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Khan MA, Amin A, Farid A, Ullah A, Waris A, Shinwari K, Hussain Y, Alsharif KF, Alzahrani KJ, Khan H. Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines. Pharmaceutics 2022; 15:pharmaceutics15010152. [PMID: 36678781 PMCID: PMC9863128 DOI: 10.3390/pharmaceutics15010152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023] Open
Abstract
Infectious diseases continue to be a leading cause of morbidity and mortality worldwide. The majority of infectious diseases are caused by intracellular pathogenic bacteria (IPB). Historically, conventional vaccination drives have helped control the pathogenesis of intracellular bacteria and the emergence of antimicrobial resistance, saving millions of lives. However, in light of various limitations, many diseases that involve IPB still do not have adequate vaccines. In response to increasing demand for novel vaccine development strategies, a new area of vaccine research emerged following the advent of genomics technology, which changed the paradigm of vaccine development by utilizing the complete genomic data of microorganisms against them. It became possible to identify genes related to disease virulence, genetic patterns linked to disease virulence, as well as the genetic components that supported immunity and favorable vaccine responses. Complete genomic databases, and advancements in transcriptomics, metabolomics, structural genomics, proteomics, immunomics, pan-genomics, synthetic genomics, and population biology have allowed researchers to identify potential vaccine candidates and predict their effects in patients. New vaccines have been created against diseases for which previously there were no vaccines available, and existing vaccines have been improved. This review highlights the key issues and explores the evolution of vaccines. The increasing volume of IPB genomic data, and their application in novel genome-based techniques for vaccine development, were also examined, along with their characteristics, and the opportunities and obstacles involved. Critically, the application of genomics technology has helped researchers rapidly select and evaluate candidate antigens. Novel vaccines capable of addressing the limitations associated with conventional vaccines have been developed and pressing healthcare issues are being addressed.
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Affiliation(s)
- Muhammad Ajmal Khan
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- Correspondence: (M.A.K.); or (H.K.)
| | - Aftab Amin
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Awais Farid
- Division of Environment and Sustainability, Hong Kong University of Science and Technology, Hong Kong, China
| | - Amin Ullah
- Molecular Virology Laboratory, Department of Microbiology and Biotechnology, Abasyn University, Peshawar 25000, Pakistan
| | - Abdul Waris
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Khyber Shinwari
- Institute of Chemical Engineering, Department Immuno-Chemistry, Ural Federal University, Yekaterinbiurg 620002, Russia
| | - Yaseen Hussain
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Khalaf F. Alsharif
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Khalid J. Alzahrani
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Haroon Khan
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Correspondence: (M.A.K.); or (H.K.)
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A New Kind of Quinonic-Antibiotic Useful Against Multidrug-Resistant S. aureus and E. faecium Infections. Molecules 2018; 23:molecules23071776. [PMID: 30029513 PMCID: PMC6100241 DOI: 10.3390/molecules23071776] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/11/2018] [Accepted: 07/17/2018] [Indexed: 01/21/2023] Open
Abstract
A rapid emergence of resistant bacteria is occurring worldwide, endangering the efficacy of antibiotics and reducing the therapeutic arsenal available for treatment of infectious diseases. In the present study, we developed a new class of compounds with antibacterial activity obtained by a simple, two step synthesis and screened the products for in vitro antibacterial activity against ATCC® strains using the broth microdilution method. The compounds exhibited minimum inhibitory concentrations (MIC) of 1⁻32 μg/mL against Gram-positive ATCC® strains. The structure⁻activity relationship indicated that the thiophenol ring is essential for antibacterial activity and the substituents on the thiophenol ring module, for antibacterial activity. The most promising compounds detected by screening were tested against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VREF) clinical isolates. We found remarkable activity against VREF for compounds 7 and 16, were the MIC50/90 were 2/4 µg/mL and 4/4 µg/mL, respectively, while for vancomycin the MIC50/90 was 256/512 µg/mL. Neither compound affected cell viability in any of the mammalian cell lines at any of the concentrations tested. These in vitro data show that compounds 7 and 16 have an interesting potential to be developed as new antibacterial drugs against infections caused by VREF.
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Small Molecules That Sabotage Bacterial Virulence. Trends Pharmacol Sci 2017; 38:339-362. [PMID: 28209403 DOI: 10.1016/j.tips.2017.01.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/01/2017] [Accepted: 01/06/2017] [Indexed: 02/08/2023]
Abstract
The continued rise of antibiotic-resistant bacterial infections has motivated alternative strategies for target discovery and treatment of infections. Antivirulence therapies function through inhibition of in vivo required virulence factors to disarm the pathogen instead of directly targeting viability or growth. This approach to treating bacteria-mediated diseases may have advantages over traditional antibiotics because it targets factors specific for pathogenesis, potentially reducing selection for resistance and limiting collateral damage to the resident microbiota. This review examines vulnerable molecular mechanisms used by bacteria to cause disease and the antivirulence compounds that sabotage these virulence pathways. By expanding the study of antimicrobial targets beyond those that are essential for growth, antivirulence strategies offer new and innovative opportunities to combat infectious diseases.
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Salunke SB, Azad AK, Kapuriya NP, Balada-Llasat JM, Pancholi P, Schlesinger LS, Chen CS. Design and synthesis of novel anti-tuberculosis agents from the celecoxib pharmacophore. Bioorg Med Chem 2015; 23:1935-43. [PMID: 25818768 DOI: 10.1016/j.bmc.2015.03.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/03/2015] [Accepted: 03/15/2015] [Indexed: 11/15/2022]
Abstract
The identification of compounds with anti-mycobacterial activity within classes of molecules that have been developed for other purposes is a fruitful approach for the development of anti-tuberculosis (TB) agents. In this study we used the scaffold of celecoxib which exhibits several activities against different pathogens, for the design and focused synthesis of a library of 64 compounds. For the primary screen, we used a bioluminescence-based method by constructing a luciferase-expressing reporter M.tb strain which contains the entire bacterial Lux operon cloned in a mycobacterial integrative expression vector. Through the screening of this library, we identified 6 hit compounds with high in vitro anti-mycobacterial activity (IC₅₀ ∼0.18-0.48 μM). In particular, compounds 41, 51 and 53 were capable of inhibiting M.tb as effectively as the anti-TB drug isoniazid (INH) at 5 μM over a 72-h period, as analyzed by both bioluminescence- and colony forming unit (CFU)-based assays. All hit compounds also showed anti-M.tb activities against several multi-drug-resistant (MDR) strains. Most of the hit compounds showed no cytotoxicity for human macrophages at concentrations as high as 40 μM, setting the stage for further optimization and development of these anti-TB hit compounds both ex vivo and in vivo.
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Affiliation(s)
- Santosh B Salunke
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, United States
| | - Abul K Azad
- Center for Microbial Interface Biology, The Ohio State University, 460 W 12th Avenue, Columbus, OH 43210, United States; Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Wexner Medical Center, 460 W 12th Avenue, Columbus, OH 43210, United States
| | - Naval P Kapuriya
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, United States; Division of Pharmaceutical and Organic Chemistry, M. & N. Virani Science College, Saurashtra University, Rajkot 360005, Gujarat, India
| | - Joan-Miquel Balada-Llasat
- Department of Pathology, The Ohio State University, 410 W. 10th Avenue, Columbus, OH 43210, United States
| | - Preeti Pancholi
- Department of Pathology, The Ohio State University, 410 W. 10th Avenue, Columbus, OH 43210, United States
| | - Larry S Schlesinger
- Center for Microbial Interface Biology, The Ohio State University, 460 W 12th Avenue, Columbus, OH 43210, United States; Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Wexner Medical Center, 460 W 12th Avenue, Columbus, OH 43210, United States.
| | - Ching-Shih Chen
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, United States; Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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Cozzone AJ. An insight into future antibacterial therapy. Emerg Microbes Infect 2012; 1:e38. [PMID: 26038407 PMCID: PMC3636425 DOI: 10.1038/emi.2012.35] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 08/06/2012] [Accepted: 09/17/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Alain J Cozzone
- Institute of Biology and Chemistry of Proteins, University of Lyon, 7 passage du Vercors , 69007 Lyon, France
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Abstract
PURPOSE OF REVIEW Giardiasis is one of the most common causes of diarrheal disease worldwide, yet existing antimicrobial therapies are not always effective and drug resistance occurs in vivo and in vitro. The review focuses on recent advances in the development of new antigiardial drug candidates. RECENT FINDINGS Modification of existing drug leads is a major strategy to develop new high-potency drugs. Complex derivatives of 5-nitroimidazole, the core structure of the most commonly used antigiardial drug, metronidazole, have shown significantly improved activities against Giardia and the ability to overcome metronidazole resistance. Derivatives of benzimidazole, the structural core of the effective antigiardial albendazole, are also exhibiting promising new activities. Beyond lead modifications, several new classes of antigiardial drug candidates have recently been identified by high-throughput screening of large compound libraries, and first efforts have been reported on the development of drugs tailored to known molecular targets in Giardia. SUMMARY The pipeline of new antigiardial drug candidates has significantly expanded over the last few years, but this expansion has so far not been accompanied by demonstration of efficacy in animal models or by a clear understanding of the action mechanisms, particularly in regard to new nitro antimicrobials. Many challenges are still to be expected before clinical utility of new antigiardial drugs can be established.
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Wecke T, Mascher T. Antibiotic research in the age of omics: from expression profiles to interspecies communication. J Antimicrob Chemother 2011; 66:2689-704. [DOI: 10.1093/jac/dkr373] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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Harris F, Pierpoint L. Photodynamic therapy based on 5-aminolevulinic acid and its use as an antimicrobial agent. Med Res Rev 2011; 32:1292-327. [PMID: 21793017 DOI: 10.1002/med.20251] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Exogenous 5-aminolevulinic acid (ALA) is taken up directly by bacteria, yeasts, fungi, and some parasites, which then induces the accumulation of protoporphyrin IX (PPIX). Subsequent light irradiation of PPIX leads to the inactivation of these organisms via photodamage to their cellular structures. ALA uptake and light irradiation of PPIX produced by host cells leads to the inactivation of other parasites, along with some viruses, via the induction of an immune response. ALA-mediated PPIX production by host cells and light irradiation result in the inactivation of other viruses via either the induction of a host cell response or direct photodynamic attack on viral particles. This ALA-mediated production of light-activated PPIX has been extensively used as a form of photodynamic therapy (PDT) and has shown varying levels of efficacy in treating conditions that are associated with microbial infection, ranging from acne and verrucae to leishmaniasis and onychomycosis. However, for the treatment of some of these conditions by ALA-based PDT, the role of an antimicrobial effect has been disputed and in general, the mechanisms by which the technique inactivates microbes are not well understood. In this study, we review current understanding of the antimicrobial mechanisms used by ALA-based PDT and its role in the treatment of microbial infections along with its potential medical and nonmedical applications.
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Affiliation(s)
- Frederick Harris
- School of Forensic and Investigative Sciences, University of Central Lancashire, Preston, Lancashire, United Kingdom. fharris1@.ac.uk
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Miller CH, O'Toole RF. Navigating tuberculosis drug discovery with target-based screening. Expert Opin Drug Discov 2011; 6:839-54. [DOI: 10.1517/17460441.2011.586999] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Dötsch A, Klawonn F, Jarek M, Scharfe M, Blöcker H, Häussler S. Evolutionary conservation of essential and highly expressed genes in Pseudomonas aeruginosa. BMC Genomics 2010; 11:234. [PMID: 20380691 PMCID: PMC2864246 DOI: 10.1186/1471-2164-11-234] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Accepted: 04/09/2010] [Indexed: 11/26/2022] Open
Abstract
Background The constant increase in development and spread of bacterial resistance to antibiotics poses a serious threat to human health. New sequencing technologies are now on the horizon that will yield massive increases in our capacity for DNA sequencing and will revolutionize the drug discovery process. Since essential genes are promising novel antibiotic targets, the prediction of gene essentiality based on genomic information has become a major focus. Results In this study we demonstrate that pooled sequencing is applicable for the analysis of sequence variations of strain collections with more than 10 individual isolates. Pooled sequencing of 36 clinical Pseudomonas aeruginosa isolates revealed that essential and highly expressed proteins evolve at lower rates, whereas extracellular proteins evolve at higher rates. We furthermore refined the list of experimentally essential P. aeruginosa genes, and identified 980 genes that show no sequence variation at all. Among the conserved nonessential genes we found several that are involved in regulation, motility and virulence, indicating that they represent factors of evolutionary importance for the lifestyle of a successful environmental bacterium and opportunistic pathogen. Conclusion The detailed analysis of a comprehensive set of P. aeruginosa genomes in this study clearly disclosed detailed information of the genomic makeup and revealed a large set of highly conserved genes that play an important role for the lifestyle of this microorganism. Sequencing strain collections enables for a detailed and extensive identification of sequence variations as potential bacterial adaptation processes, e.g., during the development of antibiotic resistance in the clinical setting and thus may be the basis to uncover putative targets for novel treatment strategies.
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Affiliation(s)
- Andreas Dötsch
- Chronic Pseudomonas Infections Research Group, Helmholtz-Center for Infection Research, Braunschweig, Germany
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Antibiotic sensitivity profiles determined with an Escherichia coli gene knockout collection: generating an antibiotic bar code. Antimicrob Agents Chemother 2010; 54:1393-403. [PMID: 20065048 DOI: 10.1128/aac.00906-09] [Citation(s) in RCA: 216] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We have defined a sensitivity profile for 22 antibiotics by extending previous work testing the entire KEIO collection of close to 4,000 single-gene knockouts in Escherichia coli for increased susceptibility to 1 of 14 different antibiotics (ciprofloxacin, rifampin [rifampicin], vancomycin, ampicillin, sulfamethoxazole, gentamicin, metronidazole, streptomycin, fusidic acid, tetracycline, chloramphenicol, nitrofurantoin, erythromycin, and triclosan). We screened one or more subinhibitory concentrations of each antibiotic, generating more than 80,000 data points and allowing a reduction of the entire collection to a set of 283 strains that display significantly increased sensitivity to at least one of the antibiotics. We used this reduced set of strains to determine a profile for eight additional antibiotics (spectinomycin, cephradine, aztreonem, colistin, neomycin, enoxacin, tobramycin, and cefoxitin). The profiles for the 22 antibiotics represent a growing catalog of sensitivity fingerprints that can be separated into two components, multidrug-resistant mutants and those mutants that confer relatively specific sensitivity to the antibiotic or type of antibiotic tested. The latter group can be represented by a set of 20 to 60 strains that can be used for the rapid typing of antibiotics by generating a virtual bar code readout of the specific sensitivities. Taken together, these data reveal the complexity of intrinsic resistance and provide additional targets for the design of codrugs (or combinations of drugs) that potentiate existing antibiotics.
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Abstract
It can be argued that the arrival of the “genomics era” has significantly shifted the paradigm of vaccine and therapeutics development from microbiological to sequence-based approaches. Genome sequences provide a previously unattainable route to investigate the mechanisms that underpin pathogenesis. Genomics, transcriptomics, metabolomics, structural genomics, proteomics, and immunomics are being exploited to perfect the identification of targets, to design new vaccines and drugs, and to predict their effects in patients. Furthermore, human genomics and related studies are providing insights into aspects of host biology that are important in infectious disease. This ever-growing body of genomic data and new genome-based approaches will play a critical role in the future to enable timely development of vaccines and therapeutics to control emerging infectious diseases.
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A class of selective antibacterials derived from a protein kinase inhibitor pharmacophore. Proc Natl Acad Sci U S A 2009; 106:1737-42. [PMID: 19164768 DOI: 10.1073/pnas.0811275106] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As the need for novel antibiotic classes to combat bacterial drug resistance increases, the paucity of leads resulting from target-based antibacterial screening of pharmaceutical compound libraries is of major concern. One explanation for this lack of success is that antibacterial screening efforts have not leveraged the eukaryotic bias resulting from more extensive chemistry efforts targeting eukaryotic gene families such as G protein-coupled receptors and protein kinases. Consistent with a focus on antibacterial target space resembling these eukaryotic targets, we used whole-cell screening to identify a series of antibacterial pyridopyrimidines derived from a protein kinase inhibitor pharmacophore. In bacteria, the pyridopyrimidines target the ATP-binding site of biotin carboxylase (BC), which catalyzes the first enzymatic step of fatty acid biosynthesis. These inhibitors are effective in vitro and in vivo against fastidious gram-negative pathogens including Haemophilus influenzae. Although the BC active site has architectural similarity to those of eukaryotic protein kinases, inhibitor binding to the BC ATP-binding site is distinct from the protein kinase-binding mode, such that the inhibitors are selective for bacterial BC. In summary, we have discovered a promising class of potent antibacterials with a previously undescribed mechanism of action. In consideration of the eukaryotic bias of pharmaceutical libraries, our findings also suggest that pursuit of a novel inhibitor leads for antibacterial targets with active-site structural similarity to known human targets will likely be more fruitful than the traditional focus on unique bacterial target space, particularly when structure-based and computational methodologies are applied to ensure bacterial selectivity.
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