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Rani N, Surolia A. Targeted suppression of MEP pathway genes DXS, IspD and IspF to explore the mycobacterial metabolism and survival. Int J Biol Macromol 2024; 272:132727. [PMID: 38823743 DOI: 10.1016/j.ijbiomac.2024.132727] [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: 12/13/2023] [Revised: 05/10/2024] [Accepted: 05/24/2024] [Indexed: 06/03/2024]
Abstract
Due to the uniqueness and essentiality of MEP pathway for the synthesis of crucial metabolites- isoprenoids, hopanoids, menaquinone etc. in mycobacterium, enzymes of this pathway are considered promising anti-tubercular drug targets. In the present study we seek to understand the consequences of downregulation of three of the essential genes- DXS, IspD, and IspF of MEP pathway using CRISPRi approach combined with transcriptomics in Mycobacterium smegmatis. Conditional knock down of either DXS or IspD or IspF gene showed strong bactericidal effect and a profound change in colony morphology. Impaired MEP pathway due to downregulation of these genes increased the susceptibility to frontline anti-tubercular drugs. Further, reduced EtBr accumulation in all the knock down strains in the presence and absence of efflux inhibitor indicated altered cell wall topology. Subsequently, transcriptional analysis validated by qRT-PCR of +154DXS, +128IspD, +104IspF strains showed that modifying the expression of these MEP pathway enzymes affects the regulation of mycobacterial core components. Among the DEGs, expression of small and large ribosomal binding proteins (rpsL, rpsJ, rplN, rplX, rplM, rplS, etc), essential protein translocases (secE, secY and infA, infC), transcriptional regulator (CarD and SigB) and metabolic enzymes (acpP, hydA, ald and fabD) were significantly depleted causing the bactericidal effect. However, mycobacteria survived under these damaging conditions by upregulating mostly the genes needed for the repair of DNA damage (DNA polymerase IV, dinB), synthesis of essential metabolites (serB, LeuA, atpD) and those strengthening the cell wall integrity (otsA, murA, D-alanyl-D-alanine dipeptidase etc.).
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Affiliation(s)
- Nidhi Rani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India; Dr.Reddy's Institute of Life Science, Hyderabad 500046, India.
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Manjunath P, Ahmad J, Samal J, Rani A, Sheikh JA, Zarin S, Ahuja Y, Alam A, Hasnain SE, Ehtesham NZ. Expression of a unique M. tuberculosis DNA MTase Rv1509 in M. smegmatis alters the gene expression pattern and enhances virulence. Front Microbiol 2024; 15:1344857. [PMID: 38803374 PMCID: PMC11129820 DOI: 10.3389/fmicb.2024.1344857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/15/2024] [Indexed: 05/29/2024] Open
Abstract
Mycobacterium tuberculosis (M. tb) genome encompasses 4,173 genes, about a quarter of which remain uncharacterized and hypothetical. Considering the current limitations associated with the diagnosis and treatment of tuberculosis, it is imperative to comprehend the pathomechanism of the disease and host-pathogen interactions to identify new drug targets for intervention strategies. Using in-silico comparative genome analysis, we identified one of the M. tb genes, Rv1509, as a signature protein exclusively present in M. tb. To explore the role of Rv1509, a likely methyl transferase, we constructed a knock-in Mycobacterium smegmatis (M. smegmatis) constitutively expressing Rv1509 (Ms_Rv1509). The Ms_Rv1509 led to differential expression of many transcriptional regulator genes as assessed by RNA-seq analysis. Further, in-vitro and in-vivo studies demonstrated an enhanced survival of Ms_Rv1509 inside the host macrophages. Ms_Rv1509 also promoted phagolysosomal escape inside macrophages to boost bacterial replication and dissemination. In-vivo infection studies revealed that Ms_Rv1509 survives better than BCG and causes pathological manifestations in the pancreas after intraperitoneal infection. Long-time survival of Ms_Rv1509 resulted in lymphocyte migration, increased T regulatory cells, giant cell formation, and likely granuloma formation in the pancreas, pointing toward the role of Rv1509 in M. tb pathogenesis.
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Affiliation(s)
- P. Manjunath
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India
- Department of Biotechnology, Jamia Hamdard, New Delhi, India
| | - Javeed Ahmad
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jasmine Samal
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India
| | - Anshu Rani
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
| | | | - Sheeba Zarin
- Department of Biotechnology, Jamia Hamdard, New Delhi, India
- Department of Life Science, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Yashika Ahuja
- Department of Life Science, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Anwar Alam
- Department of Biotechnology, Sharda School of Engineering Sciences and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Seyed E. Hasnain
- Department of Life Science, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Nasreen Z. Ehtesham
- Department of Life Science, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
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Zarin S, Shariq M, Rastogi N, Ahuja Y, Manjunath P, Alam A, Hasnain SE, Ehtesham NZ. Rv2231c, a unique histidinol phosphate aminotransferase from Mycobacterium tuberculosis, supports virulence by inhibiting host-directed defense. Cell Mol Life Sci 2024; 81:203. [PMID: 38698289 PMCID: PMC11065945 DOI: 10.1007/s00018-024-05200-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 02/02/2024] [Accepted: 03/04/2024] [Indexed: 05/05/2024]
Abstract
Nitrogen metabolism of M. tuberculosis is critical for its survival in infected host cells. M. tuberculosis has evolved sophisticated strategies to switch between de novo synthesis and uptake of various amino acids from host cells for metabolic demands. Pyridoxal phosphate-dependent histidinol phosphate aminotransferase-HspAT enzyme is critically required for histidine biosynthesis. HspAT is involved in metabolic synthesis of histidine, phenylalanine, tyrosine, tryptophan, and novobiocin. We showed that M. tuberculosis Rv2231c is a conserved enzyme with HspAT activity. Rv2231c is a monomeric globular protein that contains α-helices and β-sheets. It is a secretory and cell wall-localized protein that regulates critical pathogenic attributes. Rv2231c enhances the survival and virulence of recombinant M. smegmatis in infected RAW264.7 macrophage cells. Rv2231c is recognized by the TLR4 innate immune receptor and modulates the host immune response by suppressing the secretion of the antibacterial pro-inflammatory cytokines TNF, IL-12, and IL-6. It also inhibits the expression of co-stimulatory molecules CD80 and CD86 along with antigen presenting molecule MHC-I on macrophage and suppresses reactive nitrogen species formation, thereby promoting M2 macrophage polarization. Recombinant M. smegmatis expressing Rv2231c inhibited apoptosis in macrophages, promoting efficient bacterial survival and proliferation, thereby increasing virulence. Our results indicate that Rv2231c is a moonlighting protein that regulates multiple functions of M. tuberculosis pathophysiology to increase its virulence. These mechanistic insights can be used to better understand the pathogenesis of M. tuberculosis and to design strategies for tuberculosis mitigation.
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Affiliation(s)
- Sheeba Zarin
- Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, India
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, 201310, India
| | - Mohd Shariq
- Cell Signaling and Inflammation Biology Lab, ICMR-National Institute of Pathology, New Delhi, 110029, India
| | - Nilisha Rastogi
- Cell Signaling and Inflammation Biology Lab, ICMR-National Institute of Pathology, New Delhi, 110029, India
| | - Yashika Ahuja
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, 201310, India
| | - P Manjunath
- Cell Signaling and Inflammation Biology Lab, ICMR-National Institute of Pathology, New Delhi, 110029, India
| | - Anwar Alam
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, 201310, India
| | - Seyed Ehtesham Hasnain
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, 201310, India.
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, 110016, India.
| | - Nasreen Zafar Ehtesham
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, 201310, India.
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4
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Shenoy V, Gunda R, Noble C, Haraguchi A, Stevenson S, Daniel J. Fullertubes inhibit mycobacterial viability and prevent biofilm formation by disrupting the cell wall. Cell Biochem Funct 2024; 42:e3963. [PMID: 38424684 DOI: 10.1002/cbf.3963] [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: 09/21/2023] [Revised: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
Mycobacterium tuberculosis and nontuberculous mycobacteria such as Mycobacterium abscessus cause diseases that are becoming increasingly difficult to treat due to emerging antibiotic resistance. The development of new antimicrobial molecules is vital for combating these pathogens. Carbon nanomaterials (CNMs) are a class of carbon-containing nanoparticles with promising antimicrobial effects. Fullertubes (C90 ) are novel carbon allotropes with a structure unique among CNMs. The effects of fullertubes on any living cell have not been studied. In this study, we demonstrate that pristine fullertube dispersions show antimicrobial effects on Mycobacterium smegmatis and M. abscessus. Using scanning electron microscopy, light microscopy, and molecular probes, we investigated the effects of these CNMs on mycobacterial cell viability, cellular integrity, and biofilm formation. C90 fullertubes at 1 µM inhibited mycobacterial viability by 97%. Scanning electron microscopy revealed that the cell wall structure of M. smegmatis and M. abscessus was severely damaged within 24 h of exposure to fullertubes. Additionally, exposure to fullertubes nearly abrogated the acid-fast staining property of M. smegmatis. Using SYTO-9 and propidium iodide, we show that exposure to the novel fullertubes compromises the integrity of the mycobacterial cell. We also show that the permeability of the mycobacterial cell wall was increased after exposure to fullertubes from our assays utilizing the molecular probe dichlorofluorescein and ethidium bromide transport. C90 fullertubes at 0.37 µM and C60 fullerenes at 0.56 µM inhibited pellicle biofilm formation by 70% and 90%, respectively. This is the first report on the antimycobacterial activities of fullertubes and fullerenes.
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Affiliation(s)
- Varun Shenoy
- Department of Biological Sciences, Purdue University Fort Wayne, Fort Wayne, Indiana, USA
- Department of Chemistry and Biochemistry, Purdue University Fort Wayne, Fort Wayne, Indiana, USA
| | - Rashmika Gunda
- Department of Biological Sciences, Purdue University Fort Wayne, Fort Wayne, Indiana, USA
| | - Cora Noble
- Department of Chemistry and Biochemistry, Purdue University Fort Wayne, Fort Wayne, Indiana, USA
| | - Annalisa Haraguchi
- Department of Biological Sciences, Purdue University Fort Wayne, Fort Wayne, Indiana, USA
| | - Steven Stevenson
- Department of Chemistry and Biochemistry, Purdue University Fort Wayne, Fort Wayne, Indiana, USA
| | - Jaiyanth Daniel
- Department of Biological Sciences, Purdue University Fort Wayne, Fort Wayne, Indiana, USA
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Eldin ZE, Dishisha T, Sayed OM, Salama HM, Farghali A. A novel synergistic enzyme-antibiotic therapy with immobilization of mycobacteriophage Lysin B enzyme onto Rif@UiO-66 nanocomposite for enhanced inhaled anti-TB therapy; Nanoenzybiotics approach. Int J Biol Macromol 2024; 262:129675. [PMID: 38280693 DOI: 10.1016/j.ijbiomac.2024.129675] [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: 09/01/2023] [Revised: 01/01/2024] [Accepted: 01/20/2024] [Indexed: 01/29/2024]
Abstract
The emergence of antibiotic-resistant and phage-resistant strains of Mycobacterium tuberculosis (M. tuberculosis) necessitates improving new therapeutic plans. The objective of the current work was to ensure the effectiveness of rifampicin and the mycobacteriophage LysB D29 (LysB)enzyme in the treatment of multi-drug resistant tuberculosis (MDR-TB) infection, where new and safe metal-organic framework (MOF) nanoparticles were used in combination. UiO-66 nanoparticles were synthesized under mild conditions in which the antimycobacterial agent (rifampicin) was loaded (Rif@UiO-66) and LysB D29 enzyme immobilized onto Rif@UiO-66, which were further characterized. Subsequently, the antibacterial activity of different ratios of Rif@UiO-66 and LysB/Rif@uio-66 against the nonpathogenic tuberculosis model Mycobacterium smegmatis (M. smegmatis) was evaluated by minimum inhibitory concentration (MIC) tests. Impressively, the MIC of LysB/Rif@uio-66 was 16-fold lower than that of pure rifampicin. In vitro and in vivo toxicity studies proved that LysB/Rif@UiO-66 is a highly biocompatible therapy for pulmonary infection. A biodistribution assay showed that LysB/Rif@UiO-66 showed a 5.31-fold higher drug concentration in the lungs than free rifampicin. A synergistic interaction between UiO-66, rifampicin and the mycobacteriophage lysB D29 enzyme was shown in the computational method (docking). Therefore, all results indicated that the LysB/Rif@UiO-66 nanocomposite exhibited promising innovative enzyme-antibiotic therapy for tuberculosis treatment.
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Affiliation(s)
- Zienab E Eldin
- Materials Science and Nanotechnology Department, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, 62511 Beni-Suef, Egypt.
| | - Tarek Dishisha
- Department of Pharmaceutical Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, 62511 Beni-Suef, Egypt
| | - Ossama M Sayed
- Department of Pharmaceutics, Faculty of Pharmacy, Sinai University-Kantara Branch, Ismailia 41636, Egypt
| | - Hanaa M Salama
- Department of Chemistry, Faculty of Science, Port Said University, Port Said, Egypt
| | - Ahmed Farghali
- Materials Science and Nanotechnology Department, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, 62511 Beni-Suef, Egypt
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6
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Kumar N, Sharma S, Kaushal PS. Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH. Nat Commun 2024; 15:638. [PMID: 38245551 PMCID: PMC10799931 DOI: 10.1038/s41467-024-44879-y] [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: 06/02/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
Ribosome hibernation is a key survival strategy bacteria adopt under environmental stress, where a protein, hibernation promotion factor (HPF), transitorily inactivates the ribosome. Mycobacterium tuberculosis encounters hypoxia (low oxygen) as a major stress in the host macrophages, and upregulates the expression of RafH protein, which is crucial for its survival. The RafH, a dual domain HPF, an orthologue of bacterial long HPF (HPFlong), hibernates ribosome in 70S monosome form, whereas in other bacteria, the HPFlong induces 70S ribosome dimerization and hibernates its ribosome in 100S disome form. Here, we report the cryo- EM structure of M. smegmatis, a close homolog of M. tuberculosis, 70S ribosome in complex with the RafH factor at an overall 2.8 Å resolution. The N- terminus domain (NTD) of RafH binds to the decoding center, similarly to HPFlong NTD. In contrast, the C- terminus domain (CTD) of RafH, which is larger than the HPFlong CTD, binds to a distinct site at the platform binding center of the ribosomal small subunit. The two domain-connecting linker regions, which remain mostly disordered in earlier reported HPFlong structures, interact mainly with the anti-Shine Dalgarno sequence of the 16S rRNA.
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Affiliation(s)
- Niraj Kumar
- Structural Biology & Translation Regulation Laboratory, UNESCO-DBT, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121 001, India
| | - Shivani Sharma
- Structural Biology & Translation Regulation Laboratory, UNESCO-DBT, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121 001, India
| | - Prem S Kaushal
- Structural Biology & Translation Regulation Laboratory, UNESCO-DBT, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121 001, India.
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Andrés Libreros-Zúñiga G, Pavão E Pavão D, de Morais Barroso V, Cristina de Moraes Roso Mesquita N, Fehelberg Pinto Braga S, Oliva G, Salgado Ferreira R, Ishida K, Vinicius Bertacine Dias M. Integration of biophysical and biological approaches to validate fragment-like compounds targeting l,d-transpeptidases from Mycobacterium tuberculosis. Bioorg Chem 2024; 142:106960. [PMID: 37944368 DOI: 10.1016/j.bioorg.2023.106960] [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: 09/16/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Tuberculosis is one of the major causes of death worldwide; more than a million people die every year because of this infection. The constant emergency of Mycobacterium tuberculosis resistant strains against the most used treatments also contributes to the burden caused by this disease. Consequently, the development of new alternative therapies against this disease is constantly required. In recent years, only a few molecules have reached the market as new antituberculosis agents. The mycobacterial cell wall biosynthesis is for a longstanding considered an important target for drug development. Particularly, in M. tuberculosis, the peptidoglycan cross-links are predominantly formed by nonclassical bridges between the third residues of adjacent tetrapeptides. The responsible enzymes for these reactions are ld-transpeptidases (Ldts), for which M. tuberculosis has five paralogues. Although these enzymes are distinct from the penicillin-binding proteins (PBPs), they can also be inactivated by β-lactam antibiotics, but since M. tuberculosis has a chromosomal β-lactamase, most of the antibiotics of these classes can be degraded. Thus, to identify alternative scaffolds for the development of new antimicrobials against tuberculosis, we have integrated several fragment-based drug discovery techniques. Based on that, we identified and validated a number of small molecules that could be the starting point in the synthesis of more potent inhibitors against at least two Ldts from M. tuberculosis, LdtMt2 and LdtMt3. Eight identified molecules inhibited the Ldts activity in at least 20%, and three of them have antimycobacterial activity. The cell ultrastructural analysis suggested that one of the best compounds induced severe effects on the septum and cell wall morphologies, which corroborates our target-based approach to identifying new Ldts hits.
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Affiliation(s)
- Gerardo Andrés Libreros-Zúñiga
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil; IBILCE, São Paulo State University, Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo 15054-000, Brazil; Department of Microbiology, Faculty of Health, University of Valle, Calle 4B # 36-00, 760043, Cali, Valle del Cauca, Colombia.
| | - Danilo Pavão E Pavão
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil
| | - Vinicius de Morais Barroso
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil
| | | | - Saulo Fehelberg Pinto Braga
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais. Av. Antônio Carlos, 6627 - Belo Horizonte, 31270-901 Minas Gerais, Brazil
| | - Glaucius Oliva
- Institute of Physics of São Carlos, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, Brazil
| | - Rafaela Salgado Ferreira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais. Av. Antônio Carlos, 6627 - Belo Horizonte, 31270-901 Minas Gerais, Brazil
| | - Kelly Ishida
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil
| | - Marcio Vinicius Bertacine Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil; IBILCE, São Paulo State University, Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo 15054-000, Brazil; Department of Chemistry, University of Warwick, Coventry CV4 7AL, England.
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Zamakhaev M, Bespyatykh J, Goncharenko A, Shumkov M. The Benefits of Toxicity: M. smegmatis VapBC TA Module Is Induced by Tetracycline Exposure and Promotes Survival. Microorganisms 2023; 11:2863. [PMID: 38138007 PMCID: PMC10745673 DOI: 10.3390/microorganisms11122863] [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: 10/01/2023] [Revised: 11/15/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Toxin-antitoxin (TA) systems are widely present in bacterial genomes. Mycolicibacterium smegmatis, a common model organism for studying Mycobacterium tuberculosis physiology, has eight TA loci, including mazEF and vapBC. This study aims to investigate the physiological significance of these TA systems. Proteomic profiling was conducted on a culture overexpressing the VapC toxin, and the involvement of VapC in M. smegmatis stress responses to heat shock and antibiotic treatment was examined. While deciphering the underlying mechanisms of the altered stress resistance, we assessed the antibiotic susceptibility of vapBC, mazEF, and double vapBC-mazEF deletion mutants. Additionally, the mRNA levels of vapC and mazF were measured following tetracycline supplementation. The results reveal changes in the abundance of metabolic enzymes and stress response proteins associated with VapC overexpression. This activation of the general stress response leads to reduced thermosensitivity in M. smegmatis, but does not affect susceptibility to ciprofloxacin and isoniazid. Under tetracycline treatment, both vapC and mazF expression levels are increased, and the fate of the cell depends on the interaction between the corresponding TA systems.
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Affiliation(s)
- Mikhail Zamakhaev
- Federal Research Center Fundamentals of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., 119071 Moscow, Russia; (A.G.); (M.S.)
| | - Julia Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1A Malaya Pirogovskaya St., 119435 Moscow, Russia;
- Expertise Department in Anti-Doping and Drug Control, Mendeleev University of Chemical Technology of Russia, 9, Miusskaya Sq., 125047 Moscow, Russia
| | - Anna Goncharenko
- Federal Research Center Fundamentals of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., 119071 Moscow, Russia; (A.G.); (M.S.)
| | - Mikhail Shumkov
- Federal Research Center Fundamentals of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., 119071 Moscow, Russia; (A.G.); (M.S.)
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9
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Xia X. Horizontal Gene Transfer and Drug Resistance Involving Mycobacterium tuberculosis. Antibiotics (Basel) 2023; 12:1367. [PMID: 37760664 PMCID: PMC10526031 DOI: 10.3390/antibiotics12091367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/13/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) acquires drug resistance at a rate comparable to that of bacterial pathogens that replicate much faster and have a higher mutation rate. One explanation for this rapid acquisition of drug resistance in Mtb is that drug resistance may evolve in other fast-replicating mycobacteria and then be transferred to Mtb through horizontal gene transfer (HGT). This paper aims to address three questions. First, does HGT occur between Mtb and other mycobacterial species? Second, what genes after HGT tend to survive in the recipient genome? Third, does HGT contribute to antibiotic resistance in Mtb? I present a conceptual framework for detecting HGT and analyze 39 ribosomal protein genes, 23S and 16S ribosomal RNA genes, as well as several genes targeted by antibiotics against Mtb, from 43 genomes representing all major groups within Mycobacterium. I also included mgtC and the insertion sequence IS6110 that were previously reported to be involved in HGT. The insertion sequence IS6110 shows clearly that the Mtb complex participates in HGT. However, the horizontal transferability of genes depends on gene function, as was previously hypothesized. HGT is not observed in functionally important genes such as ribosomal protein genes, rRNA genes, and other genes chosen as drug targets. This pattern can be explained by differential selection against functionally important and unimportant genes after HGT. Functionally unimportant genes such as IS6110 are not strongly selected against, so HGT events involving such genes are visible. For functionally important genes, a horizontally transferred diverged homologue from a different species may not work as well as the native counterpart, so the HGT event involving such genes is strongly selected against and eliminated, rendering them invisible to us. In short, while HGT involving the Mtb complex occurs, antibiotic resistance in the Mtb complex arose from mutations in those drug-targeted genes within the Mtb complex and was not gained through HGT.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON K1N 9A7, Canada; ; Tel.: +1-613-562-5718
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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10
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Nayak T, Kakkar A, Singh RK, Jaiswal LK, Singh AK, Temple L, Gupta A. Isolation and characterization of a novel mycobacteriophage Kashi-VT1 infecting Mycobacterium species. Front Cell Infect Microbiol 2023; 13:1173894. [PMID: 37545854 PMCID: PMC10400892 DOI: 10.3389/fcimb.2023.1173894] [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: 02/28/2023] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
Mycobacteriophages are viruses that infect members of genus Mycobacterium. Because of the rise in antibiotic resistance in mycobacterial diseases such as tuberculosis, mycobacteriophages have received renewed attention as alternative therapeutic agents. Mycobacteriophages are highly diverse, and, on the basis of their genome sequences, they are grouped into 30 clusters and 10 singletons. In this article, we have described the isolation and characterization of a novel mycobacteriophage Kashi-VT1 (KVT1) infecting Mycobacterium >smegmatis mc2 155 (M. smegmatis) and Mycobacterium fortuitum isolated from Varanasi, India. KVT1 is a cluster K1 temperate phage that belongs to Siphoviridae family as visualized in transmission electron microscopy. The phage genome is 61,010 base pairs with 66.5% Guanine/Cytosine (GC) content, encoding 101 putative open reading frames. The KVT1 genome encodes an immunity repressor, a tyrosine integrase, and an excise protein, which are the characteristics of temperate phages. It also contains genes encoding holin, lysin A, and lysin B involved in host cell lysis. The one-step growth curve demonstrated that KVT1 has a latency time of 90 min and an average burst size of 101 phage particles per infected cell. It can withstand a temperature of up to 45°C and has a maximum viability between pH 8 and 9. Some mycobacteriophages from cluster K are known to infect the pathogenic Mycobacterium tuberculosis (M. tuberculosis); hence, KVT1 holds potential for the phage therapy against tuberculosis, and it can also be engineered to convert into an exclusively lytic phage.
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Affiliation(s)
- Tanmayee Nayak
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Anuja Kakkar
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Rakesh Kumar Singh
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Lav Kumar Jaiswal
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Anand Kumar Singh
- Interdisciplinary School of Life Sciences, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Louise Temple
- School of Integrated Sciences, James Madison University, Harrisonburg, VA, United States
| | - Ankush Gupta
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
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11
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Kurosu M, Mitachi K, Pershing EV, Horowitz BD, Wachter EA, Lacey JW, Ji Y, Rodrigues DJ. Antibacterial effect of rose bengal against colistin-resistant gram-negative bacteria. J Antibiot (Tokyo) 2023:10.1038/s41429-023-00622-1. [PMID: 37076631 DOI: 10.1038/s41429-023-00622-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/15/2023] [Accepted: 03/28/2023] [Indexed: 04/21/2023]
Abstract
Increasing drug resistance in Gram-negative bacteria presents significant health problems worldwide. Despite notable advances in the development of a new generation of β-lactams, aminoglycosides, and fluoroquinolones, it remains challenging to treat multi-drug resistant Gram-negative bacterial infections. Colistin (polymyxin E) is one of the most efficacious antibiotics for the treatment of multiple drug-resistant Gram-negative bacteria and has been used clinically as a last-resort option. However, the rapid spread of the transferable gene, mcr-1 which confers colistin resistance by encoding a phosphoethanolamine transferase that modifies lipid A of the bacterial membrane, threatens the efficacy of colistin for the treatment of drug-resistant bacterial infections. Colistin-resistant strains of Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae often reduce their susceptibility to other anti-Gram-negative bacterial agents. Thus, drugs effective against colistin-resistant strains or methods to prevent the acquisition of colistin-resistance during treatment are urgently needed. To perform cell-based screenings of the collected small molecules, we have generated colistin-resistant strains of E. coli, A. baumannii, K. pneumoniae, P. aeruginosa, and S. enterica Typhimurium. In-house MIC assay screenings, we have identified that rose bengal (4,5,6,7-tetrachloro-2',4',5',7'-tetraiodofluorescein) is the only molecule that displays unique bactericidal activity against these strains at low concentrations under illumination conditions. This article reports the antibacterial activity of a pharmaceutical-grade rose bengal against colistin-resistant Gram-negative bacteria.
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Affiliation(s)
- Michio Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN, 38163, USA.
| | - Katsuhiko Mitachi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN, 38163, USA
| | - Edward V Pershing
- Provectus Biopharmaceuticals, Inc., 800 S. Gay Street, Suite 1610, Knoxville, TN, 37929, USA
| | - Bruce D Horowitz
- Provectus Biopharmaceuticals, Inc., 800 S. Gay Street, Suite 1610, Knoxville, TN, 37929, USA
| | - Eric A Wachter
- Provectus Biopharmaceuticals, Inc., 800 S. Gay Street, Suite 1610, Knoxville, TN, 37929, USA
| | - John W Lacey
- Provectus Biopharmaceuticals, Inc., 800 S. Gay Street, Suite 1610, Knoxville, TN, 37929, USA
| | - Yinduo Ji
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 205 VSB, 1971 Commonwealth Avenue, St. Paul, MN, 55108, USA
| | - Dominic J Rodrigues
- Provectus Biopharmaceuticals, Inc., 800 S. Gay Street, Suite 1610, Knoxville, TN, 37929, USA
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12
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Lewtak K, Czaplewska P, Wydrych J, Keller R, Nowicka A, Skrzypiec K, Fiołka MJ. Antimycobacterial Activity of Sida hermaphrodita (L.) Rusby (Malvaceae) Seed Extract. Cells 2023; 12:cells12030397. [PMID: 36766739 PMCID: PMC9913413 DOI: 10.3390/cells12030397] [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: 12/19/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
The current prevalence of such lifestyle diseases as mycobacteriosis and tuberculosis is a result of the growing resistance of microorganisms to the available antibiotics and their significant toxicity. Therefore, plants can successfully become a source of new therapeutic agents. The aim of this study was to investigate the effect of protein extract from Sida hermaphrodita seeds on the morphology, structure, and viability of Mycobacterium smegmatis and to carry out proteomic characterization of the protein extract. The analyses were carried out using fluorescence and transmission microscopy, atomic force microscopy, and spectroscopy. The proteomic studies were performed using liquid chromatography coupled to tandem mass spectrometry. The studies showed that the seed extract applied at concentrations of 50-150 µg/mL exerted a statistically significant effect on M. smegmatis cells, that is, a reduction of the viability of the bacteria and induction of changes in the structure of the mycobacterial cell wall. Additionally, the SEM analysis confirmed that the extract did not have a cytotoxic or cytopathic effect on fibroblast cells. The proteomic analysis revealed the presence of structural, storage, and enzymatic proteins and peptides in the extract, which are typical for seeds. Proteins and peptides with antimicrobial activity identified as vicillins and lipid-transporting proteins were also determined in the protein profile of the extract.
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Affiliation(s)
- Kinga Lewtak
- Department of Cell Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
- Correspondence: (K.L.); (M.J.F.)
| | - Paulina Czaplewska
- Laboratory of Mass Spectrometry, Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Jerzy Wydrych
- Department of Functional Anatomy and Cytobiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Radosław Keller
- Analytical Laboratory, Institute of Chemical Sciences, Department of Chemistry, Maria Curie-Skłodowska University, Pl. M. Curie-Skłodowskiej 2, 20-031 Lublin, Poland
| | - Aldona Nowicka
- Analytical Laboratory, Institute of Chemical Sciences, Department of Chemistry, Maria Curie-Skłodowska University, Pl. M. Curie-Skłodowskiej 2, 20-031 Lublin, Poland
| | - Krzysztof Skrzypiec
- Analytical Laboratory, Institute of Chemical Sciences, Department of Chemistry, Maria Curie-Skłodowska University, Pl. M. Curie-Skłodowskiej 2, 20-031 Lublin, Poland
| | - Marta Julia Fiołka
- Department of Immunobiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
- Correspondence: (K.L.); (M.J.F.)
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13
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VapC toxin switches M. smegmatis cells into dormancy through 23S rRNA cleavage. Arch Microbiol 2023; 205:28. [DOI: 10.1007/s00203-022-03363-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/18/2022] [Accepted: 12/04/2022] [Indexed: 12/23/2022]
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14
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Jugreet BS, Lall N, Anina Lambrechts I, Reid AM, Maphutha J, Nel M, Hassan AH, Khalid A, Abdalla AN, Van BL, Mahomoodally MF. In Vitro and In Silico Pharmacological and Cosmeceutical Potential of Ten Essential Oils from Aromatic Medicinal Plants from the Mascarene Islands. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248705. [PMID: 36557842 PMCID: PMC9788324 DOI: 10.3390/molecules27248705] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/23/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
In this study, 10 essential oils (EOs), from nine plants (Cinnamomum camphora, Curcuma longa, Citrus aurantium, Morinda citrifolia, Petroselinum crispum, Plectranthus amboinicus, Pittosporum senacia, Syzygium coriaceum, and Syzygium samarangense) were assessed for their antimicrobial, antiaging and antiproliferative properties. While only S. coriaceum, P. amboinicus (MIC: 0.50 mg/mL) and M. citrifolia (MIC: 2 mg/mL) EOs showed activity against Cutibacterium acnes, all EOs except S. samarangense EO demonstrated activity against Mycobacterium smegmatis (MIC: 0.125-0.50 mg/mL). The EOs were either fungistatic or fungicidal against one or both tested Candida species with minimum inhibitory/fungicidal concentrations of 0.016-32 mg/mL. The EOs also inhibited one or both key enzymes involved in skin aging, elastase and collagenase (IC50: 89.22-459.2 µg/mL; 0.17-0.18 mg/mL, respectively). Turmerone, previously identified in the C. longa EO, showed the highest binding affinity with the enzymes (binding energy: -5.11 and -6.64 kcal/mol). Only C. aurantium leaf, C. longa, P. amboinicus, P. senacia, S. coriaceum, and S. samarangense EOs were cytotoxic to the human malignant melanoma cells, UCT-MEL1 (IC50: 88.91-277.25 µg/mL). All the EOs, except M. citrifolia EO, were also cytotoxic to the human keratinocytes non-tumorigenic cells, HaCat (IC50: 33.73-250.90 µg/mL). Altogether, some interesting therapeutic properties of the EOs of pharmacological/cosmeceutical interests were observed, which warrants further investigations.
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Affiliation(s)
- Bibi Sharmeen Jugreet
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Réduit 80837, Mauritius
| | - Namrita Lall
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria 0002, South Africa
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
- College of Pharmacy, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Isa Anina Lambrechts
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria 0002, South Africa
| | - Anna-Mari Reid
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria 0002, South Africa
| | - Jacqueline Maphutha
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria 0002, South Africa
| | - Marizé Nel
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria 0002, South Africa
| | - Abdallah H. Hassan
- Chemistry Department, College of Education, Salahaddin University, Erbil 44002, Iraq
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, Jazan 45142, Saudi Arabia
- Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, Khartoum P.O. Box 2404, Sudan
| | - Ashraf N. Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Bao Le Van
- Institute of Research and Development, Duy Tan University, Da Nang 550000, Vietnam
- Faculty of Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
- Correspondence:
| | - Mohamad Fawzi Mahomoodally
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Réduit 80837, Mauritius
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Institute of Medical and Technical Science, Saveetha Dental College, Chennai 600077, India
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa
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15
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Ang CW, Lee BM, Jackson CJ, Wang Y, Franzblau SG, Francisco AF, Kelly JM, Bernhardt PV, Tan L, West NP, Sykes ML, Hinton AO, Bolisetti R, Avery VM, Cooper MA, Blaskovich MA. Nitroimidazopyrazinones with Oral Activity against Tuberculosis and Chagas Disease in Mouse Models of Infection. J Med Chem 2022; 65:13125-13142. [DOI: 10.1021/acs.jmedchem.2c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chee Wei Ang
- Center for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
- School of Science, Monash University Malaysia, Subang Jaya, 47500 Selangor, Malaysia
| | - Brendon M. Lee
- Research School of Chemistry, Australian National University, Sullivans Creek Road, Acton ACT 2601, Australia
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10021, United States
| | - Colin J. Jackson
- Research School of Chemistry, Australian National University, Sullivans Creek Road, Acton ACT 2601, Australia
| | - Yuehong Wang
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Scott G. Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Amanda F. Francisco
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - John M. Kelly
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lendl Tan
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Nicholas P. West
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Melissa L. Sykes
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Queensland 4111, Australia
| | - Alexandra O. Hinton
- Center for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Raghu Bolisetti
- Center for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Vicky M. Avery
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Queensland 4111, Australia
- School of Environment and Science, Griffith University, Nathan, Queensland 4111, Australia
| | - Matthew A. Cooper
- Center for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mark A.T. Blaskovich
- Center for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
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16
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Arega AM, Dhal AK, Nayak S, Mahapatra RK. In silico and in vitro study of Mycobacterium tuberculosis H37Rv uncharacterized protein (RipD): an insight on tuberculosis therapeutics. J Mol Model 2022; 28:171. [PMID: 35624324 DOI: 10.1007/s00894-022-05148-1] [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: 05/06/2021] [Accepted: 05/06/2022] [Indexed: 11/29/2022]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis (Mtb) is responsible for the highest global health problem, with the deaths of millions of people. With prevalence of multiple drug resistance (MDR) strains and extended therapeutic times, it is important to discover small molecule inhibitors against novel hypothetical proteins of the pathogen. In this study, a virtual screening protocol was carried out against MtbH37Rv hypothetical protein RipD (Rv1566c) for the identification of potential small molecule inhibitors. The 3D model of the protein structure binding site was used for virtual screening (VS) of inhibitors from the Pathogen Box, followed by its validation through a molecular docking study. The stability of the protein-ligand complex was assessed using a 150 ns molecular dynamics simulation. MM-PBSA and MM-GBSA are the two approaches that were used to perform the trajectory analysis and determine the binding free energies, respectively. The ligand binding was observed to be stable across the entire time frame with an approximate binding free energy of -22.9916 kcal/mol. The drug-likeness of the inhibitors along with a potential anti-tuberculosis compound was validated by ADMET prediction software. Furthermore, a CFU inhibition assay was used to validate the best hit compound's in vitro inhibitory efficacy against a non-pathogenic Mycobacterium smegmatis MC2155 under low nutrient culture conditions. The study reported that the compound proposed in our study (Pathogen Box ID: MMV687700) will be useful for the identification of potential inhibitors against Mtb in future.
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Affiliation(s)
- Aregitu Mekuriaw Arega
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha, India.,National Veterinary Institute, Debre Zeit, Ethiopia
| | - Ajit Kumar Dhal
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha, India
| | - Sasmita Nayak
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha, India
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17
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Design, synthesis and antibacterial activity against pathogenic mycobacteria of conjugated hydroxamic acids, hydrazides and O-alkyl/O-acyl protected hydroxamic derivatives. Bioorg Med Chem Lett 2022; 64:128692. [PMID: 35307568 DOI: 10.1016/j.bmcl.2022.128692] [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: 10/24/2021] [Revised: 03/04/2022] [Accepted: 03/15/2022] [Indexed: 11/22/2022]
Abstract
With the aim to discover new antituberculous molecules, three novel series of 23 hydroxamic acids, 13 hydrazides, and 9O-alkyl/O-acyl protected hydroxamic acid derivatives have been synthesized, and fully characterized by spectral 1H NMR, 13C NMR, HRMS) analysis. These compounds were further biologically screened for their in vitro antibacterial activities against three pathogenic mycobacteria - M. abscessus S and R, M. marinum, and M. tuberculosis - as well as for their toxicity towards murine macrophages by the resazurin microtiter assay (REMA). Among the 45 derivatives, 17 compounds (3 hydroxamic acids, 9 hydrazides, and 5O-alkyl/O-acyl protected hydroxamic acids) were nontoxic against murine macrophages. When tested for their antibacterial activity, hydroxamic acid 9 h was found to be the most potent inhibitor against M. abscessus S and R only. Regarding hydrazide series, only 7h was active against M. abscessus R, M. marinum and M. tuberculosis; while the O-acyl protected hydroxamic acid derivatives 14d and 15d displayed promising antibacterial activity against both M. marinum and M. tuberculosis. Since such hydroxamic- and hydrazide-chelating groups have been reported to impair the activity of the peptide deformylase, in silico molecular docking studies in M. tuberculosis peptide deformylase enzyme active site were further performed with 7h in order to predict the possible interaction mode and binding energy of this molecule at the molecular level.
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18
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Tuyiringire N, Taremwa Mugisha I, Tusubira D, Munyampundu JP, Mambo Muvunyi C, Vander Heyden Y. In vitro antimycobacterial activity of medicinal plants Lantana camara, Cryptolepis sanguinolenta, and Zanthoxylum leprieurii. J Clin Tuberc Other Mycobact Dis 2022; 27:100307. [PMID: 35284659 PMCID: PMC8904236 DOI: 10.1016/j.jctube.2022.100307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Imperative need exists to search for new anti-TB drugs that are safer, and more effective against drug-resistant strains. Medicinal plants have been the source of active ingredients for drug development. However, the slow growth and biosafety level requirements of M. tuberculosis culture are considerable challenges. M. smegmatis can be used as a surrogate for M. tuberculosis. In the current study, preliminary phytochemical screening and antimycobacterial activity evaluation of crude methanolic extracts of medicinal plants against M. smegmatis, and two M. tuberculosis strains, were conducted. Materials and Methods Crude methanolic extracts, obtained from the leaves of L. camara, roots of C. sanguinolenta, and stem barks of Z. leprieurii, were tested for antimycobacterial activity against M. smegmatis (mc2155), pan-sensitive (H37Rv), and rifampicin-resistant (TMC-331) M. tuberculosis, using visual Resazurin Microtiter Assay (REMA) on 96 well plates. Preliminary qualitative phytochemical screening tests were performed using standard chemical methods. Results The three methanolic extracts inhibited mycobacterial growth in vitro. They were more active against rifampicin-resistant strain with MICs of 176, 97, and 45 µg/mL for L. camara, C. sanguinolenta, and Z. leprieurii extracts, respectively. The lowest activity was observed against M. smegmatis with MICs of 574, 325, and 520 µg/mL, respectively. Against H37Rv, activity was intermediate to those of TMC-331 and mc2155. However, L. camara extract showed the same activity against H37Rv and M. smegmatis. Preliminary phytochemical analysis revealed alkaloids, flavonoids, phenolic compounds, saponins, tannins, and terpenoids. Conclusions Leaves of L. camara, roots of C. sanguinolenta, and stem barks of Z. leprieurii exhibit antimycobacterial activity against M. smegmatis, pan-sensitive, and rifampicin-resistant M. tuberculosis. This offers the possibilities for novel therapeutic opportunities against TB including multidrug-resistant TB. Further investigations on safety and mechanisms of action are required. These studies could be done using M. smegmatis as a surrogate for the highly pathogenic M. tuberculosis.
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Affiliation(s)
- Naasson Tuyiringire
- Pharm-BioTechnology and Traditional Medicine Centre (PHARMBIOTRAC), Department of Pharmacy, Mbarara University of Science & Technology, P. O. Box 1410, Mbarara, Uganda
- School of Nursing and Midwifery, College of Medicine and Health Sciences, University of Rwanda, KG11 Ave, 47St/P.O. Box 3286, Kigali, Rwanda
- Corresponding author.
| | - Ivan Taremwa Mugisha
- Institute of Applied Health Sciences, Clarke International University, P.O. Box 7782, Kampala, Uganda
| | - Deusdedit Tusubira
- Department of Biochemistry, Mbarara University of Science and Technology, P. O. Box 1410, Mbarara, Uganda
| | - Jean-Pierre Munyampundu
- School of Science, College of Science and Technology, University of Rwanda, KN 67 Street Nyarugenge, P.O. Box 3900, Kigali, Rwanda
| | - Claude Mambo Muvunyi
- College of Medicine and Health Sciences, University of Rwanda, KG11 Ave, 47St/P.O. Box 3286, Kigali, Rwanda
| | - Yvan Vander Heyden
- Department of Analytical Chemistry, Applied Chemometrics and Molecular Modelling, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, Belgium
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19
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Structure-activity relationship of 2-aminodibenzothiophene pharmacophore and the discovery of aminobenzothiophenes as potent inhibitors of Mycobacterium smegmatis. Bioorg Med Chem Lett 2022; 63:128650. [PMID: 35245664 DOI: 10.1016/j.bmcl.2022.128650] [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: 11/02/2021] [Revised: 02/21/2022] [Accepted: 02/27/2022] [Indexed: 11/24/2022]
Abstract
Tuberculosis (TB) is one of the deadliest infectious diseases worldwide and its current treatments have been complicated with the emergence of multi-drug resistant (MDR-TB) and extensively drug-resistant (XDR-TB) strains. Therefore, the discovery of new antitubercular agents is in need to overcome this problem. In our efforts to discover novel candidates for the treatment of tuberculosis, we describe in this work in vitro activityagainstM. smegmatis for a series of aminated benzo-fused heterocycles, particularly, dibenzothiophene to explore the structure-activity relationship of 2-aminodibenzothiophene 3aa. From these studies, three compounds 5-aminobenzothiophene 3ia, 6-aminobenzothiophene 3ma (MIC: 0.78 µg/mL) and 5-aminobenzofuran 3ja (MIC: 1.56 µg/mL) were identified as potent inhibitors of M. smegmatis with low cytotoxicity. These results suggested the significance of these compounds 3ia, 3ja and 3ma for the future development of candidate agents to treat tuberculosis.
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20
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Inactivation of a New Potassium Channel Increases Rifampicin Resistance and Induces Collateral Sensitivity to Hydrophilic Antibiotics in Mycobacterium smegmatis. Antibiotics (Basel) 2022; 11:antibiotics11040509. [PMID: 35453260 PMCID: PMC9025972 DOI: 10.3390/antibiotics11040509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 12/10/2022] Open
Abstract
Rifampicin is a critical first-line antibiotic for treating mycobacterial infections such as tuberculosis, one of the most serious infectious diseases worldwide. Rifampicin resistance in mycobacteria is mainly caused by mutations in the rpoB gene; however, some rifampicin-resistant strains showed no rpoB mutations. Therefore, alternative mechanisms must explain this resistance in mycobacteria. In this work, a library of 11,000 Mycobacterium smegmatis mc2 155 insertion mutants was explored to search and characterize new rifampicin-resistance determinants. A transposon insertion in the MSMEG_1945 gene modified the growth rate, pH homeostasis and membrane potential in M. smegmatis, producing rifampicin resistance and collateral susceptibility to other antitubercular drugs such as isoniazid, ethionamide and aminoglycosides. Our data suggest that the M. smegmatis MSMEG_1945 protein is an ion channel, dubbed MchK, essential for maintaining the cellular ionic balance and membrane potential, modulating susceptibility to antimycobacterial agents. The functions of this new gene point once again to potassium homeostasis impairment as a proxy to resistance to rifampicin. This study increases the known repertoire of mycobacterial ion channels involved in drug susceptibility/resistance to antimycobacterial drugs and suggests novel intervention opportunities, highlighting ion channels as druggable pathways.
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21
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Antibacterial and Sporicidal Activity Evaluation of Theaflavin-3,3'-digallate. Int J Mol Sci 2022; 23:ijms23042153. [PMID: 35216265 PMCID: PMC8877948 DOI: 10.3390/ijms23042153] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 02/04/2023] Open
Abstract
Theaflavin-3,3'-digallate (TFDG), a polyphenol derived from the leaves of Camellia sinensis, is known to have many health benefits. In this study, the antibacterial effect of TFDG against nine bacteria and the sporicidal activities on spore-forming Bacillus spp. have been investigated. Microplate assay, colony-forming unit, BacTiter-GloTM, and Live/Dead Assays showed that 250 µg/mL TFDG was able to inhibit bacterial growth up to 99.97%, while 625 µg/mL TFDG was able to inhibit up to 99.92% of the spores from germinating after a one-hour treatment. Binding analysis revealed the favorable binding affinity of two germination-associated proteins, GPR and Lgt (GerF), to TFDG, ranging from -7.6 to -10.3 kcal/mol. Semi-quantitative RT-PCR showed that TFDG treatment lowered the expression of gpr, ranging from 0.20 to 0.39 compared to the control in both Bacillus spp. The results suggest that TFDG not only inhibits the growth of vegetative cells but also prevents the germination of bacterial spores. This report indicates that TFDG is a promising broad-spectrum antibacterial and anti-spore agent against Gram-positive, Gram-negative, acid-fast bacteria, and endospores. The potential anti-germination mechanism has also been elucidated.
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22
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Shin S, Kwon S, Yeo Y. Meta-Analysis of Drug Delivery Approaches for Treating Intracellular Infections. Pharm Res 2022; 39:1085-1114. [PMID: 35146592 PMCID: PMC8830998 DOI: 10.1007/s11095-022-03188-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/01/2022] [Indexed: 12/20/2022]
Abstract
This meta-analysis aims to evaluate the trend, methodological quality and completeness of studies on intracellular delivery of antimicrobial agents. PubMed, Embase, and reference lists of related reviews were searched to identify original articles that evaluated carrier-mediated intracellular delivery and pharmacodynamics (PD) of antimicrobial therapeutics against intracellular pathogens in vitro and/or in vivo. A total of 99 studies were included in the analysis. The most commonly targeted intracellular pathogens were bacteria (62.6%), followed by viruses (16.2%) and parasites (15.2%). Twenty-one out of 99 (21.2%) studies performed neither microscopic imaging nor flow cytometric analysis to verify that the carrier particles are present in the infected cells. Only 31.3% of studies provided comparative inhibitory concentrations against a free drug control. Approximately 8% of studies, albeit claimed for intracellular delivery of antimicrobial therapeutics, did not provide any experimental data such as microscopic imaging, flow cytometry, and in vitro PD. Future research on intracellular delivery of antimicrobial agents needs to improve the methodological quality and completeness of supporting data in order to facilitate clinical translation of intracellular delivery platforms for antimicrobial therapeutics.
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Affiliation(s)
- Sooyoung Shin
- College of Pharmacy, Ajou University, Suwon, Gyeonggi-do, 16499, Republic of Korea. .,Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, Gyeonggi-do, 16499, Republic of Korea.
| | - Soonbum Kwon
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47906, USA
| | - Yoon Yeo
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47906, USA. .,Weldon School of Biomedical Engineering, Purdue University, 206 S Martin Jischke Dr., West Lafayette, IN, 47907, USA.
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In Silico Drug Repurposing Approach: Investigation of Mycobacterium tuberculosis FadD32 Targeted by FDA-Approved Drugs. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030668. [PMID: 35163931 PMCID: PMC8840176 DOI: 10.3390/molecules27030668] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/27/2021] [Accepted: 01/09/2022] [Indexed: 12/17/2022]
Abstract
Background: Despite the enormous efforts made towards combating tuberculosis (TB), the disease remains a major global threat. Hence, new drugs with novel mechanisms against TB are urgently needed. Fatty acid degradation protein D32 (FadD32) has been identified as a promising drug target against TB, the protein is required for the biosynthesis of mycolic acids, hence, essential for the growth and multiplication of the mycobacterium. However, the FadD32 mechanism upon the binding of FDA-approved drugs is not well established. Herein, we applied virtual screening (VS), molecular docking, and molecular dynamic (MD) simulation to identify potential FDA-approved drugs against FadD32. Methodology/Results: VS technique was found promising to identify four FDA-approved drugs (accolate, sorafenib, mefloquine, and loperamide) with higher molecular docking scores, ranging from -8.0 to -10.0 kcal/mol. Post-MD analysis showed that the accolate hit displayed the highest total binding energy of -45.13 kcal/mol. Results also showed that the accolate hit formed more interactions with FadD32 active site residues and all active site residues displayed an increase in total binding contribution. RMSD, RMSF, Rg, and DCCM analysis further supported that the presence of accolate exhibited more structural stability, lower bimolecular flexibility, and more compactness into the FadD32 protein. Conclusions: Our study revealed accolate as the best potential drug against FadD32, hence a prospective anti-TB drug in TB therapy. In addition, we believe that the approach presented in the current study will serve as a cornerstone to identifying new potential inhibitors against a wide range of biological targets.
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Kurosu M, Mitachi K, Yang J, Pershing EV, Horowitz BD, Wachter EA, Lacey JW, Ji Y, Rodrigues DJ. Antibacterial Activity of Pharmaceutical-Grade Rose Bengal: An Application of a Synthetic Dye in Antibacterial Therapies. Molecules 2022; 27:322. [PMID: 35011554 PMCID: PMC8746496 DOI: 10.3390/molecules27010322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/21/2021] [Accepted: 12/27/2021] [Indexed: 11/27/2022] Open
Abstract
Rose bengal has been used in the diagnosis of ophthalmic disorders and liver function, and has been studied for the treatment of solid tumor cancers. To date, the antibacterial activity of rose bengal has been sporadically reported; however, these data have been generated with a commercial grade of rose bengal, which contains major uncontrolled impurities generated by the manufacturing process (80-95% dye content). A high-purity form of rose bengal formulation (HP-RBf, >99.5% dye content) kills a battery of Gram-positive bacteria, including drug-resistant strains at low concentrations (0.01-3.13 μg/mL) under fluorescent, LED, and natural light in a few minutes. Significantly, HP-RBf effectively eradicates Gram-positive bacterial biofilms. The frequency that Gram-positive bacteria spontaneously developed resistance to HP-RB is extremely low (less than 1 × 10-13). Toxicity data obtained through our research programs indicate that HP-RB is feasible as an anti-infective drug for the treatment of skin and soft tissue infections (SSTIs) involving multidrug-resistant (MDR) microbial invasion of the skin, and for eradicating biofilms. This article summarizes the antibacterial activity of pharmaceutical-grade rose bengal, HP-RB, against Gram-positive bacteria, its cytotoxicity against skin cells under illumination conditions, and mechanistic insights into rose bengal's bactericidal activity under dark conditions.
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Affiliation(s)
- Michio Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA;
| | - Katsuhiko Mitachi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA;
| | - Junshu Yang
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 205 VSB, 1971 Commonwealth Avenue, Saint Paul, MN 55108, USA; (J.Y.); (Y.J.)
| | - Edward V. Pershing
- Provectus Biopharmaceuticals, Inc., 10025 Investment Drive, Suite 250, Knoxville, TN 37932, USA; (E.V.P.); (B.D.H.); (E.A.W.); (J.W.L.III); (D.J.R.)
| | - Bruce D. Horowitz
- Provectus Biopharmaceuticals, Inc., 10025 Investment Drive, Suite 250, Knoxville, TN 37932, USA; (E.V.P.); (B.D.H.); (E.A.W.); (J.W.L.III); (D.J.R.)
| | - Eric A. Wachter
- Provectus Biopharmaceuticals, Inc., 10025 Investment Drive, Suite 250, Knoxville, TN 37932, USA; (E.V.P.); (B.D.H.); (E.A.W.); (J.W.L.III); (D.J.R.)
| | - John W. Lacey
- Provectus Biopharmaceuticals, Inc., 10025 Investment Drive, Suite 250, Knoxville, TN 37932, USA; (E.V.P.); (B.D.H.); (E.A.W.); (J.W.L.III); (D.J.R.)
| | - Yinduo Ji
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 205 VSB, 1971 Commonwealth Avenue, Saint Paul, MN 55108, USA; (J.Y.); (Y.J.)
| | - Dominic J. Rodrigues
- Provectus Biopharmaceuticals, Inc., 10025 Investment Drive, Suite 250, Knoxville, TN 37932, USA; (E.V.P.); (B.D.H.); (E.A.W.); (J.W.L.III); (D.J.R.)
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Kopiasz RJ, Zabost A, Myszka M, Kuźmińska A, Drężek K, Mierzejewska J, Tomaszewski W, Iwańska A, Augustynowicz-Kopeć E, Ciach T, Jańczewski D. Main-chain flexibility and hydrophobicity of ionenes strongly impact their antimicrobial activity: an extended study on drug resistance strains and Mycobacterium. RSC Adv 2022; 12:26220-26232. [PMID: 36275090 PMCID: PMC9477016 DOI: 10.1039/d2ra04121a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/30/2022] [Indexed: 11/22/2022] Open
Abstract
The spread of antibiotic-resistant pathogens and the resurgence of tuberculosis disease are major motivations to search for novel antimicrobial agents. Some promising candidates in this respect are cationic polymers, also known as synthetic mimics of antimicrobial peptides (SMAMPs), which act through the membrane-lytic mechanism. Development of resistance toward SMAMPs is less likely than toward currently employed antibiotics; however, further studies are needed to better understand their structure–activity relationship. The main objective of this work is to understand the cross-influence of hydrophobicity, main-chain flexibility, and the topology of ionenes (polycations containing a cationic moiety within the main-chain) on activity. To fulfill this goal, a library of ionenes was developed and compared with previously investigated molecules. The obtained compounds display promising activity against the model microorganisms and drug-resistance clinical isolates, including Mycobacterium tuberculosis. The killing efficiency was also investigated, and results confirm a strong effect of hydrophobicity, revealing higher activity for molecules possessing the flexible linker within the polymer main-chain. A high significance of the main chain flexibility and an unexpected effect of hydrophobicity on the biological activity in series of ionenes was observed. The most potent among the tested polycations showed high activity toward clinical bacterial isolates.![]()
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Affiliation(s)
- Rafał Jerzy Kopiasz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, Warsaw 00-664, Poland
| | - Anna Zabost
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Płocka 26, Warsaw 01-138, Poland
| | - Magdalena Myszka
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, Warsaw 00-664, Poland
| | - Aleksandra Kuźmińska
- Faculty of Chemical and Process Engineering, Warsaw University of Technology, Waryńskiego 1, Warsaw 00-645, Poland
| | - Karolina Drężek
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, Warsaw 00-664, Poland
| | - Jolanta Mierzejewska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, Warsaw 00-664, Poland
| | - Waldemar Tomaszewski
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, Warsaw 00-664, Poland
| | - Agnieszka Iwańska
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Płocka 26, Warsaw 01-138, Poland
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Płocka 26, Warsaw 01-138, Poland
| | - Tomasz Ciach
- Faculty of Chemical and Process Engineering, Warsaw University of Technology, Waryńskiego 1, Warsaw 00-645, Poland
| | - Dominik Jańczewski
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, Warsaw 00-664, Poland
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Green RM, Bicker KL. Discovery and Characterization of a Rapidly Fungicidal and Minimally Toxic Peptoid against Cryptococcus neoformans. ACS Med Chem Lett 2021; 12:1470-1477. [PMID: 34531956 DOI: 10.1021/acsmedchemlett.1c00327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/20/2021] [Indexed: 01/20/2023] Open
Abstract
A limited number of antifungals are available to treat infections caused by fungal pathogens such as Cryptococcus neoformans and Candida albicans. Current clinical antifungals are generally toxic, and increasing resistance to these therapies is being observed, necessitating new, effective, and safe antifungals. Peptoids, or N-substituted glycines, have shown promise as antimicrobial agents against bacteria, fungi, and parasites. Herein we report the discovery and characterization of an antifungal peptoid termed RMG8-8. This compound was originally discovered from a combinatorial peptoid library using the Peptoid Library Agar Diffusion assay to screen against C. albicans. Though the efficacy of RMG8-8 against C. albicans was modest (25 μg/mL), the efficacy against C. neoformans was excellent (1.56 μg/mL). Cytotoxicity against a panel of cell lines proved RMG8-8 to be minimally toxic, with selectivity ratios ranging from 34 to 121. Additional studies were carried out to determine the pharmacological importance of each peptoid monomer in RMG8-8, characterize the killing kinetics of this compound against C. neoformans (t 1/2 = 6.5 min), and evaluate plasma protein binding and proteolytic stability. Finally, a liposomal lysis assay suggested that RMG8-8 likely exerts fungal killing through membrane permeabilization, the generally accepted mechanism of action for most antimicrobial peptides and peptoids.
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Affiliation(s)
- R. Madison Green
- Department of Chemistry, Middle Tennessee State University, 1301 E. Main St., Murfreesboro, Tennessee 37132, United States
| | - Kevin L. Bicker
- Department of Chemistry, Middle Tennessee State University, 1301 E. Main St., Murfreesboro, Tennessee 37132, United States
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Yamazaki H. Exploration of marine natural resources in Indonesia and development of efficient strategies for the production of microbial halogenated metabolites. J Nat Med 2021; 76:1-19. [PMID: 34415546 PMCID: PMC8732978 DOI: 10.1007/s11418-021-01557-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 07/29/2021] [Indexed: 11/12/2022]
Abstract
Nature is a prolific source of organic products with diverse scaffolds and biological activities. The process of natural product discovery has gradually become more challenging, and advances in novel strategic approaches are essential to evolve natural product chemistry. Our focus has been on surveying untouched marine resources and fermentation to enhance microbial productive performance. The first topic is the screening of marine natural products isolated from Indonesian marine organisms for new types of bioactive compounds, such as antineoplastics, antimycobacterium substances, and inhibitors of protein tyrosine phosphatase 1B, sterol O-acyl-transferase, and bone morphogenetic protein-induced osteoblastic differentiation. The unique biological properties of marine organohalides are discussed herein and attempts to efficiently produce fungal halogenated metabolites are documented. This review presents an overview of our recent work accomplishments based on the MONOTORI study.
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Affiliation(s)
- Hiroyuki Yamazaki
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, 981-8558, Japan.
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Kumar N, Sharma S, Kaushal PS. Protein synthesis in Mycobacterium tuberculosis as a potential target for therapeutic interventions. Mol Aspects Med 2021; 81:101002. [PMID: 34344520 DOI: 10.1016/j.mam.2021.101002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 07/11/2021] [Accepted: 07/16/2021] [Indexed: 12/18/2022]
Abstract
Mycobacterium tuberculosis (Mtb) causes one of humankind's deadliest diseases, tuberculosis. Mtb protein synthesis machinery possesses several unique species-specific features, including its ribosome that carries two mycobacterial specific ribosomal proteins, bL37 and bS22, and ribosomal RNA segments. Since the protein synthesis is a vital cellular process that occurs on the ribosome, a detailed knowledge of the structure and function of mycobacterial ribosomes is essential to understand the cell's proteome by translation regulation. Like in many bacterial species such as Bacillus subtilis and Streptomyces coelicolor, two distinct populations of ribosomes have been identified in Mtb. Under low-zinc conditions, Mtb ribosomal proteins S14, S18, L28, and L33 are replaced with their non-zinc binding paralogues. Depending upon the nature of physiological stress, species-specific modulation of translation by stress factors and toxins that interact with the ribosome have been reported. In addition, about one-fourth of messenger RNAs in mycobacteria have been reported to be leaderless, i.e., without 5' UTR regions. However, the mechanism by which they are recruited to the Mtb ribosome is not understood. In this review, we highlight the mycobacteria-specific features of the translation apparatus and propose exploiting these features to improve the efficacy and specificity of existing antibiotics used to treat tuberculosis.
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Affiliation(s)
- Niraj Kumar
- Structural Biology & Translation Regulation Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121 001, India
| | - Shivani Sharma
- Structural Biology & Translation Regulation Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121 001, India
| | - Prem S Kaushal
- Structural Biology & Translation Regulation Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121 001, India.
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Sakallioglu IT, Barletta RG, Dussault PH, Powers R. Deciphering the mechanism of action of antitubercular compounds with metabolomics. Comput Struct Biotechnol J 2021; 19:4284-4299. [PMID: 34429848 PMCID: PMC8358470 DOI: 10.1016/j.csbj.2021.07.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 01/08/2023] Open
Abstract
Tuberculosis (TB), one of the oldest and deadliest bacterial diseases, continues to cause serious global economic, health, and social problems. Current TB treatments are lengthy, expensive, and routinely ineffective against emerging drug resistant strains. Thus, there is an urgent need for the identification and development of novel TB drugs possessing comprehensive and specific mechanisms of action (MoAs). Metabolomics is a valuable approach to elucidating the MoA, toxicity, and potency of promising chemical leads, which is a critical step of the drug discovery process. Recent advances in metabolomics methodologies for deciphering MoAs include high-throughput screening techniques, the integration of multiple omics methods, mass spectrometry imaging, and software for automated analysis. This review describes recently introduced metabolomics methodologies and techniques for drug discovery, highlighting specific applications to the discovery of new antitubercular drugs and the elucidation of their MoAs.
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Affiliation(s)
- Isin T. Sakallioglu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Raúl G. Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska Lincoln, Lincoln, NE 68583-0905, USA
| | - Patrick H. Dussault
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
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Evaluation of the Antimicrobial Effect of the Extracts of the Pods of Piliostigma thonningii (Schumach.) Milne-Redh. (Fabaceae). Adv Pharmacol Pharm Sci 2021; 2021:6616133. [PMID: 33629066 PMCID: PMC7896843 DOI: 10.1155/2021/6616133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/12/2021] [Accepted: 01/30/2021] [Indexed: 11/17/2022] Open
Abstract
Plants have been used traditionally by people in treating and the management of diseases since time immemorial. Traditional medicines including the herbal medicines are used for primary healthcare in some domains in almost every country. Approximately 80% of the population in developing coutries depend on plants as their source of medicine for combating diseases. New and effective antimicrobial agents that have novel mechanism of actions are required. Piliostigma thonningii (Schumach.) Milne-Redh. is a species of flowering plants in the legume family, Fabaceae. Different parts of the P. thonningii plants such as the roots, leaves, seeds, and fruits have been used in treating wounds, heart pain, and gingivitis and as cough remedy. This study focused on determining the antimicrobial properties found in the pods of P. thonningii. The sample was prepared by grinding the dried pods into a fine powder. Successive extraction and extraction with 1 : 1 DCM: methanol was used. The antimicrobial assay was carried out using the broth microdilution and MTT assay. The microorganism used for the tests was Pseudomonas aeruginosa, Candida krusei and Mycobacterium smegmatis. The most potent extract was then used to determine its effect on microbial cell membrane integrity. The results showed that methanol extract had the highest percentage yield of 5%. The extract with the highest antimicrobial effects was ethanol extract with the 100 μg/mL concentration inhibiting the growth of cells to 26%, 87%, and 90% for P. aeruginosa, M. smegmatis, and C. krusei, respectively. The ethanol extracts caused significant leakage of proteins in these microorganisms. In conclusion, the pods of P. thonningii contain phytochemicals with antimicrobial properties. The pods of the plant can be a source of phytochemicals that can serve as sources of lead compounds with antimicrobial effects. One of the mechanisms of action of these phytochemicals is via membrane-damaging effects on microbes.
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Minias A, Żukowska L, Lechowicz E, Gąsior F, Knast A, Podlewska S, Zygała D, Dziadek J. Early Drug Development and Evaluation of Putative Antitubercular Compounds in the -Omics Era. Front Microbiol 2021; 11:618168. [PMID: 33603720 PMCID: PMC7884339 DOI: 10.3389/fmicb.2020.618168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/30/2020] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis. According to the WHO, the disease is one of the top 10 causes of death of people worldwide. Mycobacterium tuberculosis is an intracellular pathogen with an unusually thick, waxy cell wall and a complex life cycle. These factors, combined with M. tuberculosis ability to enter prolonged periods of latency, make the bacterium very difficult to eradicate. The standard treatment of TB requires 6-20months, depending on the drug susceptibility of the infecting strain. The need to take cocktails of antibiotics to treat tuberculosis effectively and the emergence of drug-resistant strains prompts the need to search for new antitubercular compounds. This review provides a perspective on how modern -omic technologies facilitate the drug discovery process for tuberculosis treatment. We discuss how methods of DNA and RNA sequencing, proteomics, and genetic manipulation of organisms increase our understanding of mechanisms of action of antibiotics and allow the evaluation of drugs. We explore the utility of mathematical modeling and modern computational analysis for the drug discovery process. Finally, we summarize how -omic technologies contribute to our understanding of the emergence of drug resistance.
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Affiliation(s)
- Alina Minias
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Lidia Żukowska
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- BioMedChem Doctoral School of the University of Lodz and the Institutes of the Polish Academy of Sciences in Lodz, Lodz, Poland
| | - Ewelina Lechowicz
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Filip Gąsior
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- BioMedChem Doctoral School of the University of Lodz and the Institutes of the Polish Academy of Sciences in Lodz, Lodz, Poland
| | - Agnieszka Knast
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Sabina Podlewska
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Krakow, Poland
- Maj Institute of Pharmacology, Polish Academy of Sciences, Krakow, Poland
| | - Daria Zygała
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
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Bespyatykh J, Bespiatykh D, Malakhova M, Klimina K, Bespyatykh A, Varizhuk A, Tevyashova A, Nikolenko T, Pozmogova G, Ilina E, Shitikov E. Aureolic Acid Group of Agents as Potential Antituberculosis Drugs. Antibiotics (Basel) 2020; 9:E715. [PMID: 33086595 PMCID: PMC7650759 DOI: 10.3390/antibiotics9100715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium tuberculosis is one of the most dangerous pathogens. Bacterial resistance to antituberculosis drugs grows each year, but searching for new drugs is a long process. Testing for available drugs to find active against mycobacteria may be a good alternative. In this work, antibiotics of the aureolic acid group were tested on a model organism Mycobacterium smegmatis. We presumed that antibiotics of this group may be potential G4 ligands. However, this was not confirmed in our analyses. We determined the antimicrobial activity of these drugs and revealed morphological changes in the cell structure upon treatment. Transcriptomic analysis documented increased expression of MSMEG_3743/soj and MSMEG_4228/ftsW, involved in cell division. Therefore, drugs may affect cell division, possibly disrupting the function of the Z-ring and the formation of a septum. Additionally, a decrease in the transcription level of several indispensable genes, such as nitrate reductase subunits (MSMEG_5137/narI and MSMEG_5139/narX) and MSMEG_3205/hisD was shown. We concluded that the mechanism of action of aureolic acid and its related compounds may be similar to that bedaquiline and disturb the NAD+/NADH balance in the cell. All of this allowed us to conclude that aureolic acid derivatives can be considered as potential antituberculosis drugs.
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Affiliation(s)
- Julia Bespyatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Dmitry Bespiatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Maja Malakhova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Ksenia Klimina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Andrey Bespyatykh
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia;
| | - Anna Varizhuk
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | | | - Tatiana Nikolenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700 Moscow, Russia
| | - Galina Pozmogova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Elena Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Egor Shitikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
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