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Dombach JL, Christensen GL, Allgood SC, Quintana JLJ, Detweiler CS. Inhibition of multiple staphylococcal growth states by a small molecule that disrupts membrane fluidity and voltage. mSphere 2024; 9:e0077223. [PMID: 38445864 PMCID: PMC10964410 DOI: 10.1128/msphere.00772-23] [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: 12/12/2023] [Accepted: 01/26/2024] [Indexed: 03/07/2024] Open
Abstract
New molecular approaches to disrupting bacterial infections are needed. The bacterial cell membrane is an essential structure with diverse potential lipid and protein targets for antimicrobials. While rapid lysis of the bacterial cell membrane kills bacteria, lytic compounds are generally toxic to whole animals. In contrast, compounds that subtly damage the bacterial cell membrane could disable a microbe, facilitating pathogen clearance by the immune system with limited compound toxicity. A previously described small molecule, D66, terminates Salmonella enterica serotype Typhimurium (S. Typhimurium) infection of macrophages and reduces tissue colonization in mice. The compound dissipates bacterial inner membrane voltage without rapid cell lysis under broth conditions that permeabilize the outer membrane or disable efflux pumps. In standard media, the cell envelope protects Gram-negative bacteria from D66. We evaluated the activity of D66 in Gram-positive bacteria because their distinct envelope structure, specifically the absence of an outer membrane, could facilitate mechanism of action studies. We observed that D66 inhibited Gram-positive bacterial cell growth, rapidly increased Staphylococcus aureus membrane fluidity, and disrupted membrane voltage while barrier function remained intact. The compound also prevented planktonic staphylococcus from forming biofilms and a disturbed three-dimensional structure in 1-day-old biofilms. D66 furthermore reduced the survival of staphylococcal persister cells and of intracellular S. aureus. These data indicate that staphylococcal cells in multiple growth states germane to infection are susceptible to changes in lipid packing and membrane conductivity. Thus, agents that subtly damage bacterial cell membranes could have utility in preventing or treating disease.IMPORTANCEAn underutilized potential antibacterial target is the cell membrane, which supports or associates with approximately half of bacterial proteins and has a phospholipid makeup distinct from mammalian cell membranes. Previously, an experimental small molecule, D66, was shown to subtly damage Gram-negative bacterial cell membranes and to disrupt infection of mammalian cells. Here, we show that D66 increases the fluidity of Gram-positive bacterial cell membranes, dissipates membrane voltage, and inhibits the human pathogen Staphylococcus aureus in several infection-relevant growth states. Thus, compounds that cause membrane damage without lysing cells could be useful for mitigating infections caused by S. aureus.
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Affiliation(s)
- Jamie L. Dombach
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Grace L. Christensen
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Samual C. Allgood
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Joaquin L. J. Quintana
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Corrella S. Detweiler
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
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Perveen S, Negi A, Saini S, Gangwar A, Sharma R. Identification of Chemical Scaffolds Targeting Drug-Resistant and Latent Mycobacterium tuberculosis through High-Throughput Whole-Cell Screening. ACS Infect Dis 2024; 10:513-526. [PMID: 38238154 DOI: 10.1021/acsinfecdis.3c00463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Identification of structurally unique chemical entities targeting unexplored bacterial targets is a prerequisite to combat increasing drug resistance against Mycobacterium tuberculosis. This study employed a whole-cell screening approach as an initial filter to scrutinize a 10,000-compound chemical library, resulting in the discovery of seven potent compounds with MIC values ranging from 1.56 to 25 μM. These compounds were categorized into four distinct chemical groups. Remarkably, they demonstrated efficacy against drug-resistant and nonreplicating tuberculosis strains, highlighting their effectiveness across different infection states. With a favorable selectivity index (>10), these compounds showed a safe therapeutic range and exhibited potency in an intracellular model of Mtb infection, mimicking the in vivo setup. Combining these identified hits with established anti-TB drugs revealed additive effects with rifampicin, isoniazid, and bedaquiline. Notably, IIIM-IDD-01 exhibited synergy with isoniazid and bedaquiline, likely due to their complementary mechanisms of targeting Mtb. Most potent hits, IIIM-IDD-01 and IIIM-IDD-02, displayed time- and concentration-dependent killing of Mtb. Mechanistic insights were sought through SEM and docking studies, although comprehensive evaluation is ongoing to unravel the hits' specific targets and modes of action. The hits demonstrated favorable pharmacokinetic properties (ADME-Tox) and showed a low risk of adverse effects, along with a predicted high level of oral bioavailability. These promising hits can serve as an initial basis for subsequent medicinal chemistry endeavors aimed at developing a new series of anti-TB agents. Moreover, the study affirms the significance of high-throughput in vitro assays for the TB drug discovery. It also emphasizes the necessity of targeting diverse TB strains to address the heterogeneity of tuberculosis bacteria.
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Affiliation(s)
- Summaya Perveen
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anjali Negi
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sapna Saini
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anjali Gangwar
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rashmi Sharma
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Desenko SM, Gorobets MY, Lipson VV, Sakhno YI, Chebanov VA. Dihydroazolopyrimidines: Past, Present and Perspectives in Synthesis, Green Chemistry and Drug Discovery. CHEM REC 2024; 24:e202300244. [PMID: 37668291 DOI: 10.1002/tcr.202300244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/22/2023] [Indexed: 09/06/2023]
Abstract
Dihydroazolopyrimidines are an important class of heterocycles that are isosteric to natural purines and are therefore of great interest primarily as drug-like molecules. In contrast to the heteroaromatic analogs, synthetic approaches to these compounds were developed much later, and their chemical properties and biological activity have not been studied in detail until recently. In the review, different ways to build dihydroazolopyrimidine systems from different building blocks are described - via the initial formation of a partially hydrogenated pyrimidine ring or an azole ring, as well as a one-pot assembly of azole and azine fragments. Special attention is given to modern approaches: multicomponent reactions, green chemistry, and the use of non-classical activation methods. Information on the chemical properties of dihydroazolopyrimidines and the prospects for their use in the design of drugs of various profiles are also summarized in this review.
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Affiliation(s)
- Serhiy M Desenko
- Department of Organic and Bioorganic Chemistry, State Scientific Institution "Institute for Single Crystals" NAS of Ukraine, Nauky ave. 60, Kharkiv, Ukraine, 61072
| | - Mykola Yu Gorobets
- Department of Organic and Bioorganic Chemistry, State Scientific Institution "Institute for Single Crystals" NAS of Ukraine, Nauky ave. 60, Kharkiv, Ukraine, 61072
| | - Victoria V Lipson
- Department of Organic and Bioorganic Chemistry, State Scientific Institution "Institute for Single Crystals" NAS of Ukraine, Nauky ave. 60, Kharkiv, Ukraine, 61072
- Faculty of Chemistry, V.N. Karazin Kharkiv National University, Svobody sq. 4, Kharkiv, Ukraine, 61022
- Department of Medicinal Chemistry, State Institution "V. Ya. Danilevsky Institute for Endocrine Pathology Problems" NAMS of Ukraine, Alchevskikh St. 10, Kharkiv, Ukraine, 61002
| | - Yana I Sakhno
- Department of Organic and Bioorganic Chemistry, State Scientific Institution "Institute for Single Crystals" NAS of Ukraine, Nauky ave. 60, Kharkiv, Ukraine, 61072
| | - Valentyn A Chebanov
- Department of Organic and Bioorganic Chemistry, State Scientific Institution "Institute for Single Crystals" NAS of Ukraine, Nauky ave. 60, Kharkiv, Ukraine, 61072
- Faculty of Chemistry, V.N. Karazin Kharkiv National University, Svobody sq. 4, Kharkiv, Ukraine, 61022
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Zmyslia M, Fröhlich K, Dao T, Schmidt A, Jessen-Trefzer C. Deep Proteomic Investigation of Metabolic Adaptation in Mycobacteria under Different Growth Conditions. Proteomes 2023; 11:39. [PMID: 38133153 PMCID: PMC10747050 DOI: 10.3390/proteomes11040039] [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: 09/26/2023] [Revised: 11/22/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Understanding the complex mechanisms of mycobacterial pathophysiology and adaptive responses presents challenges that can hinder drug development. However, employing physiologically relevant conditions, such as those found in human macrophages or simulating physiological growth conditions, holds promise for more effective drug screening. A valuable tool in this pursuit is proteomics, which allows for a comprehensive analysis of adaptive responses. In our study, we focused on Mycobacterium smegmatis, a model organism closely related to the pathogenic Mycobacterium tuberculosis, to investigate the impact of various carbon sources on mycobacterial growth. To facilitate this research, we developed a cost-effective, straightforward, and high-quality pipeline for proteome analysis and compared six different carbon source conditions. Additionally, we have created an online tool to present and analyze our data, making it easily accessible to the community. This user-friendly platform allows researchers and interested parties to explore and interpret the results effectively. Our findings shed light on mycobacterial adaptive physiology and present potential targets for drug development, contributing to the fight against tuberculosis.
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Affiliation(s)
- Mariia Zmyslia
- Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; (M.Z.); (T.D.)
| | - Klemens Fröhlich
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland; (K.F.); (A.S.)
| | - Trinh Dao
- Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; (M.Z.); (T.D.)
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19A, 79104 Freiburg, Germany
- The Center for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland; (K.F.); (A.S.)
| | - Claudia Jessen-Trefzer
- Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; (M.Z.); (T.D.)
- The Center for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
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Ahmed S, Chowdhury S, Gomez J, Hung DT, Parish T. Benzene Amide Ether Scaffold is Active against Non-replicating and Intracellular Mycobacterium tuberculosis. ACS Infect Dis 2023; 9:1981-1992. [PMID: 37708378 PMCID: PMC10580325 DOI: 10.1021/acsinfecdis.3c00275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Indexed: 09/16/2023]
Abstract
New drugs to treat tuberculosis which target intractable bacterial populations are required to develop shorter and more effective treatment regimens. The benzene amide ether scaffold has activity against intracellular Mycobacterium tuberculosis, but low activity against extracellular, actively replicating M. tuberculosis. We determined that these molecules have bactericidal activity against non-replicating M. tuberculosis but not actively replicating bacteria. Exposure to compounds depleted ATP levels in non-replicating bacteria and increased the oxygen consumption rate; a subset of molecules led to the accumulation of intrabacterial reactive oxygen species. A comprehensive screen of M. tuberculosis strains identified a number of under-expressing strains as more sensitive to compounds under replicating conditions including QcrA and QcrB hypomorphs. We determined the global gene expression profile after compound treatment for both replicating and nutrient-starved M. tuberculosis. We saw compound-dependent changes in the expression of genes involved in energy metabolism under both conditions. Taken together, our data suggest that the scaffold targets respiration in M. tuberculosis.
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Affiliation(s)
- Sara Ahmed
- TB
Discovery Research, Infectious Disease Research
Institute, Seattle, Washington 98104, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Sultan Chowdhury
- TB
Discovery Research, Infectious Disease Research
Institute, Seattle, Washington 98104, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - James Gomez
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Deborah T. Hung
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Tanya Parish
- TB
Discovery Research, Infectious Disease Research
Institute, Seattle, Washington 98104, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
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Chemical Exploration of a Highly Selective Scaffold with Activity against Intracellular Mycobacterium tuberculosis. Microbiol Spectr 2022; 10:e0116122. [PMID: 35612308 PMCID: PMC9241686 DOI: 10.1128/spectrum.01161-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
We previously identified a phenylthiourea series with activity against intracellular Mycobacterium tuberculosis using a high-throughput, high-content assay. We conducted a catalog structure-activity relationship study with a collection of 35 analogs. We identified several thiourea derivatives with excellent potency against intracellular bacteria and good selectivity over eukaryotic cells. Compounds had much lower activity against extracellular bacteria, which was not increased by using cholesterol as the sole carbon source. Compounds were equally active against strains with mutations in QcrB or MmpL3, thereby excluding common, promiscuous targets as the mode of action. The phenylthiourea series represents a good starting point for further exploration to develop novel antitubercular agents. IMPORTANCEMycobacterium tuberculosis is responsible for the highest number of deaths from a bacterial pathogen, with >1.5 million in 2020. M. tuberculosis is a sophisticated pathogen that can replicate inside immune cells. There is an urgent need for new drugs to combat M. tuberculosis and to shorten therapy from 6 to 24 months. We have identified a series of molecules that inhibit the growth of M. tuberculosis inside macrophages; we tested a number of derivatives to link structural features to biological activity. The compounds are likely to have novel mechanism of action and so could be developed as new agents for drug-resistant tuberculosis.
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