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Basharat Z, Meshal A. Pan-genome mediated therapeutic target mining in Kingella kingae and inhibition assessment using traditional Chinese medicinal compounds: an informatics approach. J Biomol Struct Dyn 2024; 42:2872-2885. [PMID: 37144759 DOI: 10.1080/07391102.2023.2208221] [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: 02/21/2023] [Accepted: 04/23/2023] [Indexed: 05/06/2023]
Abstract
Kingella kingae causes bacteremia, endocarditis, osteomyelitis, septic arthritis, meningitis, spondylodiscitis, and lower respiratory tract infections in pediatric patients. Usually it demonstrates disease after inflammation of mouth, lips or infections of the upper respiratory tract. To date, therapeutic targets in this bacterium remain unexplored. We have utilized a battery of bioinformatics tools to mine these targets in this study. Core genes were initially inferred from 55 genomes of K. kingae and 39 therapeutic targets were mined using an in-house pipeline. We selected aroG product (KDPG aldolase) involved in chorismate pathway, for inhibition analysis of this bacterium using lead-like metabolites from traditional Chinese medicinal plants. Pharmacophore generation was done using control ZINC36444158 (1,16-bis[(dihydroxyphosphinyl)oxy]hexadecane), followed by molecular docking of top hits from a library of 36,000 compounds. Top prioritized compounds were ZINC95914016, ZINC33833283 and ZINC95914219. ADME profiling and simulation of compound dosing (100 mg tablet) was done to infer compartmental pharmacokinetics in a population of 300 individuals in fasting state. PkCSM based toxicity analysis revealed the compounds ZINC95914016 and ZINC95914219 as safe and with almost similar bioavailability. However, ZINC95914016 takes less time to reach maximum concentration in the plasma and shows several optimal parameters compared to other leads. In light of obtained data, we recommend this compound for further testing and induction in experimental drug design pipeline.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Alotaibi Meshal
- Department of Pharmacy Practice, College of Pharmacy, University of Hafr Albatin, Saudi Arabia
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Basharat Z, Murtaza Z, Siddiqa A, Alnasser SM, Meshal A. Therapeutic target mapping from the genome of Kingella negevensis and biophysical inhibition assessment through PNP synthase binding with traditional medicinal compounds. Mol Divers 2024; 28:581-594. [PMID: 36645537 PMCID: PMC9842218 DOI: 10.1007/s11030-023-10604-y] [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: 11/02/2022] [Accepted: 01/10/2023] [Indexed: 01/17/2023]
Abstract
Kingella negevensis belongs to the Neisseriaceae family. It is implied that it has significant virulence potential due to RTX toxin production, which can cause hemolysis. It usually colonizes the orophayrynx of pediatric population, along with Kingella kingae but has also been isolated from vagina. Todate no report on its drug targets is present, therefore putative therapeutic targets were identified from its genomic sequence data. Traditional Chinese (n > 36,000) and Indian medicinal compounds (n > 2000) were then screened against its pyridoxine 5'-phosphate synthase, a vital therapeutic target. Prioritized TCM compounds included ZINC02525131, ZINC33833737 and ZINC85486932, and Cadiyenol, 9,11,13-Octadecatrienoic acid and 6-Gingerol from Indian medicinal library. Molecular dynamics simulation of top compounds revealed ZINC02525131 as having best stability for 100 ns, compared to Cadiyenol. ADMET profiling was then done, along with physiologically based pharmacokinetic simulation of these compounds in a population of 200 individuals, for 12 h to see fate of the ingested compound. Additionally, the impact of these compounds in a population with cirrhosis and renal impairment was also simulated. We imply in light of all the studied parameters of safety and bioavailability, etc., that 6-Gingerol from Zingiber officinalis rhizome must be proceeded further for in vitro and in vivo testing for inhibition of K. negevensis.
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Affiliation(s)
- Zarrin Basharat
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
| | - Zainab Murtaza
- Department of Zoology, Government College University, Lahore, 54000, Pakistan
| | - Aisha Siddiqa
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Sulaiman Mohammed Alnasser
- Department of Pharmacology and Toxicology, Unaizah College of Pharmacy, Qassim University, Buraydah, 52571, Saudi Arabia
| | - Alotaibi Meshal
- Department of Pharmacy Practice, College of Pharmacy, University of Hafr Albatin, Hafr Albatin, Saudi Arabia
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Rahman WU, Fiser R, Osicka R. Kingella kingae RtxA toxin interacts with sialylated gangliosides. Microb Pathog 2023:106200. [PMID: 37315629 DOI: 10.1016/j.micpath.2023.106200] [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: 04/14/2023] [Revised: 06/11/2023] [Accepted: 06/12/2023] [Indexed: 06/16/2023]
Abstract
The membrane-damaging RTX family cytotoxin RtxA is a key virulence factor of the emerging pediatric pathogen Kingella kingae, but little is known about the mechanism of RtxA binding to host cells. While we have previously shown that RtxA binds cell surface glycoproteins, here we demonstrate that the toxin also binds different types of gangliosides. The recognition of gangliosides by RtxA depended on sialic acid side groups of ganglioside glycans. Moreover, binding of RtxA to epithelial cells was significantly decreased in the presence of free sialylated gangliosides, which inhibited cytotoxic activity of the toxin. These results suggest that RtxA utilizes sialylated gangliosides as ubiquitous cell membrane receptor molecules on host cells to exert its cytotoxic action and support K. kingae infection.
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Affiliation(s)
- Waheed Ur Rahman
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radovan Fiser
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Radim Osicka
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
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Diagnostic Utility of Synovial Fluid Cell Counts and CRP in Pediatric Knee Arthritis: A 10-Year Monocentric, Retrospective Study. CHILDREN 2022; 9:children9091367. [PMID: 36138676 PMCID: PMC9498181 DOI: 10.3390/children9091367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022]
Abstract
Background: Orthopedic surgeons often use the intra-articular white blood counts (WBCs) and the percentage of polymorphonuclear cells (PMN) in the diagnosis of an acute swollen and painful knee joint in children. Today, there is no established threshold for the synovial WBC, and their differentiation, as indicative of native joint knee bacterial arthritis. We determine the sensitivity and specificity of synovial WBCs and PMN percentages in the prediction of a community-acquired, acute bacterial native joint septic arthritis (SA) in the pediatric population. Methods: A retrospective study on healthy children 0–16 years of age who underwent knee joint aspiration for a community-acquired, acute irritable knee effusion in our tertiary-care children’s hospital between May 2009 and April 2019 was conducted. We divided the study population into two groups according to the detection of bacterial arthritis in the synovial fluid (bacterial arthritis versus its absence) and compared the intra-articular leukocyte and C-reactive protein (CRP) levels. Results: Overall, we found a statistically significant difference regarding the total CRP (p = 0.017), leukocyte or PMN counts (p ≤ 0.001 in favor of a bacterial arthritis). In contrast, the percentage of the neutrophils was not determinant for the later confirmation of bacterial pathogens, and we were unable to establish diagnostically determining minimal thresholds of the intra-articular CRP and leukocyte levels. Conclusions: This pilot study suggests that either the leukocyte or PMN counts may be associated with a bacterial origin of knee arthritis in children. We plan a larger prospective interventional study in the future to confirm these findings including the investigation of other joint aspirate biomarkers.
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Filipi K, Rahman WU, Osickova A, Osicka R. Kingella kingae RtxA Cytotoxin in the Context of Other RTX Toxins. Microorganisms 2022; 10:microorganisms10030518. [PMID: 35336094 PMCID: PMC8953716 DOI: 10.3390/microorganisms10030518] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/04/2022] Open
Abstract
The Gram-negative bacterium Kingella kingae is part of the commensal oropharyngeal flora of young children. As detection methods have improved, K. kingae has been increasingly recognized as an emerging invasive pathogen that frequently causes skeletal system infections, bacteremia, and severe forms of infective endocarditis. K. kingae secretes an RtxA cytotoxin, which is involved in the development of clinical infection and belongs to an ever-growing family of cytolytic RTX (Repeats in ToXin) toxins secreted by Gram-negative pathogens. All RTX cytolysins share several characteristic structural features: (i) a hydrophobic pore-forming domain in the N-terminal part of the molecule; (ii) an acylated segment where the activation of the inactive protoxin to the toxin occurs by a co-expressed toxin-activating acyltransferase; (iii) a typical calcium-binding RTX domain in the C-terminal portion of the molecule with the characteristic glycine- and aspartate-rich nonapeptide repeats; and (iv) a C-proximal secretion signal recognized by the type I secretion system. RTX toxins, including RtxA from K. kingae, have been shown to act as highly efficient ‘contact weapons’ that penetrate and permeabilize host cell membranes and thus contribute to the pathogenesis of bacterial infections. RtxA was discovered relatively recently and the knowledge of its biological role remains limited. This review describes the structure and function of RtxA in the context of the most studied RTX toxins, the knowledge of which may contribute to a better understanding of the action of RtxA in the pathogenesis of K. kingae infections.
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Munson E, Carroll KC. Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019. J Clin Microbiol 2021; 59:e01309-20. [PMID: 32967902 PMCID: PMC8111135 DOI: 10.1128/jcm.01309-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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A comprehensive review of bacterial osteomyelitis with emphasis on Staphylococcus aureus. Microb Pathog 2020; 148:104431. [PMID: 32801004 DOI: 10.1016/j.micpath.2020.104431] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 02/04/2023]
Abstract
Osteomyelitis, a significant infection of bone tissue, gives rise to two main groups of infection: acute and chronic. These groups are further categorized in terms of the duration of infection. Usually, children and adults are more susceptible to acute and chronic infections, respectively. The aforementioned groups of osteomyelitis share almost 80% of the corresponding bacterial pathogens. Among all bacteria, Staphylococcus aureus (S. aureus) is a significant pathogen and is associated with a high range of osteomyelitis symptoms. S. aureus has many strategies for interacting with host cells including Small Colony Variant (SCV), biofilm formation, and toxin secretion. In addition, it induces an inflammatory response and causes host cell death by apoptosis and necrosis. However, any possible step to take in this respect is dependent on the conditions and host responses. In the absence of any immune responses and antibiotics, bacteria actively duplicate themselves; however, in the presence of phagocytic cell and harassing conditions, they turn into a SCV, remaining sustainable for a long time. SCV is characterized by notable advantages such as (a) intracellular life that mediates a dam against immune cells and (b) low ATP production that mediates resistance against antibiotics.
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Samara E, Spyropoulou V, Tabard-Fougère A, Merlini L, Valaikaite R, Dhouib A, Manzano S, Juchler C, Dayer R, Ceroni D. Kingella kingae and Osteoarticular Infections. Pediatrics 2019; 144:peds.2019-1509. [PMID: 31722963 DOI: 10.1542/peds.2019-1509] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/12/2019] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES In this study, we aimed to contrast the bacteriologic epidemiology of osteoarticular infections (OAIs) between 2 patient groups in successive 10-year periods, before and after the extensive use of nucleic acid amplification assays in the diagnostic process. METHODS Epidemiologic data and bacteriologic etiologies of all children presenting with OAIs on admission to our institution over 20 years (1997-2016) were assessed retrospectively. The population was divided into 2 cohorts, using the standardized use of polymerase chain reaction as the cutoff point (2007). The conventional cohort included children with OAIs mainly investigated by using classic cultures, whereas the molecular cohort referred to patients also investigated by using molecular assays. RESULTS Kingella kingae was the most frequently isolated pathogen, responsible for 51% of OAIs, whereas other classic pathogens were responsible for 39.7% of cases in the molecular cohort. A statistically significant increase in the mean incidence of OAIs was observed, as was a decrease in the mean age at diagnosis after 2007. After 2007, the pathogen remained unidentified in 21.6% of OAIs in our pediatric population. CONCLUSIONS Extensive use of nucleic acid amplification assays improved the detection of fastidious pathogens and has increased the observed incidence of OAI, especially in children aged between 6 and 48 months. We propose the incorporation of polymerase chain reaction assays into modern diagnostic algorithms for OAIs to better identify the bacteriologic etiology of OAIs.
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Affiliation(s)
| | | | | | | | | | | | - Sergio Manzano
- Paediatric Emergency, Geneva University Hospitals, Geneva, Switzerland
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Osickova A, Balashova N, Masin J, Sulc M, Roderova J, Wald T, Brown AC, Koufos E, Chang EH, Giannakakis A, Lally ET, Osicka R. Cytotoxic activity of Kingella kingae RtxA toxin depends on post-translational acylation of lysine residues and cholesterol binding. Emerg Microbes Infect 2018; 7:178. [PMID: 30405113 PMCID: PMC6221878 DOI: 10.1038/s41426-018-0179-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 11/28/2022]
Abstract
Kingella kingae is a member of the commensal oropharyngeal flora of young children. Improvements in detection methods have led to the recognition of K. kingae as an emerging pathogen that frequently causes osteoarticular infections in children and a severe form of infective endocarditis in children and adults. Kingella kingae secretes a membrane-damaging RTX (Repeat in ToXin) toxin, RtxA, which is implicated in the development of clinical infections. However, the mechanism by which RtxA recognizes and kills host cells is largely unexplored. To facilitate structure-function studies of RtxA, we have developed a procedure for the overproduction and purification of milligram amounts of biologically active recombinant RtxA. Mass spectrometry analysis revealed the activation of RtxA by post-translational fatty acyl modification on the lysine residues 558 and/or 689 by the fatty-acyltransferase RtxC. Acylated RtxA was toxic to various human cells in a calcium-dependent manner and possessed pore-forming activity in planar lipid bilayers. Using various biochemical and biophysical approaches, we demonstrated that cholesterol facilitates the interaction of RtxA with artificial and cell membranes. The results of analyses using RtxA mutant variants suggested that the interaction between the toxin and cholesterol occurs via two cholesterol recognition/interaction amino acid consensus motifs located in the C-terminal portion of the pore-forming domain of the toxin. Based on our observations, we conclude that the cytotoxic activity of RtxA depends on post-translational acylation of the K558 and/or K689 residues and on the toxin binding to cholesterol in the membrane.
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Affiliation(s)
- Adriana Osickova
- Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Nataliya Balashova
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jiri Masin
- Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic
| | - Miroslav Sulc
- Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Jana Roderova
- Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic
| | - Tomas Wald
- Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic.,Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, CA, USA
| | - Angela C Brown
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA
| | - Evan Koufos
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA
| | - En Hyung Chang
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA
| | - Alexander Giannakakis
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.,The Department of Cell and Molecular Biology at Karolinska Institutet, Stockholm, Sweden
| | - Edward T Lally
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Radim Osicka
- Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic.
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