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Jeon G, Kim S, Kim YJ, Kim S, Han K, Oh K, Lee HJ, Choi J. Identification of fluoroquinolone-resistant Mycobacterium tuberculosis through high-level data fusion of Raman and laser-induced breakdown spectroscopy. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 39221494 DOI: 10.1039/d4ay01331j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Accurate and rapid diagnosis of drug susceptibility of Mycobacterium tuberculosis is crucial for the successful treatment of tuberculosis, a persistent global public health threat. To shorten diagnosis times and enhance accuracy, this study introduces a fusion model combining laser-induced breakdown spectroscopy (LIBS) and Raman spectroscopy. This model offers a rapid and accurate method for diagnosing drug-resistance. LIBS and Raman spectroscopy provide complementary information, enabling accurate identification of drug resistance in tuberculosis. Although individual use of LIBS or Raman spectroscopy achieved approximately 90% accuracy in identifying drug resistance, the fusion model significantly improved identification accuracy to 98.3%. Given the fast measurement capabilities of both techniques, this fusion approach is expected to markedly decrease the time required for diagnosis.
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Affiliation(s)
- Gookseon Jeon
- Industrial Transformation Technology Department, Research Institute of Sustainable Development Technology, Korea Institute of Industrial Technology, 89, Yangdaegiro-gil, Ipjang-myeon, Seobuk-gu, Cheonan-Si, Chungcheongnam-do 31056, Republic of Korea.
- Photonic Device Physics Laboratory, Institute of Physics and Applied Physics, Yonsei University, 50, Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Soogeun Kim
- Advanced Photonics Research Institute (APRI), Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Young Jin Kim
- Department of Laboratory Medicine, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul, Republic of Korea
| | - Seungmo Kim
- Laboratory Medicine Center, Korean National Tuberculosis Association, The Korean Institute of Tuberculosis, Cheongju, Republic of Korea
| | - Kyungmin Han
- Clinical Laboratory Medicine Center, Korean National Tuberculosis Association, Seoul, Republic of Korea.
| | - Kyunghwan Oh
- Photonic Device Physics Laboratory, Institute of Physics and Applied Physics, Yonsei University, 50, Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hee Joo Lee
- Clinical Laboratory Medicine Center, Korean National Tuberculosis Association, Seoul, Republic of Korea.
| | - Janghee Choi
- Industrial Transformation Technology Department, Research Institute of Sustainable Development Technology, Korea Institute of Industrial Technology, 89, Yangdaegiro-gil, Ipjang-myeon, Seobuk-gu, Cheonan-Si, Chungcheongnam-do 31056, Republic of Korea.
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2
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Kotev M, Diaz Gonzalez C. Molecular Dynamics and Other HPC Simulations for Drug Discovery. Methods Mol Biol 2024; 2716:265-291. [PMID: 37702944 DOI: 10.1007/978-1-0716-3449-3_12] [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: 09/14/2023]
Abstract
High performance computing (HPC) is taking an increasingly important place in drug discovery. It makes possible the simulation of complex biochemical systems with high precision in a short time, thanks to the use of sophisticated algorithms. It promotes the advancement of knowledge in fields that are inaccessible or difficult to access through experimentation and it contributes to accelerating the discovery of drugs for unmet medical needs while reducing costs. Herein, we report how computational performance has evolved over the past years, and then we detail three domains where HPC is essential. Molecular dynamics (MD) is commonly used to explore the flexibility of proteins, thus generating a better understanding of different possible approaches to modulate their activity. Modeling and simulation of biopolymer complexes enables the study of protein-protein interactions (PPI) in healthy and disease states, thus helping the identification of targets of pharmacological interest. Virtual screening (VS) also benefits from HPC to predict in a short time, among millions or billions of virtual chemical compounds, the best potential ligands that will be tested in relevant assays to start a rational drug design process.
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Affiliation(s)
- Martin Kotev
- Evotec SE, Integrated Drug Discovery, Molecular Architects, Campus Curie, Toulouse, France
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Rosconi F, Rudmann E, Li J, Surujon D, Anthony J, Frank M, Jones DS, Rock C, Rosch JW, Johnston CD, van Opijnen T. A bacterial pan-genome makes gene essentiality strain-dependent and evolvable. Nat Microbiol 2022; 7:1580-1592. [PMID: 36097170 PMCID: PMC9519441 DOI: 10.1038/s41564-022-01208-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/21/2022] [Indexed: 11/09/2022]
Abstract
Many bacterial species are represented by a pan-genome, whose genetic repertoire far outstrips that of any single bacterial genome. Here we investigate how a bacterial pan-genome might influence gene essentiality and whether essential genes that are initially critical for the survival of an organism can evolve to become non-essential. By using Transposon insertion sequencing (Tn-seq), whole-genome sequencing and RNA-seq on a set of 36 clinical Streptococcus pneumoniae strains representative of >68% of the species' pan-genome, we identify a species-wide 'essentialome' that can be subdivided into universal, core strain-specific and accessory essential genes. By employing 'forced-evolution experiments', we show that specific genetic changes allow bacteria to bypass essentiality. Moreover, by untangling several genetic mechanisms, we show that gene essentiality can be highly influenced by and/or be dependent on: (1) the composition of the accessory genome, (2) the accumulation of toxic intermediates, (3) functional redundancy, (4) efficient recycling of critical metabolites and (5) pathway rewiring. While this functional characterization underscores the evolvability potential of many essential genes, we also show that genes with differential essentiality remain important antimicrobial drug target candidates, as their inactivation almost always has a severe fitness cost in vivo.
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Affiliation(s)
| | - Emily Rudmann
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Jien Li
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Defne Surujon
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Jon Anthony
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Matthew Frank
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Dakota S Jones
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Charles Rock
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher D Johnston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Preparation and Characterization of Calcium-Incorporated Rosa roxburghii Tratt and Its Efficacy on Bone Mineral Density in Rats. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:5122396. [PMID: 35497912 PMCID: PMC9045994 DOI: 10.1155/2022/5122396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/16/2022] [Indexed: 11/25/2022]
Abstract
The deficiency of traditional calcium preparation will gradually be replaced by the new type of calcium preparation. Rosa roxburghii fruit (R. roxburghii) is popular for its rich nutrients and functional ingredients. The fermentation broth of R. roxburghii, involving amino acids, flavonoids, triterpenes, polysaccharides, and other compounds, is favorable for calcium chelation. Thus, this study fabricated calcium-incorporated R. roxburghii (FECa) and further illustrated its efficacy on bone mineral density (BMD) in rats. The calcium holding capacity of FECa was identified and confirmed using AAS. Ion complexation of FECa was characterized using 1H-NMR, UV, SEM and EDS, and FTIR. The calcium contents of femurs were increased by 36%, and the bone trabeculae of femurs were significantly increased. Net calcium balance was enhanced to further improve BMD by oral administration of FECa. The above results indicate that FECa can be a potential and efficient calcium supplementation agent.
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Pihan E, Kotev M, Rabal O, Beato C, Diaz Gonzalez C. Fine tuning for success in structure-based virtual screening. J Comput Aided Mol Des 2021; 35:1195-1206. [PMID: 34799816 DOI: 10.1007/s10822-021-00431-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/08/2021] [Indexed: 11/30/2022]
Abstract
Structure-based virtual screening plays a significant role in drug-discovery. The method virtually docks millions of compounds from corporate or public libraries into a binding site of a disease-related protein structure, allowing for the selection of a small list of potential ligands for experimental testing. Many algorithms are available for docking and assessing the affinity of compounds for a targeted protein site. The performance of affinity estimation calculations is highly dependent on the size and nature of the site, therefore a rationale for selecting the best protocol is required. To address this issue, we have developed an automated calibration process, implemented in a Knime workflow. It consists of four steps: preparation of a protein test set with structures and models of the target, preparation of a compound test set with target-related ligands and decoys, automatic test of 24 scoring/rescoring protocols for each target structure and model, and graphical display of results. The automation of the process combined with execution on high performance computing resources greatly reduces the duration of the calibration phase, and the test of many combinations of algorithms on various target conformations results in a rational and optimal choice of the best protocol. Here, we present this tool and exemplify its application in setting-up an optimal protocol for SBVS against Retinoid X Receptor alpha.
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Affiliation(s)
- Emilie Pihan
- Computational Drug Discovery, Evotec (France) SAS, Campus Curie, 195 Route d'Espagne, 31036, Toulouse, France.
| | - Martin Kotev
- Computational Drug Discovery, Evotec (France) SAS, Campus Curie, 195 Route d'Espagne, 31036, Toulouse, France
| | - Obdulia Rabal
- Computational Drug Discovery, Evotec (France) SAS, Campus Curie, 195 Route d'Espagne, 31036, Toulouse, France
| | - Claudia Beato
- Aptuit (Verona) Srl, an Evotec Company, Via Alessandro Fleming, 4, 37135, Verona, Italy
| | - Constantino Diaz Gonzalez
- Computational Drug Discovery, Evotec (France) SAS, Campus Curie, 195 Route d'Espagne, 31036, Toulouse, France
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Yuan T, Werman JM, Sampson NS. The pursuit of mechanism of action: uncovering drug complexity in TB drug discovery. RSC Chem Biol 2021; 2:423-440. [PMID: 33928253 PMCID: PMC8081351 DOI: 10.1039/d0cb00226g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 12/23/2020] [Indexed: 12/21/2022] Open
Abstract
Whole cell-based phenotypic screens have become the primary mode of hit generation in tuberculosis (TB) drug discovery during the last two decades. Different drug screening models have been developed to mirror the complexity of TB disease in the laboratory. As these culture conditions are becoming more and more sophisticated, unraveling the drug target and the identification of the mechanism of action (MOA) of compounds of interest have additionally become more challenging. A good understanding of MOA is essential for the successful delivery of drug candidates for TB treatment due to the high level of complexity in the interactions between Mycobacterium tuberculosis (Mtb) and the TB drug used to treat the disease. There is no single "standard" protocol to follow and no single approach that is sufficient to fully investigate how a drug restrains Mtb. However, with the recent advancements in -omics technologies, there are multiple strategies that have been developed generally in the field of drug discovery that have been adapted to comprehensively characterize the MOAs of TB drugs in the laboratory. These approaches have led to the successful development of preclinical TB drug candidates, and to a better understanding of the pathogenesis of Mtb infection. In this review, we describe a plethora of efforts based upon genetic, metabolomic, biochemical, and computational approaches to investigate TB drug MOAs. We assess these different platforms for their strengths and limitations in TB drug MOA elucidation in the context of Mtb pathogenesis. With an emphasis on the essentiality of MOA identification, we outline the unmet needs in delivering TB drug candidates and provide direction for further TB drug discovery.
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Affiliation(s)
- Tianao Yuan
- Department of Chemistry, Stony Brook UniversityStony BrookNY 11794-3400USA+1-631-632-5738+1-631-632-7952
| | - Joshua M. Werman
- Department of Chemistry, Stony Brook UniversityStony BrookNY 11794-3400USA+1-631-632-5738+1-631-632-7952
| | - Nicole S. Sampson
- Department of Chemistry, Stony Brook UniversityStony BrookNY 11794-3400USA+1-631-632-5738+1-631-632-7952
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Kolbe K, Bell AC, Prosser GA, Assmann M, Yang HJ, Forbes HE, Gallucci S, Mayer-Barber KD, Boshoff HI, Barry Iii CE. Development and Optimization of Chromosomally-Integrated Fluorescent Mycobacterium tuberculosis Reporter Constructs. Front Microbiol 2020; 11:591866. [PMID: 33362741 PMCID: PMC7755994 DOI: 10.3389/fmicb.2020.591866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/13/2020] [Indexed: 11/25/2022] Open
Abstract
Mycobacterium tuberculosis resides in the lungs in various lesion types with unique microenvironmental conditions. This diversity is in line with heterogeneous disease progression and divergent drug efficiency. Fluorescent reporter strains can be used to decipher the micromilieu and to guide future treatment regimens. Current reporters using replicating plasmids, however, are not suitable for long-term mouse infections or studies in non-human primates. Using a combination of recombinant DNA and protein optimization techniques, we have developed reporter strains based on integrative plasmids, which exhibit stimulus-response characteristics and fluorescence intensities comparable to those based on replicating plasmids. We successfully applied the concepts by constructing a multi-color reporter strain able to detect simultaneous changes in environmental pH, Mg2+ concentrations, and protein expression levels.
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Affiliation(s)
- Katharina Kolbe
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Alice C Bell
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Gareth A Prosser
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States.,Drug Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee, United Kingdom
| | - Maike Assmann
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Hee-Jeong Yang
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - He Eun Forbes
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Sophia Gallucci
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Katrin D Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Helena I Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Clifton E Barry Iii
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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Inhibition of CorA-Dependent Magnesium Homeostasis Is Cidal in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2019; 63:AAC.01006-19. [PMID: 31383669 DOI: 10.1128/aac.01006-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/02/2019] [Indexed: 01/24/2023] Open
Abstract
Mechanisms of magnesium homeostasis in Mycobacterium tuberculosis are poorly understood. Here, we describe the characterization of a pyrimidinetrione amide scaffold that disrupts magnesium homeostasis in the pathogen by direct binding to the CorA Mg2+/Co2+ transporter. Mutations in domains of CorA that are predicted to regulate the pore opening in response to Mg2+ ions conferred resistance to this scaffold. The pyrimidinetrione amides were cidal against the pathogen under both actively replicating and nonreplicating conditions in vitro and were efficacious against the organism during macrophage infection. However, the compound lacked efficacy in infected mice, possibly due to limited exposure. Our results indicate that inhibition of Mg2+ homeostasis by CorA is an attractive target for tuberculosis drug discovery and encourage identification of improved CorA inhibitors.
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