference Laboratory for STIs, WHO Collaborating Centre for Gonorrhoea and Other STIs, Örebro University Hospital, Örebro, Sweden.
| | - Daniel Golparian
- National Reference Laboratory for STIs, WHO Collaborating Centre for Gonorrhoea and Other STIs, Örebro University Hospital, Örebro, Sweden
| | - David W Eyre
- Big Data Institute, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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Vázquez-Laslop N, Mankin AS. How Macrolide Antibiotics Work. Trends Biochem Sci 2018; 43:668-684. [PMID: 30054232 PMCID: PMC6108949 DOI: 10.1016/j.tibs.2018.06.011] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/17/2018] [Accepted: 06/29/2018] [Indexed: 01/24/2023]
Abstract
Macrolide antibiotics inhibit protein synthesis by targeting the bacterial ribosome. They bind at the nascent peptide exit tunnel and partially occlude it. Thus, macrolides have been viewed as 'tunnel plugs' that stop the synthesis of every protein. More recent evidence, however, demonstrates that macrolides selectively inhibit the translation of a subset of cellular proteins, and that their action crucially depends on the nascent protein sequence and on the antibiotic structure. Therefore, macrolides emerge as modulators of translation rather than as global inhibitors of protein synthesis. The context-specific action of macrolides is the basis for regulating the expression of resistance genes. Understanding the details of the mechanism of macrolide action may inform rational design of new drugs and unveil important principles of translation regulation.
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Affiliation(s)
- Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
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Population Pharmacokinetics and Safety of Solithromycin following Intravenous and Oral Administration in Infants, Children, and Adolescents. Antimicrob Agents Chemother 2018; 62:AAC.00692-18. [PMID: 29891609 DOI: 10.1128/aac.00692-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/04/2018] [Indexed: 01/10/2023] Open
Abstract
Solithromycin is a novel fluoroketolide antibiotic which was under investigation for the treatment of community-acquired bacterial pneumonia (CABP). A phase 1 study was performed to characterize the pharmacokinetics (PK) and safety of solithromycin in children. Eighty-four subjects (median age, 6 years [age range, 4 days to 17 years]) were administered intravenous (i.v.) or oral (capsules or suspension) solithromycin (i.v., 6 to 8 mg/kg of body weight; capsules/suspension, 14 to 16 mg/kg on days 1 and 7 to 15 mg/kg on days 2 to 5). PK samples were collected after the first and multidose administration. Data from 83 subjects (662 samples) were combined with previously collected adolescent PK data (n = 13; median age, 16 years [age range, 12 to 17 years]) following capsule administration to perform a population PK analysis. A 2-compartment PK model characterized the data well, and postmenstrual age was the only significant covariate after accounting for body size differences. Dosing simulations suggested that 8 mg/kg i.v. daily and oral dosing of 20 mg/kg on day 1 (800-mg adult maximum) followed by 10 mg/kg on days 2 to 5 (400-mg adult maximum) would achieve a pediatric solithromycin exposure consistent with the exposures observed in adults. Seventy-six treatment-emergent adverse events (TEAEs) were reported in 40 subjects. Diarrhea (6 subjects) and infusion site pain or phlebitis (3 subjects) were the most frequently reported adverse events related to treatment. Two subjects experienced TEAEs of increased hepatic enzymes that were deemed not to be related to the study treatment. (The phase 1 pediatric studies discussed in this paper have been registered at ClinicalTrials.gov under identifiers NCT01966055 and NCT02268279.).
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Metabolism, Excretion, and Mass Balance of Solithromycin in Humans. Antimicrob Agents Chemother 2018; 62:AAC.01474-17. [PMID: 29507061 DOI: 10.1128/aac.01474-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/07/2018] [Indexed: 11/20/2022] Open
Abstract
Solithromycin, a novel macrolide and the first fluoroketolide, is being developed as a therapy for community-acquired bacterial pneumonia, with a distinct mechanism that provides activity against macrolide-resistant bacteria. The pharmacokinetics, metabolism, and excretion of solithromycin were studied in healthy male subjects after oral administration of a single 800-mg (∼100-μCi) dose of [14C]solithromycin. Solithromycin was well tolerated, and absorption from the solution occurred with a median time to peak concentration of 4.0 h. Solithromycin and the total radioactivity had similar profiles with no long-lived metabolites. The whole-blood total radioactivity was approximately 75% of the plasma total radioactivity. Recovery was essentially complete (mean, 90.6%), with 76.5% and 14.1% of the dose recovered in feces and urine, respectively. Unchanged solithromycin (CEM-101) was the predominant circulating radioactive component in plasma (77% of the total radioactivity area under the concentration-time curve [AUC]), with two minor plasma metabolites, CEM-214 and CEM-122 (N-acetyl-CEM-101), each accounting for approximately 5% of the total radioactivity. Urinary excretion was predominantly like that of the parent. Solithromycin was primarily eliminated in the feces after extensive metabolism via a complex metabolic pathway with CEM-262 as the major constituent (27.36% of the administered dose). Overall oxidative pathways, presumably carried out mostly by CYP3A4, represented the majority of the metabolism, with N-acetylation present to a lesser extent. No disproportionate human metabolites were observed.
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Zhu Y, Han J, Wang J, Shibata N, Sodeoka M, Soloshonok VA, Coelho JAS, Toste FD. Modern Approaches for Asymmetric Construction of Carbon-Fluorine Quaternary Stereogenic Centers: Synthetic Challenges and Pharmaceutical Needs. Chem Rev 2018; 118:3887-3964. [PMID: 29608052 DOI: 10.1021/acs.chemrev.7b00778] [Citation(s) in RCA: 423] [Impact Index Per Article: 70.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
New methods for preparation of tailor-made fluorine-containing compounds are in extremely high demand in nearly every sector of chemical industry. The asymmetric construction of quaternary C-F stereogenic centers is the most synthetically challenging and, consequently, the least developed area of research. As a reflection of this apparent methodological deficit, pharmaceutical drugs featuring C-F stereogenic centers constitute less than 1% of all fluorine-containing medicines currently on the market or in clinical development. Here we provide a comprehensive review of current research activity in this area, including such general directions as asymmetric electrophilic fluorination via organocatalytic and transition-metal catalyzed reactions, asymmetric elaboration of fluorine-containing substrates via alkylations, Mannich, Michael, and aldol additions, cross-coupling reactions, and biocatalytic approaches.
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Affiliation(s)
- Yi Zhu
- School of Chemistry and Chemical Engineering, State Key laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials , Nanjing University , 210093 Nanjing , China
| | - Jianlin Han
- School of Chemistry and Chemical Engineering, State Key laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials , Nanjing University , 210093 Nanjing , China
| | - Jiandong Wang
- Department of Nanopharmaceutical Sciences & Department of Frontier Materials , Nagoya Institute of Technology , Gokiso, Showa-ku , Nagoya 466-8555 , Japan
| | - Norio Shibata
- Department of Nanopharmaceutical Sciences & Department of Frontier Materials , Nagoya Institute of Technology , Gokiso, Showa-ku , Nagoya 466-8555 , Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory , RIKEN, and RIKEN Center for Sustainable Resourse Science , 2-1 Hirosawa , Wako 351-0198 , Japan
| | - Vadim A Soloshonok
- Department of Organic Chemistry I, Faculty of Chemistry , University of the Basque Country UPV/EHU , 20018 San Sebastian , Spain.,IKERBASQUE, Basque Foundation for Science , 48011 Bilbao , Spain
| | - Jaime A S Coelho
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - F Dean Toste
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
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45
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Lin J, Zhou D, Steitz TA, Polikanov YS, Gagnon MG. Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design. Annu Rev Biochem 2018; 87:451-478. [PMID: 29570352 DOI: 10.1146/annurev-biochem-062917-011942] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic information is translated into proteins by the ribosome. Structural studies of the ribosome and of its complexes with factors and inhibitors have provided invaluable information on the mechanism of protein synthesis. Ribosome inhibitors are among the most successful antimicrobial drugs and constitute more than half of all medicines used to treat infections. However, bacterial infections are becoming increasingly difficult to treat because the microbes have developed resistance to the most effective antibiotics, creating a major public health care threat. This has spurred a renewed interest in structure-function studies of protein synthesis inhibitors, and in few cases, compounds have been developed into potent therapeutic agents against drug-resistant pathogens. In this review, we describe the modes of action of many ribosome-targeting antibiotics, highlight the major resistance mechanisms developed by pathogenic bacteria, and discuss recent advances in structure-assisted design of new molecules.
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Affiliation(s)
- Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China;
| | - Dejian Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China;
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA; .,Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
| | - Yury S Polikanov
- Department of Biological Sciences, and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60607, USA;
| | - Matthieu G Gagnon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA; .,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA.,Current affiliation: Department of Microbiology and Immunology, and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA;
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46
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Alihodžić S, Bukvić M, Elenkov IJ, Hutinec A, Koštrun S, Pešić D, Saxty G, Tomašković L, Žiher D. Current Trends in Macrocyclic Drug Discovery and beyond -Ro5. PROGRESS IN MEDICINAL CHEMISTRY 2018; 57:113-233. [DOI: 10.1016/bs.pmch.2018.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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47
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Evans D, Yalkowsky S, Wu S, Pereira D, Fernandes P. Overcoming the Challenges of Low Drug Solubility in the Intravenous Formulation of Solithromycin. J Pharm Sci 2018; 107:412-418. [DOI: 10.1016/j.xphs.2017.10.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 10/16/2017] [Accepted: 10/17/2017] [Indexed: 10/18/2022]
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48
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Donald BJ, Surani S, Deol HS, Mbadugha UJ, Udeani G. Spotlight on solithromycin in the treatment of community-acquired bacterial pneumonia: design, development, and potential place in therapy. Drug Des Devel Ther 2017; 11:3559-3566. [PMID: 29263651 PMCID: PMC5732564 DOI: 10.2147/dddt.s119545] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Community-acquired bacterial pneumonia (CABP) is a leading cause of death worldwide. However, antibacterial agents used to treat common pathogens in CABP are marked by adverse drug events and increasing antimicrobial resistance. Solithromycin is a new ketolide antibiotic, based on the macrolide antibiotic structure, being studied for use in CABP. It has efficacy in vitro against the common causative pathogens in CABP including Streptococcus pneumoniae, Haemophilus influenzae, and atypical pathogens. In Phase II and Phase III clinical trials, it has been demonstrated efficacious as a single agent for treatment of CABP with an apparently milder adverse event profile than alternative agents.
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Affiliation(s)
- Bryan J Donald
- Department of Pharmacy, Corpus Christi Medical Center, Corpus Christi, TX.,Department of Clinical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, LA
| | - Salim Surani
- Department of Pulmonology/Critical Care, Corpus Christi Medical Center, Corpus Christi, TX.,Department of Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX.,Department of Medicine, College of Osteopathic Medicine, University of North Texas Health Science Center, Denton, TX
| | - Harmeet S Deol
- Department of Pharmacy, Corpus Christi Medical Center, Corpus Christi, TX.,Department of Pharmacy Services, Yale New Haven Hospital, New Haven, CT
| | - Uche J Mbadugha
- Department of Pharmacy, Corpus Christi Medical Center, Corpus Christi, TX
| | - George Udeani
- Department of Pharmacy, Corpus Christi Medical Center, Corpus Christi, TX.,Pharmacy Practice, College of Pharmacy, Texas A&M University Health Science Center, Kingsville, TX, USA
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49
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Kinetics of drug-ribosome interactions defines the cidality of macrolide antibiotics. Proc Natl Acad Sci U S A 2017; 114:13673-13678. [PMID: 29229833 DOI: 10.1073/pnas.1717168115] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Antibiotics can cause dormancy (bacteriostasis) or induce death (cidality) of the targeted bacteria. The bactericidal capacity is one of the most important properties of antibacterial agents. However, the understanding of the fundamental differences in the mode of action of bacteriostatic or bactericidal antibiotics, especially those belonging to the same chemical class, is very rudimentary. Here, by examining the activity and binding properties of chemically distinct macrolide inhibitors of translation, we have identified a key difference in their interaction with the ribosome, which correlates with their ability to cause cell death. While bacteriostatic and bactericidal macrolides bind in the nascent peptide exit tunnel of the large ribosomal subunit with comparable affinities, the bactericidal antibiotics dissociate from the ribosome with significantly slower rates. The sluggish dissociation of bactericidal macrolides correlates with the presence in their structure of an extended alkyl-aryl side chain, which establishes idiosyncratic interactions with the ribosomal RNA. Mutations or chemical alterations of the rRNA nucleotides in the drug binding site can protect cells from macrolide-induced killing, even with inhibitor concentrations that significantly exceed those required for cell growth arrest. We propose that the increased translation downtime due to slow dissociation of the antibiotic may damage cells beyond the point where growth can be reinitiated upon the removal of the drug due to depletion of critical components of the gene-expression pathway.
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50
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Koch M, Willi J, Pradère U, Hall J, Polacek N. Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain. Nucleic Acids Res 2017; 45:6717-6728. [PMID: 28369621 PMCID: PMC5499644 DOI: 10.1093/nar/gkx195] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/14/2017] [Indexed: 12/25/2022] Open
Abstract
The nascent peptide exit tunnel has recently been identified as a functional region of ribosomes contributing to translation regulation and co-translational protein folding. Inducible expression of the erm resistance genes depends on ribosome stalling at specific codons of an upstream open reading frame in the presence of an exit tunnel-bound macrolide antibiotic. The molecular basis for this translation arrest is still not fully understood. Here, we used a nucleotide analog interference approach to unravel important functional groups on 23S rRNA residues in the ribosomal exit tunnel for ribosome stalling on the ErmC leader peptide. By replacing single nucleobase functional groups or even single atoms we were able to demonstrate the importance of A2062, A2503 and U2586 for drug-dependent ribosome stalling. Our data show that the universally conserved A2062 and A2503 are capable of forming a non-Watson–Crick base pair that is critical for sensing and transmitting the stalling signal from the exit tunnel back to the peptidyl transferase center of the ribosome. The nucleobases of A2062, A2503 as well as U2586 do not contribute significantly to the overall mechanism of protein biosynthesis, yet their elaborate role for co-translational monitoring of nascent peptide chains inside the exit tunnel can explain their evolutionary conservation.
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Affiliation(s)
- Miriam Koch
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jessica Willi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Ugo Pradère
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Norbert Polacek
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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