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Krivitskaya AV, Kuryshkina MS, Eremina MY, Smirnov IV, Khrenova MG. Molecular Basis of Influence of A501X Mutations in Penicillin-Binding Protein 2 of Neisseria gonorrhoeae Strain 35/02 on Ceftriaxone Resistance. Int J Mol Sci 2024; 25:8260. [PMID: 39125830 PMCID: PMC11312080 DOI: 10.3390/ijms25158260] [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: 06/14/2024] [Revised: 07/20/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
The increase in the resistance of mutant strains of Neisseria gonorrhoeae to the antibiotic ceftriaxone is pronounced in the decrease in the second-order acylation rate constant, k2/KS, by penicillin-binding protein 2 (PBP2). These changes can be caused by both the decrease in the acylation rate constant, k2, and the weakening of the binding affinity, i.e., an increase in the substrate constant, KS. A501X mutations in PBP2 affect second-order acylation rate constants. The PBP2A501V variant exhibits a higher k2/KS value, whereas for PBP2A501R and PBP2A501P variants, these values are lower. We performed molecular dynamic simulations with both classical and QM/MM potentials to model both acylation energy profiles and conformational dynamics of four PBP2 variants to explain the origin of k2/KS changes. The acylation reaction occurs in two elementary steps, specifically, a nucleophilic attack by the oxygen atom of the Ser310 residue and C-N bond cleavage in the β-lactam ring accompanied by the elimination of the leaving group of ceftriaxone. The energy barrier of the first step increases for PBP2 variants with a decrease in the observed k2/KS value. Submicrosecond classic molecular dynamic trajectories with subsequent cluster analysis reveal that the conformation of the β3-β4 loop switches from open to closed and its flexibility decreases for PBP2 variants with a lower k2/KS value. Thus, the experimentally observed decrease in the k2/KS in A501X variants of PBP2 occurs due to both the decrease in the acylation rate constant, k2, and the increase in KS.
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Affiliation(s)
- Alexandra V. Krivitskaya
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia;
| | - Maria S. Kuryshkina
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.S.K.); (I.V.S.)
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Maria Y. Eremina
- Biology Department, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Ivan V. Smirnov
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.S.K.); (I.V.S.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Maria G. Khrenova
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia;
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.S.K.); (I.V.S.)
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Vitiello A, Ferrara F, Boccellino M, Ponzo A, Sabbatucci M, Zovi A. Antimicrobial Resistance in Gonorrhea. Microb Drug Resist 2024; 30:297-303. [PMID: 38579162 DOI: 10.1089/mdr.2023.0259] [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] [Indexed: 04/07/2024] Open
Abstract
Antimicrobial resistance is a global public health emergency. The World Health Organization recently highlighted the growing number of new sexually transmitted infections such as gonorrhea, syphilis, and Chlamydia, which are resistant to common antibiotics. The phenomenon is also on the rise due to increasing intercontinental travel. Emerging antibiotic-resistant strains of gonorrhea are particularly associated with international spread from Southeast Asian travelers. Infection with Neisseria gonorrhoeae can cause a wide spectrum of associated diseases such as dermatitis, arthritis and septic arthritis, and pelvic inflammatory disease, and can even lead to serious health consequences for the individual. Natural infection confers no immunity, and vaccination is not available currently, although in several countries, it has been reported that the antimeningococcal vaccine may protect against gonorrhea. Implementing all necessary preventive measures is crucial, as well as appropriate and timely diagnostic methods and effective antimicrobial therapeutic treatments in the correct modalities to avoid the increase of forms of gonorrhea that are resistant to common antibiotics and difficult to eradicate.
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Affiliation(s)
| | | | | | - Annarita Ponzo
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Michela Sabbatucci
- Department Infectious Diseases, Italian National Institute of Health, Rome, Italy
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Liao Y, Xie Q, Yin X, Li X, Xie J, Wu X, Tang S, Liu M, Zeng L, Pan Y, Yang J, Feng Z, Qin X, Zheng H. penA profile of Neisseria gonorrhoeae in Guangdong, China: Novel penA alleles are related to decreased susceptibility to ceftriaxone or cefixime. Int J Antimicrob Agents 2024; 63:107101. [PMID: 38325722 DOI: 10.1016/j.ijantimicag.2024.107101] [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: 02/09/2023] [Revised: 12/15/2023] [Accepted: 01/29/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND Resistance to extended-spectrum cephalosporins (ESCs) has become a public health concern with the spread of Neisseria gonorrhoeae and increasing antimicrobial resistance. Mutation of penA, encoding penicillin-binding protein 2, represents a mechanism of ESC resistance. This study sought to assess penA alleles and mutations associated with decreased susceptibility (DS) to ESCs in N. gonorrhoeae. MATERIALS AND METHODS In 2021, 347 gonococci were collected in Guangdong, China. Minimum inhibitory concentations (MICs) of ceftriaxone and cefixime were determined, and whole-genome sequencing and phylogenetic analysis were performed. Multi-locus sequence typing (MLST) and conventional resistance determinants such as penA, mtrR, PonA and PorB were analysed. penA was genotyped and sequence-aligned using PubMLST. RESULTS Genome-wide phylogenetic analysis revealed that the prevalence of DS to ESCs was highest in Clade 11.1 (100.0%), Clade 2 (66.7%) and Clade 0 (55.7%), and the leading cause was strains with penA-60.001 or new penA alleles in clades. The penA phylogenetic tree is divided into two branches: non-mosaic penA and mosaic penA. The latter contained penA-60.001, penA-10 and penA-34. penA profile analysis indicated that A311V and T483S are closely related to DS to ESCs in mosaic penA. The new alleles NEIS1753_2840 and NEIS1753_2837 are closely related to penA-60.001, with DS to ceftriaxone and cefixime of 100%. NEIS1753_2660, a derivative of penA-10 (A486V), has increased DS to ceftriaxone. NEIS1753_2846, a derivative of penA-34.007 (G546S), has increased DS to cefixime. CONCLUSION This study identified critical penA alleles related to elevated MICs, and trends of gonococcus-evolved mutated penA associated with DS to ESCs in Guangdong.
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Affiliation(s)
- Yiwen Liao
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Qinghui Xie
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaona Yin
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaoxiao Li
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Junhui Xie
- The Affiliated Cancer Hospital of Gannan Medical University, Ganzhou, Jiang Xi, China
| | - Xingzhong Wu
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Sanmei Tang
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Mingjing Liu
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Lihong Zeng
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yuying Pan
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jianjiang Yang
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhanqin Feng
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaolin Qin
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory for Sexually Transmitted Disease Control, Guangzhou, Guangdong, China
| | - Heping Zheng
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory for Sexually Transmitted Disease Control, Guangzhou, Guangdong, China.
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Zhu L, Liang J, Zheng Y, Chen S, Xu Q, Yin S, Hong Y, Cao W, Lai W, Gong Z. Combined mutations of the penA with ftsX genes contribute to ceftriaxone resistance in Neisseria gonorrhoeae and peptide nucleic acids targeting these genes reverse ceftriaxone resistance. J Glob Antimicrob Resist 2023; 35:19-25. [PMID: 37567469 DOI: 10.1016/j.jgar.2023.08.005] [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: 04/23/2023] [Revised: 06/26/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
OBJECTIVES To investigate the gene mutations associated with ceftriaxone (CRO) resistance among gonococcal isolates, and to determine the effects of the mutated genes on CRO minimum inhibitory concentrations (MICs) with transformation assays and antisense peptide nucleic acids (asPNAs). METHODS Ceftriaxone-resistant (CROR) and ceftriaxone-susceptible (CROS) isolates were identified using EUCAST and paired according to similarity in their MICs to other antimicrobials. The two groups of gonococci were sequenced and analysed. Mutated genes that showed a statistical difference between the two groups were transformed into gonococcal reference strains to determine their functions. AsPNAs were designed and transformed into the former transformant to further confirm the effects of the mutated genes. RESULTS Twenty-two paired CROR and CROS isolates were obtained. The incidence of the penA-A501T and penA-G542S mutations individually, as well as combined mutations (penA-A501T and ftsX-R251H, penA-G542S and ftsX R251H), was statistically different between the two groups. The MIC of ATCC43069 (A43) increased 2 times following transformation with penA-A501T, and the MICs of A43 and ATCC49226 (A49) increased 32 times and 2 times following transformation with penA-A501T and ftsX-R251H, respectively. Antisense PNA-P3 reduced the MIC of the A43 transformant most significantly when transformed individually. PNA-P3 and PNA-F1 (asPNAs of the penA and ftsX) restored CRO susceptibility. CONCLUSIONS PenA-A501T and penA-G542S mutations are important in CRO resistance among gonococci isolates. The ftsX-R251H mutation is also related to CRO resistance, and combined mutations of ftsX-R251H and penA-A501T comediate a significant reduction in CRO susceptibility. The combined application of PNA-P3 and PNA-F1 could effectively reverse the resistance to CRO in N. gonorrhoeae.
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Affiliation(s)
- Lin Zhu
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Jingyao Liang
- Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou, China
| | - Yue Zheng
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Shaochun Chen
- Institute of Dermatology and Hospital for Skin Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Qingfang Xu
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Songchao Yin
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Yiyong Hong
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Wenling Cao
- Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou, China
| | - Wei Lai
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Zijian Gong
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
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Hunashal Y, Kumar GS, Choy MS, D'Andréa ÉD, Da Silva Santiago A, Schoenle MV, Desbonnet C, Arthur M, Rice LB, Page R, Peti W. Molecular basis of β-lactam antibiotic resistance of ESKAPE bacterium E. faecium Penicillin Binding Protein PBP5. Nat Commun 2023; 14:4268. [PMID: 37460557 DOI: 10.1038/s41467-023-39966-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
Penicillin-binding proteins (PBPs) are essential for the formation of the bacterial cell wall. They are also the targets of β-lactam antibiotics. In Enterococcus faecium, high levels of resistance to β-lactams are associated with the expression of PBP5, with higher levels of resistance associated with distinct PBP5 variants. To define the molecular mechanism of PBP5-mediated resistance we leveraged biomolecular NMR spectroscopy of PBP5 - due to its size (>70 kDa) a challenging NMR target. Our data show that resistant PBP5 variants show significantly increased dynamics either alone or upon formation of the acyl-enzyme inhibitor complex. Furthermore, these variants also exhibit increased acyl-enzyme hydrolysis. Thus, reducing sidechain bulkiness and expanding surface loops results in increased dynamics that facilitates acyl-enzyme hydrolysis and, via increased β-lactam antibiotic turnover, facilitates β-lactam resistance. Together, these data provide the molecular basis of resistance of clinical E. faecium PBP5 variants, results that are likely applicable to the PBP family.
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Affiliation(s)
- Yamanappa Hunashal
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Ganesan Senthil Kumar
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
- National Institute of Immunology, New Delhi, India
| | - Meng S Choy
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Éverton D D'Andréa
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | | | - Marta V Schoenle
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Charlene Desbonnet
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Michel Arthur
- INSERM, Sorbonne Université, Université Paris Cité, Paris, France
| | - Louis B Rice
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Rebecca Page
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA.
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Evolution of Ceftriaxone Resistance of Penicillin-Binding Proteins 2 Revealed by Molecular Modeling. Int J Mol Sci 2022; 24:ijms24010176. [PMID: 36613627 PMCID: PMC9820184 DOI: 10.3390/ijms24010176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Penicillin-binding proteins 2 (PBP2) are critically important enzymes in the formation of the bacterial cell wall. Inhibition of PBP2 is utilized in the treatment of various diseases, including gonorrhea. Ceftriaxone is the only drug used to treat gonorrhea currently, and recent growth in PBP2 resistance to this antibiotic is a serious threat to human health. Our study reveals mechanistic aspects of the inhibition reaction of PBP2 from the wild-type FA19 strain and mutant 35/02 and H041 strains of Neisseria Gonorrhoeae by ceftriaxone. QM(PBE0-D3/6-31G**)/MM MD simulations show that the reaction mechanism for the wild-type PBP2 consists of three elementary steps including nucleophilic attack, C-N bond cleavage in the β-lactam ring and elimination of the leaving group in ceftriaxone. In PBP2 from the mutant strains, the second and third steps occur simultaneously. For all considered systems, the acylation rate is determined by the energy barrier of the first step that increases in the order of PBP2 from FA19, 35/02 and H041 strains. Dynamic behavior of ES complexes is analyzed using geometry and electron density features including Fukui electrophilicity index and Laplacian of electron density maps. It reveals that more efficient activation of the carbonyl group of the antibiotic leads to the lower energy barrier of nucleophilic attack and larger stabilization of the first reaction intermediate. Dynamical network analysis of MD trajectories explains the differences in ceftriaxone binding affinity: in PBP2 from the wild-type strain, the β3-β4 loop conformation facilitates substrate binding, whereas in PBP2 from the mutant strains, it exists in the conformation that is unfavorable for complex formation. Thus, we clarify that the experimentally observed decrease in the second-order rate constant of acylation (k2/KS) in PBP2 from the mutant strains is due to both a decrease in the acylation rate constant k2 and an increase in the dissociation constant KS.
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Molecular Mechanisms of Drug Resistance and Epidemiology of Multidrug-Resistant Variants of Neisseria gonorrhoeae. Int J Mol Sci 2022; 23:ijms231810499. [PMID: 36142410 PMCID: PMC9505821 DOI: 10.3390/ijms231810499] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 01/16/2023] Open
Abstract
The paper presents various issues related to the increasing drug resistance of Neisseria gonorrhoeae and the occurrence and spread of multidrug-resistant clones. One of the most important is the incidence and evolution of resistance mechanisms of N. gonorrhoeae to beta-lactam antibiotics. Chromosomal resistance to penicillins and oxyimino-cephalosporins and plasmid resistance to penicillins are discussed. Chromosomal resistance is associated with the presence of mutations in the PBP2 protein, containing mosaic variants and nonmosaic amino acid substitutions in the transpeptidase domain, and their correlation with mutations in the mtrR gene and its promoter regions (the MtrCDE membrane pump repressor) and in several other genes, which together determine reduced sensitivity or resistance to ceftriaxone and cefixime. Plasmid resistance to penicillins results from the production of beta-lactamases. There are different types of beta-lactamases as well as penicillinase plasmids. In addition to resistance to beta-lactam antibiotics, the paper covers the mechanisms and occurrence of resistance to macrolides (azithromycin), fluoroquinolones and some other antibiotics. Moreover, the most important epidemiological types of multidrug-resistant N. gonorrhoeae, prevalent in specific years and regions, are discussed. Epidemiological types are defined as sequence types, clonal complexes and genogroups obtained by various typing systems such as NG-STAR, NG-MAST and MLST. New perspectives on the treatment of N. gonorrhoeae infections are also presented, including new drugs active against multidrug-resistant strains.
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Salleh MZ, Banga Singh KK, Deris ZZ. Structural Insights into Substrate Binding and Antibiotic Inhibition of Enterobacterial Penicillin-Binding Protein 6. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071022. [PMID: 35888109 PMCID: PMC9320039 DOI: 10.3390/life12071022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/03/2022] [Accepted: 07/07/2022] [Indexed: 11/16/2022]
Abstract
Shigella sonnei remains the second most common cause of shigellosis in young children and is now increasingly dominant across developing countries. The global emergence of drug resistance has become a main burden in the treatment of S. sonnei infections and β-lactam antibiotics, such as pivmecillinam and ceftriaxone, are recommended to be used as second-line treatment. They work by inhibiting the biosynthesis of the peptidoglycan layer of bacterial cell walls, in which the final transpeptidation step is facilitated by penicillin-binding proteins (PBPs). In this study, using protein homology modelling, we modelled the structure of PBP6 from S. sonnei and comprehensively examined the molecular interactions between PBP6 and its pentapeptide substrate and two antibiotic inhibitors. The docked complex of S. sonnei PBP6 with pentapeptides showed that the substrate bound to the active site groove of the DD-carboxypeptidase domain, via hydrogen bonding interactions with the residues S79, V80, Q101, G144, D146 and R240, in close proximity to the catalytic nucleophile S36 for the nucleophilic attack. Two residues, R240 and T208, were found to be important in ligand recognition and binding, where they formed strong hydrogen bonds with the substrate and β-lactams, respectively. Our results provide valuable information on the molecular interactions essential for ligand recognition and catalysis by PBP6. Understanding these interactions will be helpful in the development of effective drugs to treat S. sonnei infections.
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