1
|
Ayon NJ. High-Throughput Screening of Natural Product and Synthetic Molecule Libraries for Antibacterial Drug Discovery. Metabolites 2023; 13:625. [PMID: 37233666 PMCID: PMC10220967 DOI: 10.3390/metabo13050625] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Due to the continued emergence of resistance and a lack of new and promising antibiotics, bacterial infection has become a major public threat. High-throughput screening (HTS) allows rapid screening of a large collection of molecules for bioactivity testing and holds promise in antibacterial drug discovery. More than 50% of the antibiotics that are currently available on the market are derived from natural products. However, with the easily discoverable antibiotics being found, finding new antibiotics from natural sources has seen limited success. Finding new natural sources for antibacterial activity testing has also proven to be challenging. In addition to exploring new sources of natural products and synthetic biology, omics technology helped to study the biosynthetic machinery of existing natural sources enabling the construction of unnatural synthesizers of bioactive molecules and the identification of molecular targets of antibacterial agents. On the other hand, newer and smarter strategies have been continuously pursued to screen synthetic molecule libraries for new antibiotics and new druggable targets. Biomimetic conditions are explored to mimic the real infection model to better study the ligand-target interaction to enable the designing of more effective antibacterial drugs. This narrative review describes various traditional and contemporaneous approaches of high-throughput screening of natural products and synthetic molecule libraries for antibacterial drug discovery. It further discusses critical factors for HTS assay design, makes a general recommendation, and discusses possible alternatives to traditional HTS of natural products and synthetic molecule libraries for antibacterial drug discovery.
Collapse
Affiliation(s)
- Navid J Ayon
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| |
Collapse
|
2
|
Kalra R, Conlan XA, Goel M. Recent advances in research for potential utilization of unexplored lichen metabolites. Biotechnol Adv 2023; 62:108072. [PMID: 36464145 DOI: 10.1016/j.biotechadv.2022.108072] [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: 07/26/2021] [Revised: 10/28/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022]
Abstract
Several research studies have shown that lichens are productive organisms for the synthesis of a broad range of secondary metabolites. Lichens are a self-sustainable stable microbial ecosystem comprising an exhabitant fungal partner (mycobiont) and at least one or more photosynthetic partners (photobiont). The successful symbiosis is responsible for their persistence throughout time and allows all the partners (holobionts) to thrive in many extreme habitats, where without the synergistic relationship they would be rare or non-existent. The ability to survive in harsh conditions can be directly correlated with the production of some unique metabolites. Despite the potential applications, these unique metabolites have been underutilised by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability and technical challenges involved in their artificial cultivation. However, recent development of biotechnological tools such as molecular phylogenetics, modern tissue culture techniques, metabolomics and molecular engineering are opening up a new opportunity to exploit these compounds within the lichen holobiome for industrial applications. This review also highlights the recent advances in culturing the symbionts and the computational and molecular genetics approaches of lichen gene regulation recognized for the enhanced production of target metabolites. The recent development of multi-omics novel biodiscovery strategies aided by synthetic biology in order to study the heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offers a promising means for a sustainable supply of specialized metabolites.
Collapse
Affiliation(s)
- Rishu Kalra
- Sustainable Agriculture Program, The Energy and Resources Institute, Gurugram, Haryana, India
| | - Xavier A Conlan
- Deakin University, School of Life and Environmental Sciences, Geelong, Victoria, Australia
| | - Mayurika Goel
- Sustainable Agriculture Program, The Energy and Resources Institute, Gurugram, Haryana, India.
| |
Collapse
|
3
|
Karagöz Y, Öztürk Karagöz B. Lichens in Pharmacological Action: What Happened in the Last Decade? Eurasian J Med 2022; 54:195-208. [PMID: 36655467 PMCID: PMC11163341 DOI: 10.5152/eurasianjmed.2022.22335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/04/2022] [Indexed: 01/19/2023] Open
Abstract
Lichens are a unique group of organisms, which can produce compounds that are named secondary metabolites and rarely or are not produced in other organisms. Lichens possess pharmacological actions related to their secondary metabolites. Our knowledge of lichens and their pharmacological actions rapidly increases as new technologies and devices, which facilitate the investigation of the chemical profile and biological activities of lichens, are introduced and become more readily available. In addition, new methods and perspectives, as well as suggestions for pharmacological mechanisms, accumulate daily. Furthermore, lichen substances stand as a relatively untapped source of natural products. Accordingly, researchers investigate the pharmacological actions of lichen-derived material more frequently than it was in the past. This review focused on the pharmacological activities of lichens published in the last 11 years (2012-2022). Literature data obtained from WebOfScience and PubMed databases using related search keywords revealed that anti-genotoxicity, anticancer, and anti-microbial activity studies have constantly been conducted. More recently, immunomodulatory and inflammation-related studies took to the stage. Enzyme inhibition actions were popular as well. Our selection was based on the novelty and mechanistic insight that papers presented.
Collapse
Affiliation(s)
- Yalçın Karagöz
- Department of Pharmaceutical Botany, Ağrı İbrahim Çeçen University Faculty of Pharmacy, Ağrı, Turkey
| | - Berna Öztürk Karagöz
- Department of Pharmacology, Ağrı İbrahim Çeçen University Faculty of Pharmacy, Ağrı, Turkey
| |
Collapse
|
4
|
Wang C, Sarotti AM, Zaman KHAU, Wu X, Cao S. New Alkaloids From a Hawaiian Fungal Strain Aspergillus felis FM324. Front Chem 2021; 9:724617. [PMID: 34434921 PMCID: PMC8380829 DOI: 10.3389/fchem.2021.724617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/28/2021] [Indexed: 11/15/2022] Open
Abstract
Two new alkaloids tryptoquivaline Y (1) and pseurotin I (2), together with eight known compounds (3-10), were purified from a fungal strain Aspergillus felis FM324, which was isolated from a Hawaiian beach soil sample. The absolute configuration and physicochemical data of tryptoquivaline Z (3) were reported for the first time here in this paper. Compound 1 is an uncommon tryptoquivaline analog containing a 3-O-isobutanoyl group. The structures of the new compounds 1-2 and known compound 3 were elucidated through HRESIMS, NMR spectroscopy and ECD analysis. All the compounds were evaluated for their antiproliferative, antibacterial and NF-κB inhibitory activities. Compound 4 showed weak antibacterial activity against Staphylococcus aureus, methicillin resistant Staphylococcus aureus and Bacillus subtilis with the same MIC value of 59.2 µM. Compounds 3 and 2 inhibited NF-κB with IC50 values of 26.7 and 30.9 μM, respectively.
Collapse
Affiliation(s)
- Cong Wang
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai’i at Hilo, Hilo, HI, United States
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning, China
| | - Ariel M. Sarotti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (CONICET), Universidad Nacional de Rosario, Rosario, Argentina
| | - KH Ahammad Uz Zaman
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai’i at Hilo, Hilo, HI, United States
| | - Xiaohua Wu
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai’i at Hilo, Hilo, HI, United States
| | - Shugeng Cao
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai’i at Hilo, Hilo, HI, United States
| |
Collapse
|
5
|
Wang C, Wu X, Bai H, Zaman KAU, Hou S, Saito J, Wongwiwatthananukit S, Kim KS, Cao S. Antibacterial and NF-κB Inhibitory Lumazine Peptides, Aspochalasin, γ-Butyrolactone Derivatives, and Cyclic Peptides from a Hawaiian Aspergillus flavipes. JOURNAL OF NATURAL PRODUCTS 2020; 83:2233-2240. [PMID: 32568536 DOI: 10.1021/acs.jnatprod.0c00344] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Five new lumazine peptides (1-5), a new aspochalasin derivative (6), and a new γ-butyrolactone derivative (7), together with seven known compounds (8-14), were isolated from a Hawaiian fungal strain, Aspergillus flavipes FS888. Compound 1 is an uncommon natural product containing an isocyano group. The structures of the new compounds 1-7 were elucidated by NMR spectroscopy, HRESIMS, chemical derivatization, and ECD analysis. Compounds 12-14 showed significant antibacterial activity against S. aureus when in combination with disulfiram. Additionally, compounds 9 and 13 showed NF-κB inhibitory activity with IC50 values of 3.1 ± 1.0 and 10.3 ± 2.0 μM, respectively.
Collapse
Affiliation(s)
- Cong Wang
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, Hawaii 96720, United States
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530006, People's Republic of China
| | - Xiaohua Wu
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, Hawaii 96720, United States
| | - Helong Bai
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, Hawaii 96720, United States
- College of Chemistry, Changchun Normal University, 677 ChangJibei Road, Changchun, Jilin 130032, People's Republic of China
| | - Kh Ahammad Uz Zaman
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, Hawaii 96720, United States
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics (ASGPB), University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
| | - Jennifer Saito
- Advanced Studies in Genomics, Proteomics and Bioinformatics (ASGPB), University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
| | - Supakit Wongwiwatthananukit
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, Hawaii 96720, United States
| | - Kyung Sik Kim
- School of Pharmacy, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Shugeng Cao
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, Hawaii 96720, United States
| |
Collapse
|
6
|
Zaman KAU, Hu Z, Wu X, Hou S, Saito J, Kondratyuk TP, Pezzuto JM, Cao S. NF-κB Inhibitory and Antibacterial Helvolic and Fumagillin Derivatives from Aspergillus terreus. JOURNAL OF NATURAL PRODUCTS 2020; 83:730-737. [PMID: 32163285 DOI: 10.1021/acs.jnatprod.9b01190] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Two new helvolic acid analogues (1 and 2) and one new fumagillin derivative containing an octahydroisobenzofuran moiety (3), together with four known compounds (4-7), were isolated from an Aspergillus terreus, isolated from soil collected from Mauna Kea, the highest mountain in Hawaii. Compound 4 was recorded in SciFinder with a CAS Registry Number of 1379525-35-5, but it was not documented in the cited reference (ACS Chem. Biol. 2012, 7, 137). The structures of compounds 1-4 were elucidated by NMR spectroscopy and HRMS and ECD analysis. Compounds 5 and 6 showed significant inhibitory activity against NF-κB with IC50 values of 2.7 ± 2.6 and 6.5 ± 0.8 μM, respectively. Compounds 1 and 2 were active against S. aureus with MICs of 6.25 and 6.25 μg/mL, respectively, while compound 5 inhibited E. coli with an MIC of 3.12 μg/mL.
Collapse
Affiliation(s)
- Kh Ahammad Uz Zaman
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, Hawaii 96720, United States
| | - Zhenquan Hu
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, People's Republic of China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Xiaohua Wu
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, Hawaii 96720, United States
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics (ASGPB), University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
| | - Jennifer Saito
- Advanced Studies in Genomics, Proteomics and Bioinformatics (ASGPB), University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
| | - Tamara P Kondratyuk
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, Hawaii 96720, United States
| | - John M Pezzuto
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, Hawaii 96720, United States
- Arnold & Mary Schwartz College of Pharmacy and Health Sciences, Long Island University, 75 DeKalb Avenue, Brooklyn, New York 11201-5497, United States
| | - Shugeng Cao
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, Hawaii 96720, United States
| |
Collapse
|
7
|
Szafran MJ, Gongerowska M, Małecki T, Elliot M, Jakimowicz D. Transcriptional Response of Streptomyces coelicolor to Rapid Chromosome Relaxation or Long-Term Supercoiling Imbalance. Front Microbiol 2019; 10:1605. [PMID: 31354687 PMCID: PMC6637917 DOI: 10.3389/fmicb.2019.01605] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/26/2019] [Indexed: 12/14/2022] Open
Abstract
Negative DNA supercoiling allows chromosome condensation and facilitates DNA unwinding, which is required for the occurrence of DNA transaction processes, i.e., DNA replication, transcription and recombination. In bacteria, changes in chromosome supercoiling impact global gene expression; however, the limited studies on the global transcriptional response have focused mostly on pathogenic species and have reported various fractions of affected genes. Furthermore, the transcriptional response to long-term supercoiling imbalance is still poorly understood. Here, we address the transcriptional response to both novobiocin-induced rapid chromosome relaxation or long-term topological imbalance, both increased and decreased supercoiling, in environmental antibiotic-producing bacteria belonging to the Streptomyces genus. During the Streptomyces complex developmental cycle, multiple copies of GC-rich linear chromosomes present in hyphal cells undergo profound topological changes, from being loosely condensed in vegetative hyphae, to being highly compacted in spores. Moreover, changes in chromosomal supercoiling have been suggested to be associated with the control of antibiotic production and environmental stress response. Remarkably, in S. coelicolor, a model Streptomyces species, topoisomerase I (TopA) is solely responsible for the removal of negative DNA supercoils. Using a S. coelicolor strain in which topA transcription is under the control of an inducible promoter, we identified genes involved in the transcriptional response to long-term supercoiling imbalance. The affected genes are preferentially organized in several clusters, and a supercoiling-hypersensitive cluster (SHC) was found to be located in the core of the S. coelicolor chromosome. The transcripts affected by long-term topological imbalance encompassed genes encoding nucleoid-associated proteins, DNA repair proteins and transcriptional regulators, including multiple developmental regulators. Moreover, using a gyrase inhibitor, we identified those genes that were directly affected by novobiocin, and found this was correlated with increased AT content in their promoter regions. In contrast to the genes affected by long-term supercoiling changes, among the novobiocin-sensitive genes, a significant fraction encoded for proteins associated with membrane transport or secondary metabolite synthesis. Collectively, our results show that long-term supercoiling imbalance globally regulates gene transcription and has the potential to impact development, secondary metabolism and DNA repair, amongst others.
Collapse
Affiliation(s)
- Marcin Jan Szafran
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Martyna Gongerowska
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Tomasz Małecki
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Marie Elliot
- Department of Biology, M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Dagmara Jakimowicz
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| |
Collapse
|
8
|
García MT, Carreño D, Tirado-Vélez JM, Ferrándiz MJ, Rodrigues L, Gracia B, Amblar M, Ainsa JA, de la Campa AG. Boldine-Derived Alkaloids Inhibit the Activity of DNA Topoisomerase I and Growth of Mycobacterium tuberculosis. Front Microbiol 2018; 9:1659. [PMID: 30087665 PMCID: PMC6066988 DOI: 10.3389/fmicb.2018.01659] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/04/2018] [Indexed: 11/13/2022] Open
Abstract
The spread of multidrug-resistant isolates of Mycobacterium tuberculosis requires the discovery of new drugs directed to new targets. In this study, we investigated the activity of two boldine-derived alkaloids, seconeolitsine (SCN) and N-methyl-seconeolitsine (N-SCN), against M. tuberculosis. These compounds have been shown to target DNA topoisomerase I enzyme and inhibit growth of Streptococcus pneumoniae. Both SCN and N-SCN inhibited M. tuberculosis growth at 1.95-15.6 μM, depending on the strain. In M. smegmatis this inhibitory effect correlated with the amount of topoisomerase I in the cell, hence demonstrating that this enzyme is the target for these alkaloids in mycobacteria. The gene coding for topoisomerase I of strain H37Rv (MtbTopoI) was cloned into pQE1 plasmid of Escherichia coli. MtbTopoI was overexpressed with an N-terminal 6-His-tag and purified by affinity chromatography. In vitro inhibition of MtbTopoI activity by SCN and N-SCN was tested using a plasmid relaxation assay. Both SCN and N-SCN inhibited 50% of the enzymatic activity at 5.6 and 8.4 μM, respectively. Cleavage of single-stranded DNA was also inhibited with SCN. The effects on DNA supercoiling were also evaluated in vivo in plasmid-containing cultures of M. tuberculosis. Plasmid supercoiling densities were -0.060 in cells untreated or treated with boldine, and -0.072 in 1 × MIC N-SCN treated cells, respectively, indicating that the plasmid became hypernegatively supercoiled in the presence of N-SCN. Altogether, these results demonstrate that the M. tuberculosis topoisomerase I enzyme is an attractive drug target, and that SCN and N-SCN are promising lead compounds for drug development.
Collapse
Affiliation(s)
- María T. García
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - David Carreño
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - José M. Tirado-Vélez
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María J. Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Liliana Rodrigues
- CIBER de Enfermedades Respiratorias, Madrid, Spain
- Departamento de Microbiología, Medicina Preventiva y Salud Pública, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
- Fundación Agencia Aragonesa para la Investigación y el Desarrollo, Zaragoza, Spain
| | - Begoña Gracia
- CIBER de Enfermedades Respiratorias, Madrid, Spain
- Departamento de Microbiología, Medicina Preventiva y Salud Pública, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Mónica Amblar
- Unidad de Patología Molecular de Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - José A. Ainsa
- CIBER de Enfermedades Respiratorias, Madrid, Spain
- Departamento de Microbiología, Medicina Preventiva y Salud Pública, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Adela G. de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Presidencia, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| |
Collapse
|
9
|
Abstract
Bacterial Topoisomerase I is a potential target for the identification of novel topoisomerase poison inhibitors that could provide leads for a new class of antibacterial compounds. Here we describe in detail a fluorescence-based cleavage assay that is successfully used in HTS for the discovery of bacterial topoisomerase Ι poisons.
Collapse
|
10
|
Garnier F, Debat H, Nadal M. Type IA DNA Topoisomerases: A Universal Core and Multiple Activities. Methods Mol Biol 2018; 1703:1-20. [PMID: 29177730 DOI: 10.1007/978-1-4939-7459-7_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
All the type IA topoisomerases display universal characteristics relying on a core region basically responsible for the transesterification and the strand passage reaction. First limited to the bacterial domain for a long time, these enzymes were further retrieved in Archaea and Eukarya as well. This is representative of an extremely ancient origin, probably due to an inheritance from the RNA world. As remaining evidence, some current topoisomerases IA have retained a RNA topoisomerase activity. Despite the presence of this core region in all of these TopoIAs, some differences exist and are originated from variable regions, located essentially within both extremities, conferring on them their specificities. During the last 2 decades the evidence of multiple activities and dedicated roles highlighted the importance of the topoisomerases IA. It is now obvious that topoisomerases IA are key enzymes involved in the maintenance of the genome stability. The discovery of these new activities was done thanks to the use of more accurate assays, based on new sophisticated DNA substrates.
Collapse
Affiliation(s)
- Florence Garnier
- Université Versailles St-Quentin, Institut Jacques Monod, UMR 7592 CNRS-Univ. Paris Diderot, 15, rue Hélène Brion, Paris, 75013, France
| | - Hélène Debat
- Université Versailles St-Quentin, Institut Jacques Monod, UMR 7592 CNRS-Univ. Paris Diderot, 15, rue Hélène Brion, Paris, 75013, France
| | - Marc Nadal
- Institut Jacques Monod, UMR 7592 CNRS-Université Paris Diderot, 15, rue Hélène Brion, Paris, 75013, France.
| |
Collapse
|
11
|
Calcott MJ, Ackerley DF, Knight A, Keyzers RA, Owen JG. Secondary metabolism in the lichen symbiosis. Chem Soc Rev 2018; 47:1730-1760. [PMID: 29094129 DOI: 10.1039/c7cs00431a] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lichens, which are defined by a core symbiosis between a mycobiont (fungal partner) and a photobiont (photoautotrophic partner), are in fact complex assemblages of microorganisms that constitute a largely untapped source of bioactive secondary metabolites. Historically, compounds isolated from lichens have predominantly been those produced by the dominant fungal partner, and these continue to be of great interest for their unique chemistry and biotechnological potential. In recent years it has become apparent that many photobionts and lichen-associated bacteria also produce a range of potentially valuable molecules. There is evidence to suggest that the unique nature of the symbiosis has played a substantial role in shaping many aspects of lichen chemistry, for example driving bacteria to produce metabolites that do not bring them direct benefit but are useful to the lichen as a whole. This is most evident in studies of cyanobacterial photobionts, which produce compounds that differ from free living cyanobacteria and are unique to symbiotic organisms. The roles that these and other lichen-derived molecules may play in communication and maintaining the symbiosis are poorly understood at present. Nonetheless, advances in genomics, mass spectrometry and other analytical technologies are continuing to illuminate the wealth of biological and chemical diversity present within the lichen holobiome. Implementation of novel biodiscovery strategies such as metagenomic screening, coupled with synthetic biology approaches to reconstitute, re-engineer and heterologously express lichen-derived biosynthetic gene clusters in a cultivable host, offer a promising means for tapping into this hitherto inaccessible wealth of natural products.
Collapse
Affiliation(s)
- Mark J Calcott
- School of Biological Sciences, Victoria University of Wellington, New Zealand.
| | | | | | | | | |
Collapse
|
12
|
Discovery of novel bacterial topoisomerase I inhibitors by use of in silico docking and in vitro assays. Sci Rep 2018; 8:1437. [PMID: 29362471 PMCID: PMC5780498 DOI: 10.1038/s41598-018-19944-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/10/2018] [Indexed: 02/07/2023] Open
Abstract
Topoisomerases are important targets for antibacterial and anticancer therapies. Bacterial topoisomerase I remains to be exploited for antibiotics that can be used in the clinic. Inhibitors of bacterial topoisomerase I may provide leads for novel antibacterial drugs against pathogens resistant to current antibiotics. TB is the leading infectious cause of death worldwide, and new TB drugs against an alternative target are urgently needed to overcome multi-drug resistance. Mycobacterium tuberculosis topoisomerase I (MtbTopI) has been validated genetically and chemically as a TB drug target. Here we conducted in silico screening targeting an active site pocket of MtbTopI. The top hits were assayed for inhibition of MtbTopI activity. The shared structural motif found in the active hits was utilized in a second round of in silico screening and in vitro assays, yielding selective inhibitors of MtbTopI with IC50s as low as 2 µM. Growth inhibition of Mycobacterium smegmatis by these compounds in combination with an efflux pump inhibitor was diminished by the overexpression of recombinant MtbTopI. This work demonstrates that in silico screening can be utilized to discover new bacterial topoisomerase I inhibitors, and identifies a novel structural motif which could be explored further for finding selective bacterial topoisomerase I inhibitors.
Collapse
|
13
|
Scott Chialvo CH, Chialvo P, Holland JD, Anderson TJ, Breinholt JW, Kawahara AY, Zhou X, Liu S, Zaspel JM. A phylogenomic analysis of lichen-feeding tiger moths uncovers evolutionary origins of host chemical sequestration. Mol Phylogenet Evol 2017; 121:23-34. [PMID: 29274497 DOI: 10.1016/j.ympev.2017.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022]
Abstract
Host species utilize a variety of defenses to deter feeding, including secondary chemicals. Some phytophagous insects have evolved tolerance to these chemical defenses, and can sequester secondary defense compounds for use against their own predators and parasitoids. While numerous studies have examined plant-insect interactions, little is known about lichen-insect interactions. Our study focused on reconstructing the evolution of lichen phenolic sequestration in the tiger moth tribe Lithosiini (Lepidoptera: Erebidae: Arctiinae), the most diverse lineage of lichen-feeding moths, with 3000 described species. We built an RNA-Seq dataset and examined the adult metabolome for the presence of lichen-derived phenolics. Using the transcriptomic dataset, we recover a well-resolved phylogeny of the Lithosiini, and determine that the metabolomes within species are more similar than those among species. Results from an initial ancestral state reconstruction suggest that the ability to sequester phenolics produced by a single chemical pathway preceded generalist sequestration of phenolics produced by multiple chemical pathways. We conclude that phenolics are consistently and selectively sequestered within Lithosiini. Furthermore, sequestration of compounds from a single chemical pathway may represent a synapomorphy of the tribe, and the ability to sequester phenolics produced by multiple pathways arose later. These findings expand on our understanding of the interactions between Lepidoptera and their lichen hosts.
Collapse
Affiliation(s)
- Clare H Scott Chialvo
- Department of Biological Sciences, PO Box 870344, University of Alabama, Tuscaloosa, AL 35487, USA.
| | - Pablo Chialvo
- Department of Biology, 320 Stanley Avenue, Lander University, Greenwood, SC 29649, USA
| | - Jeffrey D Holland
- Department of Entomology, 901 West State Street, Purdue University, West Lafayette, IN 47907, USA
| | - Timothy J Anderson
- Department of Entomology, 901 West State Street, Purdue University, West Lafayette, IN 47907, USA
| | - Jesse W Breinholt
- Florida Museum of Natural History, 3215 Hull Road, University of Florida, Gainesville, FL 32611, USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, 3215 Hull Road, University of Florida, Gainesville, FL 32611, USA
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, People's Republic of China; Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Shanlin Liu
- China National GeneBank, 8/F, Beishan Industrial Zone, Yantian District, BGI-Shenzhen, People's Republic of China; BGI-Shenzhen, Beishan Industrial Zone, Yantian District, People's Republic of China
| | - Jennifer M Zaspel
- Department of Entomology, 901 West State Street, Purdue University, West Lafayette, IN 47907, USA; Milwaukee Public Museum, 800 W Wells St, Milwaukee, WI 53233, USA
| |
Collapse
|
14
|
DNA topoisomerase I and DNA gyrase as targets for TB therapy. Drug Discov Today 2017; 22:510-518. [DOI: 10.1016/j.drudis.2016.11.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 11/20/2022]
|
15
|
Affiliation(s)
- Giovanni Capranico
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Jessica Marinello
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Giovanni Chillemi
- SCAI
SuperComputing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185 Rome, Italy
| |
Collapse
|
16
|
Ekins S, Godbole AA, Kéri G, Orfi L, Pato J, Bhat RS, Verma R, Bradley EK, Nagaraja V. Machine learning and docking models for Mycobacterium tuberculosis topoisomerase I. Tuberculosis (Edinb) 2017; 103:52-60. [PMID: 28237034 DOI: 10.1016/j.tube.2017.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 01/14/2017] [Accepted: 01/18/2017] [Indexed: 11/30/2022]
Abstract
There is a shortage of compounds that are directed towards new targets apart from those targeted by the FDA approved drugs used against Mycobacterium tuberculosis. Topoisomerase I (Mttopo I) is an essential mycobacterial enzyme and a promising target in this regard. However, it suffers from a shortage of known inhibitors. We have previously used computational approaches such as homology modeling and docking to propose 38 FDA approved drugs for testing and identified several active molecules. To follow on from this, we now describe the in vitro testing of a library of 639 compounds. These data were used to create machine learning models for Mttopo I which were further validated. The combined Mttopo I Bayesian model had a 5 fold cross validation receiver operator characteristic of 0.74 and sensitivity, specificity and concordance values above 0.76 and was used to select commercially available compounds for testing in vitro. The recently described crystal structure of Mttopo I was also compared with the previously described homology model and then used to dock the Mttopo I actives norclomipramine and imipramine. In summary, we describe our efforts to identify small molecule inhibitors of Mttopo I using a combination of machine learning modeling and docking studies in conjunction with screening of the selected molecules for enzyme inhibition. We demonstrate the experimental inhibition of Mttopo I by small molecule inhibitors and show that the enzyme can be readily targeted for lead molecule development.
Collapse
Affiliation(s)
- Sean Ekins
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94403, USA; Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay-Varina, NC 27526, USA.
| | - Adwait Anand Godbole
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - György Kéri
- Vichem Chemie Research Ltd., Herman Ottó u. 15, H-1022, Budapest, Hungary; Semmelweis Univ, Dept Med Chem, MTA SE Pathobiochem Res Grp, H-1092, Budapest, Hungary
| | - Lászlo Orfi
- Vichem Chemie Research Ltd., Herman Ottó u. 15, H-1022, Budapest, Hungary; Semmelweis Univ, Dept Med Chem, MTA SE Pathobiochem Res Grp, H-1092, Budapest, Hungary
| | - János Pato
- Vichem Chemie Research Ltd., Herman Ottó u. 15, H-1022, Budapest, Hungary
| | - Rajeshwari Subray Bhat
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Rinkee Verma
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | | | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India.
| |
Collapse
|
17
|
Abstract
DNA metabolism embodies a number of biochemical pathways, which include targets of clinically used antibiotics as well as those that are only being explored as potential targets for inhibitory compounds. We give an overview of representative cell-based and enzymatic assays suitable for high-throughput-driven search for novel DNA metabolism inhibitors of established and novel DNA metabolism targets in bacteria. The protocol for a colorimetric coupled primase-inorganic pyrophosphatase assay developed by our group is described in detail.
Collapse
|
18
|
Bansal S, Bajaj P, Pandey S, Tandon V. Topoisomerases: Resistance versus Sensitivity, How Far We Can Go? Med Res Rev 2016; 37:404-438. [PMID: 27687257 DOI: 10.1002/med.21417] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/04/2016] [Accepted: 08/29/2016] [Indexed: 12/15/2022]
Abstract
DNA topoisomerases are ubiquitously present remarkable molecular machines that help in altering topology of DNA in living cells. The crucial role played by these nucleases during DNA replication, transcription, and recombination vis-à-vis less sequence similarity among different species makes topoisomerases unique and attractive targets for different anticancer and antibacterial drugs. However, druggability of topoisomerases by the existing class of molecules is increasingly becoming questationable due to resistance development predominated by mutations in the corresponding genes. The current scenario facing a decline in the development of new molecules further comprises an important factor that may challenge topoisomerase-targeting therapy. Thus, it is imperative to wisely use the existing inhibitors lest with this rapid rate of losing grip over the target we may not go too far. Furthermore, it is important not only to design new molecules but also to develop new approaches that may avoid obstacles in therapies due to multiple resistance mechanisms. This review provides a succinct account of different classes of topoisomerase inhibitors, focuses on resistance acquired by mutations in topoisomerases, and discusses the various approaches to increase the efficacy of topoisomerase inhibitors. In a later section, we also suggest the possibility of using bisbenzimidazoles along with efflux pump inhibitors for synergistic bactericidal effects.
Collapse
Affiliation(s)
- Sandhya Bansal
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, India
| | - Priyanka Bajaj
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Stuti Pandey
- Department of Chemistry, University of Delhi, New Delhi, India
| | - Vibha Tandon
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.,Department of Chemistry, University of Delhi, New Delhi, India
| |
Collapse
|
19
|
Emsen B, Aslan A, Togar B, Turkez H. In vitro antitumor activities of the lichen compounds olivetoric, physodic and psoromic acid in rat neuron and glioblastoma cells. PHARMACEUTICAL BIOLOGY 2016; 54:1748-1762. [PMID: 26704132 DOI: 10.3109/13880209.2015.1126620] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 10/02/2015] [Accepted: 11/25/2015] [Indexed: 06/05/2023]
Abstract
Context Since methods utilised in the treatment of glioblastoma multiforme (GBM) are inadequate and have too many side effects, usage of herbal products in the treatment process comes into prominence. Lichens are symbiotic organisms used for medicinal purposes for many years. There are various anticancer treatments about components of two lichen species used in the present study. Objective Antitumor potential of three lichen secondary metabolites including olivetoric acid (OLA) and physodic acid (PHA) isolated from Pseudevernia furfuracea (L.) Zopf (Parmeliaceae) and psoromic acid (PSA) isolated from Rhizoplaca melanophthalma (DC.) Leuckert (Lecanoraceae) were investigated on human U87MG-GBM cell lines and primary rat cerebral cortex (PRCC) cells for the first time. Materials and methods PRCC cells used as healthy brain cells were obtained from Sprague-Dawley rats. The treatments were carried out on the cells cultured for 48 h. Cytotoxic effects of different concentrations (2.5, 5, 10, 20 and 40 mg/L) of metabolites on the cells were determined via 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and lactate dehydrogenase (LDH) analyses. Total antioxidant capacity (TAC) and total oxidant status (TOS) parameters were used for assessing oxidative alterations. Oxidative DNA damage potentials of metabolites were investigated via evaluating 8-hydroxy-2'-deoxyguanosine (8-OH-dG) levels. Results Median inhibitory concentration (IC50) values of OLA, PHA and PSA were 125.71, 698.19 and 79.40 mg/L for PRCC cells and 17.55, 410.72 and 56.22 mg/L for U87MG cells, respectively. It was revealed that cytotoxic effects of these metabolites showed positive correlation with concentration, LDH activity and oxidative DNA damage. Discussion and conclusion The present findings obtained in this study revealed that primarily OLA and then PSA had high potential for use in the treatment of GBM.
Collapse
Affiliation(s)
- Bugrahan Emsen
- a Department of Biology, Kamil Özdağ Faculty of Science , Karamanoğlu Mehmetbey University , Karaman , Turkey
| | - Ali Aslan
- b Department of Biology Education, Kazım Karabekir Faculty of Education , Atatürk University , Erzurum , Turkey
| | - Basak Togar
- c Department of Biology, Faculty of Science , Atatürk University , Erzurum , Turkey
| | - Hasan Turkez
- d Department of Molecular Biology and Genetics, Faculty of Science , Erzurum Technical University , Erzurum , Turkey
| |
Collapse
|
20
|
Ristić S, Ranković B, Kosanić M, Stanojković T, Stamenković S, Vasiljević P, Manojlović I, Manojlović N. Phytochemical study and antioxidant, antimicrobial and anticancer activities of Melanelia subaurifera and Melanelia fuliginosa lichens. Journal of Food Science and Technology 2016; 53:2804-16. [PMID: 27478237 DOI: 10.1007/s13197-016-2255-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 05/12/2016] [Accepted: 05/17/2016] [Indexed: 10/21/2022]
Abstract
The aim of this study was to investigate antioxidant, antimicrobial and anticancerous activity of Melanelia subaurifera and Melanelia fuliginosa. The phytochemical analysis was determined by HPLC-UV method. Antioxidant activity was evaluated by DPPH and reducing power assay while antimicrobial activity was determined by minimal inhibitory concentration. The cytotoxic activity was tested using MTT method. The method for quantification of 2'-O-methyl anziaic acid and lecanoric acid in these lichens using RF-HPLC was also developed and validated. The depsides (lecanoric acid, gyrophoric acid, atranorin, anziaic acid and 2'-O-methyl anziaic acid), and dibenzofurane (usnic acid) were identified in these lichens. The antioxidant activity (IC50) of lichens extracts ranged from 121.52 to 424.51 μg/ml. 2'-O-Methyl anziaic acid showed the highest antimicrobial activity with MIC ranging from 0.0625 to 1 mg/ml. M. subaurifera extract showed the highest cytotoxic activity against the tested cell lines (IC50 = 9.88 to 31.64 μg/ml).
Collapse
Affiliation(s)
- Svetlana Ristić
- Department of Biology, Faculty of Science, University of Kragujevac, Kragujevac, 34000 Serbia
| | - Branislav Ranković
- Department of Biology, Faculty of Science, University of Kragujevac, Kragujevac, 34000 Serbia
| | - Marijana Kosanić
- Department of Biology, Faculty of Science, University of Kragujevac, Kragujevac, 34000 Serbia
| | | | - Slaviša Stamenković
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Nis, 18000 Serbia
| | - Perica Vasiljević
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Nis, 18000 Serbia
| | - Ivana Manojlović
- Department of Pharmacy, Faculty of Medicinal Sciences, University of Kragujevac, Kragujevac, 34000 Serbia
| | - Nedeljko Manojlović
- Department of Pharmacy, Faculty of Medicinal Sciences, University of Kragujevac, Kragujevac, 34000 Serbia
| |
Collapse
|
21
|
Targeting bacterial topoisomerase I to meet the challenge of finding new antibiotics. Future Med Chem 2016; 7:459-71. [PMID: 25875873 DOI: 10.4155/fmc.14.157] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Resistance of bacterial pathogens to current antibiotics has grown to be an urgent crisis. Approaches to overcome this challenge include identification of novel targets for discovery of new antibiotics. Bacterial topoisomerase I is present in all bacterial pathogens as a potential target for bactericidal topoisomerase poison inhibitors. Recent efforts have identified inhibitors of bacterial topoisomerase I with antibacterial activity. Additional research on the mode of action and binding site of these inhibitors would provide further validation of the target and establish that bacterial topoisomerase I is druggable. Bacterial topoisomerase I is a potentially high value target for discovery of new antibiotics. Demonstration of topoisomerase I as the cellular target of an antibacterial compound would provide proof-of-concept validation.
Collapse
|
22
|
Topoisomerase I Inhibitors Derived from Natural Products: Structure–Activity Relationships and Antitumor Potency. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/b978-0-444-63603-4.00001-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
|
23
|
Ravishankar S, Ambady A, Awasthy D, Mudugal NV, Menasinakai S, Jatheendranath S, Guptha S, Sharma S, Balakrishnan G, Nandishaiah R, Ramachandran V, Eyermann CJ, Reck F, Rudrapatna S, Sambandamurthy VK, Sharma UK. Genetic and chemical validation identifies Mycobacterium tuberculosis topoisomerase I as an attractive anti-tubercular target. Tuberculosis (Edinb) 2015; 95:589-98. [PMID: 26073894 DOI: 10.1016/j.tube.2015.05.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/30/2015] [Accepted: 05/13/2015] [Indexed: 12/21/2022]
Abstract
DNA topoisomerases perform the essential function of maintaining DNA topology in prokaryotes. DNA gyrase, an essential enzyme that introduces negative supercoils, is a clinically validated target. However, topoisomerase I (Topo I), an enzyme responsible for DNA relaxation has received less attention as an antibacterial target, probably due to the ambiguity over its essentiality in many organisms. The Mycobacterium tuberculosis genome harbors a single topA gene with no obvious redundancy in its function suggesting an essential role. The topA gene could be inactivated only in the presence of a complementing copy of the gene in M. tuberculosis. Furthermore, down-regulation of topA in a genetically engineered strain of M. tuberculosis resulted in loss of bacterial viability which correlated with a concomitant depletion of intracellular Topo I levels. The topA knockdown strain of M. tuberculosis failed to establish infection in a murine model of TB and was cleared from lungs in two months post infection. Phenotypic screening of a Topo I overexpression strain led to the identification of an inhibitor, thereby providing chemical validation of this target. Thus, our work confirms the attractiveness of Topo I as an anti-mycobacterial target.
Collapse
Affiliation(s)
- Sudha Ravishankar
- AstraZeneca India Pvt. Ltd., Bellary Road, Hebbal, Bangalore 560024, India.
| | - Anisha Ambady
- AstraZeneca India Pvt. Ltd., Bellary Road, Hebbal, Bangalore 560024, India
| | - Disha Awasthy
- AstraZeneca India Pvt. Ltd., Bellary Road, Hebbal, Bangalore 560024, India
| | | | | | | | - Supreeth Guptha
- AstraZeneca India Pvt. Ltd., Bellary Road, Hebbal, Bangalore 560024, India
| | - Sreevalli Sharma
- AstraZeneca India Pvt. Ltd., Bellary Road, Hebbal, Bangalore 560024, India
| | | | - Radha Nandishaiah
- AstraZeneca India Pvt. Ltd., Bellary Road, Hebbal, Bangalore 560024, India
| | | | - Charles J Eyermann
- AstraZeneca Infection, Innovative Medicines, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Folkert Reck
- AstraZeneca Infection, Innovative Medicines, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Suresh Rudrapatna
- AstraZeneca India Pvt. Ltd., Bellary Road, Hebbal, Bangalore 560024, India
| | | | - Umender K Sharma
- AstraZeneca India Pvt. Ltd., Bellary Road, Hebbal, Bangalore 560024, India
| |
Collapse
|
24
|
Cheng B, Annamalai T, Sandhaus S, Bansod P, Tse-Dinh YC. Inhibition of Zn(II) binding type IA topoisomerases by organomercury compounds and Hg(II). PLoS One 2015; 10:e0120022. [PMID: 25798600 PMCID: PMC4370478 DOI: 10.1371/journal.pone.0120022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 01/18/2015] [Indexed: 11/19/2022] Open
Abstract
Type IA topoisomerase activities are essential for resolving DNA topological barriers via an enzyme-mediated transient single strand DNA break. Accumulation of topoisomerase DNA cleavage product can lead to cell death or genomic rearrangement. Many antibacterial and anticancer drugs act as topoisomerase poison inhibitors that form stabilized ternary complexes with the topoisomerase covalent intermediate, so it is desirable to identify such inhibitors for type IA topoisomerases. Here we report that organomercury compounds were identified during a fluorescence based screening of the NIH diversity set of small molecules for topoisomerase inhibitors that can increase the DNA cleavage product of Yersinia pestis topoisomerase I. Inhibition of relaxation activity and accumulation of DNA cleavage product were confirmed for these organomercury compounds in gel based assays of Escherichia coli topoisomerase I. Hg(II), but not As(III), could also target the cysteines that form the multiple Zn(II) binding tetra-cysteine motifs found in the C-terminal domains of these bacterial topoisomerase I for relaxation activity inhibition. Mycobacterium tuberculosis topoisomerase I activity is not sensitive to Hg(II) or the organomercury compounds due to the absence of the Zn(II) binding cysteines. It is significant that the type IA topoisomerases with Zn(II) binding domains can still cleave DNA when interfered by Hg(II) or organomercury compounds. The Zn(II) binding domains found in human Top3α and Top3β may be potential targets of toxic metals and organometallic complexes, with potential consequence on genomic stability and development.
Collapse
Affiliation(s)
- Bokun Cheng
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, United States of America
| | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Shayna Sandhaus
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Priyanka Bansod
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- * E-mail:
| |
Collapse
|
25
|
Gómez-Serranillos MP, Fernández-Moriano C, González-Burgos E, Divakar PK, Crespo A. Parmeliaceae family: phytochemistry, pharmacological potential and phylogenetic features. RSC Adv 2014. [DOI: 10.1039/c4ra09104c] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
|
26
|
Feng L, Maddox MM, Alam MZ, Tsutsumi LS, Narula G, Bruhn DF, Wu X, Sandhaus S, Lee RB, Simmons CJ, Tse-Dinh YC, Hurdle JG, Lee RE, Sun D. Synthesis, structure-activity relationship studies, and antibacterial evaluation of 4-chromanones and chalcones, as well as olympicin A and derivatives. J Med Chem 2014; 57:8398-420. [PMID: 25238443 PMCID: PMC4207537 DOI: 10.1021/jm500853v] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
On
the basis of recently reported abyssinone II and olympicin A, a series
of chemically modified flavonoid phytochemicals were synthesized and
evaluated against Mycobacterium tuberculosis and
a panel of Gram-positive and -negative bacterial pathogens. Some of
the synthesized compounds exhibited good antibacterial activities
against Gram-positive pathogens including methicillin resistant Staphylococcus aureus with minimum inhibitory concentration
as low as 0.39 μg/mL. SAR analysis revealed that the 2-hydrophobic
substituent and the 4-hydrogen bond donor/acceptor of the 4-chromanone
scaffold together with the hydroxy groups at 5- and 7-positions enhanced
antibacterial activities; the 2′,4′-dihydroxylated A
ring and the lipophilic substituted B ring of chalcone derivatives
were pharmacophoric elements for antibacterial activities. Mode of
action studies performed on selected compounds revealed that they
dissipated the bacterial membrane potential, resulting in the inhibition
of macromolecular biosynthesis; further studies showed that selected
compounds inhibited DNA topoisomerase IV, suggesting complex mechanisms
of actions for compounds in this series.
Collapse
Affiliation(s)
- Li Feng
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo , 34 Rainbow Drive, Hilo, Hawaii 96720, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Nimesh H, Sur S, Sinha D, Yadav P, Anand P, Bajaj P, Virdi JS, Tandon V. Synthesis and Biological Evaluation of Novel Bisbenzimidazoles as Escherichia coli Topoisomerase IA Inhibitors and Potential Antibacterial Agents. J Med Chem 2014; 57:5238-57. [DOI: 10.1021/jm5003028] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hemlata Nimesh
- Department
of Chemistry, University of Delhi, Delhi 110 007, India
| | - Souvik Sur
- Department
of Chemistry, University of Delhi, Delhi 110 007, India
| | - Devapriya Sinha
- Department
of Chemistry, University of Delhi, Delhi 110 007, India
| | - Pooja Yadav
- Department
of Chemistry, University of Delhi, Delhi 110 007, India
| | - Prachi Anand
- Department of Chemistry & Biochemistry, CUNY−Hunter College, New York, New York 10065, United States
| | - Priyanka Bajaj
- Department
of Microbiology, University of Delhi, Delhi 110 021, India
| | | | - Vibha Tandon
- Department
of Chemistry, University of Delhi, Delhi 110 007, India
- Special
Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110 067, India
| |
Collapse
|
28
|
Lin H, Annamalai T, Bansod P, Tse-Dinh YC, Sun D. Synthesis and antibacterial evaluation of anziaic acid and analogues as topoisomerase I inhibitors. MEDCHEMCOMM 2013; 4:10.1039/C3MD00238A. [PMID: 24363888 PMCID: PMC3867937 DOI: 10.1039/c3md00238a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Naturally occurring anziaic acid was very recently reported as a topoisomerase I inhibitor with antibacterial activity. Herein total synthesis of anziaic acid and structural analogues is described and the preliminary structure-activity relationship (SAR) has been developed based on topoisomerase inhibition and whole cell antibacterial activity.
Collapse
Affiliation(s)
- Hao Lin
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawai’i at Hilo, 34 Rainbow Drive, Hilo, HI 96720, USA. Fax: 1-(808)-933-2974; Tel: 1-(808)-933-2960
| | - Thirunavukkarasu Annamalai
- Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8 Street, Miami, FL 33199, USA
| | - Priyanka Bansod
- Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8 Street, Miami, FL 33199, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8 Street, Miami, FL 33199, USA
| | - Dianqing Sun
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawai’i at Hilo, 34 Rainbow Drive, Hilo, HI 96720, USA. Fax: 1-(808)-933-2974; Tel: 1-(808)-933-2960
| |
Collapse
|