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Ushtanit A, Mikhailova Y, Krylova L, Grigorash D, Makarova M, Safonova S, Zimenkov D. Perchlozone Resistance in Clinical Isolates of Mycobacterium tuberculosis. Antibiotics (Basel) 2023; 12:590. [PMID: 36978456 PMCID: PMC10044601 DOI: 10.3390/antibiotics12030590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
The emergence of drug-resistant tuberculosis forced the development of new drugs and the screening of more effective or less toxic analogues. Mycolic acid biosynthesis is targeted by several antituberculosis drugs, isoniazid being one of the most important in tuberculosis therapy. Recently, perchlozone, acting on another step in the FAS-II cycle, was officially approved for tuberculosis treatment in the Russian Federation and was included in the Russian national clinical guidelines. Using the serial dilution method on 7H10 agar plates for perchlozone and a Sensititre MYCOTB microdilution plate, we analyzed the phenotypic properties of primary clinical isolates of M. tuberculosis and analyzed the molecular determinants of resistance to isoniazid, ethionamide, and perchlozone. We found a wide variation in the MIC of perchlozone from 2 to 64 mg/L, correlating with the overall resistance profile: the MIC was higher for MDR and pre-XDR isolates. The cross-resistance between ethionamide and perchlozone was driven by mutations in the ethA gene encoding monooxygenase responsible for the activation of both drugs. The presumably susceptible to perchlozone and wild-type strains had MICs ranging from 2 to 4 mg/L, and the breakpoint was estimated to be 4 or 8 mg/L. In conclusion, susceptibility to perchlozone is retained for a part of the MDR strains, as is susceptibility to ethionamide, providing the possibility of therapy for such cases based on phenotypic or molecular analysis.
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Karthikeyan A, Joseph A, Nair BG. Promising bioactive compounds from the marine environment and their potential effects on various diseases. J Genet Eng Biotechnol 2022; 20:14. [PMID: 35080679 PMCID: PMC8790952 DOI: 10.1186/s43141-021-00290-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 12/17/2021] [Indexed: 12/30/2022]
Abstract
Background The marine environment hosts a wide variety of species that have evolved to live in harsh and challenging conditions. Marine organisms are the focus of interest due to their capacity to produce biotechnologically useful compounds. They are promising biocatalysts for new and sustainable industrial processes because of their resistance to temperature, pH, salt, and contaminants, representing an opportunity for several biotechnological applications. Encouraged by the extensive and richness of the marine environment, marine organisms’ role in developing new therapeutic benefits is heading as an arable field. Main body of the abstract There is currently much interest in biologically active compounds derived from natural resources, especially compounds that can efficiently act on molecular targets, which are involved in various diseases. Studies are focused on bacteria and fungi, isolated from sediments, seawater, fish, algae, and most marine invertebrates such as sponges, mollusks, tunicates, coelenterates, and crustaceans. In addition to marine macro-organisms, such as sponges, algae, or corals, marine bacteria and fungi have been shown to produce novel secondary metabolites (SMs) with specific and intricate chemical structures that may hold the key to the production of novel drugs or leads. The marine environment is known as a rich source of chemical structures with numerous beneficial health effects. Presently, several lines of studies have provided insight into biological activities and neuroprotective effects of marine algae, including antioxidant, anti-neuroinflammatory, cholinesterase inhibitory activity, and neuronal death inhibition. Conclusion The application of marine-derived bioactive compounds has gained importance because of their therapeutic uses in several diseases. Marine natural products (MNPs) display various pharmaceutically significant bioactivities, including antibiotic, antiviral, neurodegenerative, anticancer, or anti-inflammatory properties. The present review focuses on the importance of critical marine bioactive compounds and their role in different diseases and highlights their possible contribution to humanity.
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Affiliation(s)
- Akash Karthikeyan
- School of Biotechnology, National Institute of Technology Calicut, Calicut, Kerala, India
| | - Abey Joseph
- School of Biotechnology, National Institute of Technology Calicut, Calicut, Kerala, India
| | - Baiju G Nair
- School of Biotechnology, National Institute of Technology Calicut, Calicut, Kerala, India. .,Nanomedical Engineering Laboratory, Riken, Wako, Saitama, Japan.
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Cummings JE, Abdo Z, Slayden RA. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac028. [PMID: 35350133 PMCID: PMC8947225 DOI: 10.1093/jacamr/dlac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/27/2022] [Indexed: 12/03/2022] Open
Abstract
Background NIAID has a programme for testing drug candidates against biodefense and emerging bacterial pathogens that uses defined strain panels consisting of standard laboratory reference strains and strains of clinical origin. Objectives The current studies were performed to assess the activity of standard-of-care drugs, determine benchmark criteria for new investigational antibacterial candidate prioritization and identify reduced non-redundant strain panels for candidate performance classification. Methods The susceptibilities of each strain in the screening panels to 40 standard-of-care drugs and clinical drug combinations were determined by percentage growth inhibition using multiple concentrations, a method commonly used in efficient high-throughput screening efforts. The drug susceptibility of each strain was categorized based on interpretive criteria to benchmark the activity of each standard-of-care drug and drug combination, followed by confirmation of select active drugs. Exact match and clustering analyses defined focused non-redundant species and pan-species screening panels. Results This process revealed a broad spectrum of susceptibilities among strains in each species, with important differences between the standard laboratory reference strains and strains of clinical origin. Exact match and clustering analyses identified subsets of non-redundant strains that can more efficiently classify drug activity resulting in individual species screening panels, a pan-species screening panel and a pan-species maximum resistance panel. Conclusions This study resulted in improved non-redundant species screening panels for benchmarking the performance of new investigational antibacterial candidates with the greatest potential for efficacy against clinically relevant Category A and B priority and emerging pathogens.
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Affiliation(s)
- Jason E. Cummings
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, 80523-2025 CO, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, 80523-2025 CO, USA
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Nazli A, He D, Xu H, Wang ZP, He Y. A Comparative Insight on the Newly Emerging Rifamycins: Rifametane, Rifalazil, TNP-2092 and TNP-2198. Curr Med Chem 2021; 29:2846-2862. [PMID: 34365945 DOI: 10.2174/0929867328666210806114949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/15/2021] [Accepted: 06/15/2021] [Indexed: 11/22/2022]
Abstract
Rifamycins are considered a milestone for tuberculosis (TB) treatment because of their proficient sterilizing ability. Currently, available TB treatments are complicated and need a long duration, which ultimately leads to failure of patient compliance. Some new rifamycin derivatives, i.e., rifametane, TNP-2092 (rifamycin-quinolizinonehybrid), and TNP-2198 (rifamycin-nitromidazole hybrid) are under clinical trials, which are attempting to overcome the problems associated with TB treatment. The undertaken review is intended to compare the pharmacokinetics, pharmacodynamics and safety profiles of these rifamycins, including rifalazil, another derivative terminated in phase II trials, and already approved rifamycins. The emerging resistance of microbes is an imperative consideration associated with antibiotics. Resistance development potential of microbial strains against rifamycins and an overview of chemistry, as well as structure-activity relationship (SAR) of rifamycins, are briefly described. Moreover, issues associated with rifamycins are discussed as well. We expect that newly emerging rifamycins shall appear as potential tools for TB treatment in the near future.
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Affiliation(s)
- Adila Nazli
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing. China
| | - David He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing. China
| | - Huacheng Xu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing. China
| | - Zhi-Peng Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing. China
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing. China
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Santos MSC, Matos AM, Reis M, Martins F. Lipophilicity assessment of some isoniazid derivatives active against Mycobacterium tuberculosis. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.124820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Abstract
Tuberculosis (TB) is a global health disaster and is a wide-reaching hitch. The improper use of antibiotics in chemotherapy of TB patients led to the current problem of tuberculosis therapy which gives rise to Multi-Drug Resistant (MDR) strains. Nitrogen heterocycles including azole compounds are an important class of therapeutic agent with electron-rich property. Azole-based derivatives easily bind with the enzymes and receptors in organisms through noncovalent interactions, thereby possessing various applications in medicinal chemistry. Research on azoles derivatives have been expansively carried out and have become one of the extremely active area in recent years and the progress is quite rapid. A genuine attempt to review chemistry of azoles and to describe various azole-based compounds synthesized in the last two decades having promising antitubercular potential is described in the present article. It is hopeful that azole compounds may continue to serve as an important direction for the exploitation of azole-based antitubercular drugs with better curative effect, lower toxicity, less side effects, especially fewer resistances and so on.
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Affiliation(s)
- Rina Das
- MMCP, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207. HR, India
| | - Gyati S. Asthana
- MMCP, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207. HR, India
| | | | - Dinesh Mehta
- MMCP, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207. HR, India
| | - Abhay Asthana
- MMCP, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207. HR, India
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Hou XM, Wang CY, Gerwick WH, Shao CL. Marine natural products as potential anti-tubercular agents. Eur J Med Chem 2019; 165:273-292. [PMID: 30685527 DOI: 10.1016/j.ejmech.2019.01.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/11/2019] [Accepted: 01/11/2019] [Indexed: 02/01/2023]
Abstract
Tuberculosis has been one of the greatest global health challenges of all time. Although the current first-line anti-tuberculosis (anti-TB) medicines used in the clinic have reduced mortality, multidrug-resistance and extensively drug-resistance forms of the disease have now spread worldwide and become a global problem. Even so, few new clinically approved drugs have emerged during the past 30 years. Highly biodiverse marine organisms have received considerable attention for drug discovery in the past couple of decades, and emerging TB drug resistance has motivated interest in assessing marine natural products (MNPs) in the treatment of this disease. So far, more than 170 compounds have been isolated from marine organisms with anti-TB properties, ten of which exhibit potent activity and have the potential for further development. This review systematically surveys MNPs with anti-TB activity and illustrates the impact of these compounds on drug discovery research against tuberculosis.
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Affiliation(s)
- Xue-Mei Hou
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, People's Republic of China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, People's Republic of China
| | - Chang-Yun Wang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, People's Republic of China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, People's Republic of China
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States.
| | - Chang-Lun Shao
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, People's Republic of China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, People's Republic of China.
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Naz S, Farooq U, Ali S, Sarwar R, Khan S, Abagyan R. Identification of new benzamide inhibitor against α-subunit of tryptophan synthase from Mycobacterium tuberculosis through structure-based virtual screening, anti-tuberculosis activity and molecular dynamics simulations. J Biomol Struct Dyn 2018; 37:1043-1053. [PMID: 29502488 DOI: 10.1080/07391102.2018.1448303] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Multi-drug-resistant tuberculosis and extensively drug-resistant tuberculosis has emerged as global health threat, causing millions of deaths worldwide. Identification of new drug candidates for tuberculosis (TB) by targeting novel and less explored protein targets will be invaluable for antituberculosis drug discovery. We performed structure-based virtual screening of eMolecules database against a homology model of relatively unexplored protein target: the α-subunit of tryptophan synthase (α-TRPS) from Mycobacterium tuberculosis essential for bacterial survival. Based on physiochemical properties analysis and molecular docking, the seven candidate compounds were selected and evaluated through whole cell-based activity against the H37Rv strain of M. tuberculosis. A new Benzamide inhibitor against α-subunit of tryptophan synthase (α-TRPS) from M. tuberculosis has been identified causing 100% growth inhibition at 25 μg/ml and visible bactericidal activity at 6 μg/ml. This benzamide inhibitor displayed a good predicted binding score (-48.24 kcal/mol) with the α-TRPS binding pocket and has logP value (2.95) comparable to Rifampicin. Further refinement of docking results and evaluation of inhibitor-protein complex stability were investigated through Molecular dynamic (MD) simulations studies. Following MD simulations, Root mean square deviation, Root mean square fluctuation and secondary structure analysis confirmed that protein did not unfold and ligand stayed inside the active pocket of protein during the explored time scale. This identified benzamide inhibitor against the α-subunit of TRPS from M. tuberculosis could be considered as candidate for drug discovery against TB and will be further evaluated for enzyme-based inhibition in future studies.
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Affiliation(s)
- Sadia Naz
- a Department of Chemistry , COMSATS Institute of Information Technology , Abbottabad 22060 , Pakistan.,b Skaggs School of Pharmacy & Pharmaceutical Sciences , University of California , San Diego , CA , USA
| | - Umar Farooq
- a Department of Chemistry , COMSATS Institute of Information Technology , Abbottabad 22060 , Pakistan
| | - Sajid Ali
- c Provincial TB Control Program, Khyber Pakhtunkhwa Hayatabad Medical Complex , Peshawar , Pakistan
| | - Rizwana Sarwar
- a Department of Chemistry , COMSATS Institute of Information Technology , Abbottabad 22060 , Pakistan
| | - Sara Khan
- a Department of Chemistry , COMSATS Institute of Information Technology , Abbottabad 22060 , Pakistan
| | - Ruben Abagyan
- b Skaggs School of Pharmacy & Pharmaceutical Sciences , University of California , San Diego , CA , USA
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Patil K, Bagade S, Bonde S, Sharma S, Saraogi G. Recent therapeutic approaches for the management of tuberculosis: Challenges and opportunities. Biomed Pharmacother 2018; 99:735-45. [DOI: 10.1016/j.biopha.2018.01.115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 11/19/2022] Open
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Oosthuizen C, Arbach M, Meyer D, Hamilton C, Lall N. Diallyl Polysulfides from Allium sativum as Immunomodulators, Hepatoprotectors, and Antimycobacterial Agents. J Med Food 2017; 20:685-690. [PMID: 28410455 DOI: 10.1089/jmf.2016.0137] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis remains one of the world's deadliest killers, with an annual death rate of ∼1.5 million. The medicinal effects of garlic have been well documented, and natural products have been shown to have antimycobacterial activity. The current study evaluated the efficacy of six Allium sativum L. polysulfide mixtures as antimycobacterial agents together with their cytotoxic, immunomodulatory, and hepatoprotective activities. The microtitre PrestoBlue assay was used to determine the minimum inhibitory concentrations (MIC). Cytotoxicity was evaluated by using peripheral blood mononuclear cells (PBMC). Excreted cytokine levels were determined by utilizing an enzyme-linked immunosorbent assay (ELISA), by exposing isolated PBMCs to varying concentrations of polysulfide mixtures. Human C3A liver cells were utilized in the hepatoprotective study, to assess the protective effect against the toxicity induced by acetaminophen. Samples with higher amounts of diallyl trisulfide (Sample G4) showed the highest antimycobacterial activity, exhibiting an MIC of 2.5 μg/mL against M. tuberculosis H37Rv. Five samples showed moderate toxicity in PBMC, with G1 showing no toxicity. The selective index of G4 was the highest, with a selectivity index close to one. Two samples, G3 and G6 containing higher amounts of diallyl tetrasulfide and lower amounts of diallyl trisulfide, showed >50% hepatoprotection. This is comparable to a hepatoprotective agent, Silymarin, which showed a hepatoprotective effect of 30% at the tested concentration. Diallyl tetrasulfide showed significant antimycobacterial activity. A combination of higher diallyl tetrasulfide and lower diallyl trisulfide was indicative of hepatoprotective activity.
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Affiliation(s)
- Carel Oosthuizen
- 1 Department of Plant and Soil Sciences, University of Pretoria , Pretoria, South Africa
| | - Miriam Arbach
- 2 School of Pharmacy, Norwich Research Park, University of East Anglia , Norwich, United Kingdom .,3 ECOspray Ltd. , Grange Farm, Hilborough, United Kingdom
| | - Debra Meyer
- 4 Faculty of Science, University of Johannesburg , Johannesburg, South Africa .,5 Department of Biochemistry, University of Pretoria , Pretoria, South Africa
| | - Chris Hamilton
- 1 Department of Plant and Soil Sciences, University of Pretoria , Pretoria, South Africa .,2 School of Pharmacy, Norwich Research Park, University of East Anglia , Norwich, United Kingdom
| | - Namrita Lall
- 1 Department of Plant and Soil Sciences, University of Pretoria , Pretoria, South Africa
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Patel HM, Noolvi MN, Sethi NS, Gadad AK, Cameotra SS. Synthesis and antitubercular evaluation of imidazo[2,1- b ][1,3,4]thiadiazole derivatives. ARAB J CHEM 2017. [DOI: 10.1016/j.arabjc.2013.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Desai N, Joshi V, Rajpara K, Makwana AH. A new synthetic approach and in vitro antimicrobial evaluation of novel imidazole incorporated 4-thiazolidinone motifs. ARAB J CHEM 2017. [DOI: 10.1016/j.arabjc.2012.10.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Sajja Y, Vanguru S, Jilla L, Vulupala HR, Bantu R, Yogeswari P, Sriram D, Nagarapu L. A convenient synthesis and screening of benzosuberone bearing 1,2,3-triazoles against Mycobacterium tuberculosis. Bioorg Med Chem Lett 2016; 26:4292-5. [DOI: 10.1016/j.bmcl.2016.07.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/11/2016] [Accepted: 07/19/2016] [Indexed: 11/29/2022]
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Grant SS, Wellington S, Kawate T, Desjardins CA, Silvis MR, Wivagg C, Thompson M, Gordon K, Kazyanskaya E, Nietupski R, Haseley N, Iwase N, Earl AM, Fitzgerald M, Hung DT. Baeyer-Villiger Monooxygenases EthA and MymA Are Required for Activation of Replicating and Non-replicating Mycobacterium tuberculosis Inhibitors. Cell Chem Biol 2016; 23:666-77. [PMID: 27321573 DOI: 10.1016/j.chembiol.2016.05.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 04/12/2016] [Accepted: 05/06/2016] [Indexed: 01/21/2023]
Abstract
Successful treatment of Mycobacterium tuberculosis infection typically requires a complex regimen administered over at least 6 months. Interestingly, many of the antibiotics used to treat M. tuberculosis are prodrugs that require intracellular activation. Here, we describe three small molecules, active against both replicating and non-replicating M. tuberculosis, that require activation by Baeyer-Villiger monooxygenases (BVMOs). Two molecules require BVMO EthA (Rv3854c) for activation and the third molecule requires the BVMO MymA (Rv3083). While EthA is known to activate the antitubercular drug ethionamide, this is the first description of MymA as an activating enzyme of a prodrug. Furthermore, we found that MymA also plays a role in activating ethionamide, with loss of MymA function resulting in ethionamide-resistant M. tuberculosis. These findings suggest overlap in function and specificity of the BVMOs in M. tuberculosis.
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Affiliation(s)
- Sarah Schmidt Grant
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Samantha Wellington
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Tomohiko Kawate
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Carl Wivagg
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | | | | | - Nathan Haseley
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Noriaki Iwase
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ashlee M Earl
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
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Kotapalli SS, Nallam SS, Nadella L, Banerjee T, Rode HB, Mainkar PS, Ummanni R. Identification of New Molecular Entities (NMEs) as Potential Leads against Tuberculosis from Open Source Compound Repository. PLoS One 2015; 10:e0144018. [PMID: 26642200 DOI: 10.1371/journal.pone.0144018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/12/2015] [Indexed: 02/04/2023] Open
Abstract
The purpose of this study was to provide a number of diverse and promising early-lead compounds that will feed into the drug discovery pipeline for developing new antitubercular agents. The results from the phenotypic screening of the open-source compound library against Mycobacterium smegmatis and Mycobacterium bovis (BCG) with hit validation against M. tuberculosis (H37Rv) have identified novel potent hit compounds. To determine their druglikeness, a systematic analysis of physicochemical properties of the hit compounds has been performed using cheminformatics tools. The hit molecules were analysed by clustering based on their chemical finger prints and structural similarity determining their chemical diversity. The hit compound library is also filtered for druglikeness based on the physicochemical descriptors following Lipinski filters. The robust filtration of hits followed by secondary screening against BCG, H37Rv and cytotoxicity evaluation has identified 12 compounds with potential against H37Rv (MIC range 0.4 to 12.5 μM). Furthermore in cytotoxicity assays, 12 compounds displayed low cytotoxicity against liver and lung cells providing high therapeutic index > 50. To avoid any variations in activity due to the route of chemical synthesis, the hit compounds were re synthesized independently and confirmed for their potential against H37Rv. Taken together, the hits reported here provides copious potential starting points for generation of new leads eventually adds to drug discovery pipeline against tuberculosis.
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Pinheiro M, Silva AS, Reis S. Molecular interactions of rifabutin with membrane under acidic conditions. Int J Pharm 2015; 479:63-9. [PMID: 25542991 DOI: 10.1016/j.ijpharm.2014.12.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/16/2014] [Accepted: 12/19/2014] [Indexed: 01/19/2023]
Abstract
This work focuses on the interaction of the anti-tuberculosis (anti-TB) drug, rifabutin (RFB) with cell membrane models formed by 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). The experiments were performed under acidic conditions (i.e., pH 5.0) taking into account the pH conditions that RFB may find in the course of its in vivo pharmacological activity. The partition of the drug to the membrane was quantified through the partition coefficient (Kp). Fluorescence quenching studies were performed to predict the drug's location across the cell membrane model. The effect of RFB on the biophysical parameters of the cell membrane model was studied by steady-state anisotropy and small-angle X-ray scattering (SAXS). The overall results point to a marked interaction of RFB with cell membranes under acidic pH, which may be related with its pharmacological effects. The in vivo success of RFB may be associated with the drug's disordering effect of the membranes under acidic pH values environments, and consequently drug accumulation in the gastric infected tissues and inside phagolysosomes. On the other hand, the present study allowed establishing important correlations with the gastrointestinal side effects caused by RFB.
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Affiliation(s)
- Marina Pinheiro
- REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira n.° 228, Porto 4050-313, Portugal.
| | - Ana Sofia Silva
- REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira n.° 228, Porto 4050-313, Portugal
| | - Salette Reis
- REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira n.° 228, Porto 4050-313, Portugal
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Ekins S, Freundlich JS, Reynolds RC. Are bigger data sets better for machine learning? Fusing single-point and dual-event dose response data for Mycobacterium tuberculosis. J Chem Inf Model 2014; 54:2157-65. [PMID: 24968215 DOI: 10.1021/ci500264r] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tuberculosis is a major, neglected disease for which the quest to find new treatments continues. There is an abundance of data from large phenotypic screens in the public domain against Mycobacterium tuberculosis (Mtb). Since machine learning methods can learn from past data, we were interested in addressing whether more data builds better models. We now describe using Bayesian machine learning to assess whether we can improve our models by combining the large quantities of single-point data with the much smaller (higher quality) dual-event data sets, which use both dose-response data for both whole-cell antitubercular activity and Vero cell cytotoxicity. We have evaluated 12 models ranging from different single-point, dual-event dose-response, single-point and dual-event dose-response as well as combined data sets for three distinct data sets from the same laboratory. We used a fourth data set of active and inactive compounds from the same group as well as a smaller set of 177 active compounds from GlaxoSmithKline as test sets. Our data suggest combining single-point with dual-event dose-response data does not diminish the internal or external predictive ability of the models based on the receiver operator curve (ROC) for these models (internal ROC range 0.83-0.91, external ROC range 0.62-0.83) compared to the orders of magnitude smaller dual-event models (internal ROC range 0.6-0.83 and external ROC 0.54-0.83). In conclusion, models developed with 1200-5000 compounds appear to be as predictive as those generated with 25 000-350 000 molecules. Our results have implications for justifying further high-throughput screening versus focused testing based on model predictions.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry , 5616 Hilltop Needmore Road, Fuquay-Varina, North Carolina 27526, United States
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Martins F, Santos S, Ventura C, Elvas-Leitão R, Santos L, Vitorino S, Reis M, Miranda V, Correia HF, Aires-de-Sousa J, Kovalishyn V, Latino DA, Ramos J, Viveiros M. Design, synthesis and biological evaluation of novel isoniazid derivatives with potent antitubercular activity. Eur J Med Chem 2014; 81:119-38. [DOI: 10.1016/j.ejmech.2014.04.077] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 03/08/2014] [Accepted: 04/26/2014] [Indexed: 11/28/2022]
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Pinheiro M, Pisco S, Silva AS, Nunes C, Reis S. Evaluation of the effect of rifampicin on the biophysical properties of the membranes: Significance for therapeutic and side effects. Int J Pharm 2014; 466:190-7. [DOI: 10.1016/j.ijpharm.2014.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 02/27/2014] [Accepted: 03/01/2014] [Indexed: 01/01/2023]
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Pinheiro M, Arêde M, Caio JM, Moiteiro C, Lúcio M, Reis S. Drug–membrane interaction studies applied to N′-acetyl-rifabutin. Eur J Pharm Biopharm 2013; 85:597-603. [DOI: 10.1016/j.ejpb.2013.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 02/06/2013] [Accepted: 02/28/2013] [Indexed: 12/01/2022]
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Ekins S, Reynolds RC, Kim H, Koo MS, Ekonomidis M, Talaue M, Paget SD, Woolhiser LK, Lenaerts AJ, Bunin BA, Connell N, Freundlich JS. Bayesian models leveraging bioactivity and cytotoxicity information for drug discovery. ACTA ACUST UNITED AC 2013; 20:370-8. [PMID: 23521795 DOI: 10.1016/j.chembiol.2013.01.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 12/21/2012] [Accepted: 01/03/2013] [Indexed: 12/26/2022]
Abstract
Identification of unique leads represents a significant challenge in drug discovery. This hurdle is magnified in neglected diseases such as tuberculosis. We have leveraged public high-throughput screening (HTS) data to experimentally validate a virtual screening approach employing Bayesian models built with bioactivity information (single-event model) as well as bioactivity and cytotoxicity information (dual-event model). We virtually screened a commercial library and experimentally confirmed actives with hit rates exceeding typical HTS results by one to two orders of magnitude. This initial dual-event Bayesian model identified compounds with antitubercular whole-cell activity and low mammalian cell cytotoxicity from a published set of antimalarials. The most potent hit exhibits the in vitro activity and in vitro/in vivo safety profile of a drug lead. These Bayesian models offer significant economies in time and cost to drug discovery.
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Affiliation(s)
- Sean Ekins
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010, USA.
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Pinheiro M, Arêde M, Giner-Casares JJ, Nunes C, Caio JM, Moiteiro C, Lúcio M, Camacho L, Reis S. Effects of a novel antimycobacterial compound on the biophysical properties of a pulmonary surfactant model membrane. Int J Pharm 2013; 450:268-77. [DOI: 10.1016/j.ijpharm.2013.03.062] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 03/21/2013] [Accepted: 03/23/2013] [Indexed: 10/26/2022]
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Ekins S, Reynolds RC, Franzblau SG, Wan B, Freundlich JS, Bunin BA. Enhancing hit identification in Mycobacterium tuberculosis drug discovery using validated dual-event Bayesian models. PLoS One 2013; 8:e63240. [PMID: 23667592 DOI: 10.1371/journal.pone.0063240] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 03/31/2013] [Indexed: 02/01/2023] Open
Abstract
High-throughput screening (HTS) in whole cells is widely pursued to find compounds active against Mycobacterium tuberculosis (Mtb) for further development towards new tuberculosis (TB) drugs. Hit rates from these screens, usually conducted at 10 to 25 µM concentrations, typically range from less than 1% to the low single digits. New approaches to increase the efficiency of hit identification are urgently needed to learn from past screening data. The pharmaceutical industry has for many years taken advantage of computational approaches to optimize compound libraries for in vitro testing, a practice not fully embraced by academic laboratories in the search for new TB drugs. Adapting these proven approaches, we have recently built and validated Bayesian machine learning models for predicting compounds with activity against Mtb based on publicly available large-scale HTS data from the Tuberculosis Antimicrobial Acquisition Coordinating Facility. We now demonstrate the largest prospective validation to date in which we computationally screened 82,403 molecules with these Bayesian models, assayed a total of 550 molecules in vitro, and identified 124 actives against Mtb. Individual hit rates for the different datasets varied from 15–28%. We have identified several FDA approved and late stage clinical candidate kinase inhibitors with activity against Mtb which may represent starting points for further optimization. The computational models developed herein and the commercially available molecules derived from them are now available to any group pursuing Mtb drug discovery.
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Abstract
The search for small molecules with activity against Mycobacterium tuberculosis increasingly uses -high-throughput screening and computational methods. Previously, we have analyzed recent studies in which computational tools were used for cheminformatics. We have now updated this analysis to illustrate how they may assist in finding desirable leads for tuberculosis drug discovery. We provide our thoughts on strategies for drug discovery efforts for neglected diseases.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, Fuquay Varina, NC, USA
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26
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Yan M, Ma S. Recent Advances in the Research of Heterocyclic Compounds as Antitubercular Agents. ChemMedChem 2012; 7:2063-75. [DOI: 10.1002/cmdc.201200339] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Revised: 08/28/2012] [Indexed: 11/10/2022]
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Antinarelli LM, Carmo AM, Pavan FR, Leite CQ, Da Silva AD, Coimbra ES, Salunke DB. Increase of leishmanicidal and tubercular activities using steroids linked to aminoquinoline. Org Med Chem Lett 2012; 2:16. [PMID: 22551300 DOI: 10.1186/2191-2858-2-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 01/15/2012] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED BACKGROUND Aminoquinoline/steroid conjugates were synthesized based on the fact that steroid transporters have been shown to accept and carry a variety of drugs. So, in continuing our research of antileishmanial and antitubercular drugs, aminoquinoline/steroid conjugates (12, 13, and 14) were regioselectively synthesized via 1, 3-dipolar cycloaddition of alkynes 3, 5, and 7 with azide 12. The aminoquinoline/steroids conjugates were evaluated in vitro against Leishmania major and Mycobacterium tuberculosis. RESULTS Regioselective synthesis of the novel aminoquinoline/steroid conjugates was achieved in very high yield. All aminoquinoline/steroid conjugates (12, 13, and 14) exhibited best results against Leishmania and M. tuberculosis than the respective alkyne intermediate structures (3, 5, and 7, respectively). Among them, the compound 12 exhibited the best activity for M. tuberculosis (MIC = 8.8 μM). This result is comparable to drugs commonly used in tuberculosis treatment. Also, for antileishmanial assay, the aminoquinoline/steroid conjugates demonstrated a significant activity against promastigote and amastigote forms of L. major. CONCLUSIONS Addition of a steroid group to aminoquinoline molecules enhanced the leishmanicidal and antitubercular activities. These results highlight the importance of steroids as carrier.
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Singh R, Meena A, Negi A, Shanker K. Quantitative relationships between molecular descriptors, chromatographic retention behavior, andin vitroantituberculosis activity of phytol derivatives. JPC-J PLANAR CHROMAT 2012. [DOI: 10.1556/jpc.25.2012.1.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Blaser A, Palmer BD, Sutherland HS, Kmentova I, Franzblau SG, Wan B, Wang Y, Ma Z, Thompson AM, Denny WA. Structure-activity relationships for amide-, carbamate-, and urea-linked analogues of the tuberculosis drug (6S)-2-nitro-6-{[4-(trifluoromethoxy)benzyl]oxy}-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine (PA-824). J Med Chem 2011; 55:312-26. [PMID: 22148391 DOI: 10.1021/jm2012276] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Analogues of clinical tuberculosis drug (6S)-2-nitro-6-{[4-(trifluoromethoxy)benzyl]oxy}-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine (PA-824), in which the OCH(2) linkage was replaced with amide, carbamate, and urea functionality, were investigated as an alternative approach to address oxidative metabolism, reduce lipophilicity, and improve aqueous solubility. Several soluble monoaryl examples displayed moderately improved (∼2- to 4-fold) potencies against replicating Mycobacterium tuberculosis but were generally inferior inhibitors under anaerobic (nonreplicating) conditions. More lipophilic biaryl derivatives mostly displayed similar or reduced potencies to these in contrast to the parent biaryl series. The leading biaryl carbamate demonstrated exceptional metabolic stability and a 5-fold better efficacy than the parent drug in a mouse model of acute M. tuberculosis infection but was poorly soluble. Bioisosteric replacement of this biaryl moiety by arylpiperazine resulted in a soluble, orally bioavailable carbamate analogue providing identical activity in the acute model, comparable efficacy to OPC-67683 in a chronic infection model, favorable pharmacokinetic profiles across several species, and enhanced safety.
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Affiliation(s)
- Adrian Blaser
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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Chauhan PM, Sunduru N, Sharma M. Recent advances in the design and synthesis of heterocycles as anti-tubercular agents. Future Med Chem 2010; 2:1469-500. [PMID: 21426140 DOI: 10.4155/fmc.10.227] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Due to the unusual structure and chemical composition of the mycobacterial cell wall, effective tuberculosis (TB) treatment is difficult, making many antibiotics ineffective and hindering the entry of drugs. With approximately 33% of infection, TB is still the second most deadly infectious disease worldwide. The reasons for this are drug-resistant TB (multidrug resistant and extensively drug resistant), persistent infection (latent TB) and synergism of TB with HIV; furthermore no new chemical entity has emerged in last 40 years. New data available from the recently sequenced genome of the mycobacterium and the application of methods of modern drug design promise much for the fight against this disease. In this review, we present an introduction to TB, followed by an overview of new heterocyclic anti-tubercular moieties published during the last decade.
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Labadie GR, de la Iglesia A, Morbidoni HR. Targeting tuberculosis through a small focused library of 1,2,3-triazoles. Mol Divers 2011; 15:1017-24. [PMID: 21633789 DOI: 10.1007/s11030-011-9319-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2010] [Accepted: 05/17/2011] [Indexed: 11/24/2022]
Abstract
Looking for new active molecules against Mycobacterium tuberculosis, a small focused library of 1,2,3-triazoles was efficiently prepared by click chemistry. Compounds were subsequently tested against different pathogenic and opportunistic mycobacteria including M. avium and M. tuberculosis. Two of them showed MIC at lower μg/mL concentration for M. avium and even below that for M. tuberculosis, being more potent that control drugs.
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Affiliation(s)
- Guillermo R Labadie
- Instituto de Química Rosario (IQUIR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina.
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32
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Palkar MB, Noolvi MN, Maddi VS, Ghatole M, Nargund LG. Synthesis, spectral studies and biological evaluation of a novel series of 2-substituted-5,6-diarylsubstituted imidazo(2,1-b)-1,3,4-thiadiazole derivatives as possible anti-tubercular agents. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9646-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Ekins S, Freundlich JS, Choi I, Sarker M, Talcott C. Computational databases, pathway and cheminformatics tools for tuberculosis drug discovery. Trends Microbiol 2010; 19:65-74. [PMID: 21129975 DOI: 10.1016/j.tim.2010.10.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/15/2010] [Accepted: 10/29/2010] [Indexed: 01/31/2023]
Abstract
We are witnessing the growing menace of both increasing cases of drug-sensitive and drug-resistant Mycobacterium tuberculosis strains and the challenge to produce the first new tuberculosis (TB) drug in well over 40 years. The TB community, having invested in extensive high-throughput screening efforts, is faced with the question of how to optimally leverage these data to move from a hit to a lead to a clinical candidate and potentially, a new drug. Complementing this approach, yet conducted on a much smaller scale, cheminformatic techniques have been leveraged and are examined in this review. We suggest that these computational approaches should be optimally integrated within a workflow with experimental approaches to accelerate TB drug discovery.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, 601 Runnymede Avenue, Jenkintown, PA 19046, USA.
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Ekins S, Kaneko T, Lipinski CA, Bradford J, Dole K, Spektor A, Gregory K, Blondeau D, Ernst S, Yang J, Goncharoff N, Hohman MM, Bunin BA. Analysis and hit filtering of a very large library of compounds screened against Mycobacterium tuberculosis. Mol Biosyst 2010; 6:2316-2324. [PMID: 20835433 DOI: 10.1039/c0mb00104j] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
There is an urgent need for new drugs against tuberculosis which annually claims 1.7-1.8 million lives. One approach to identify potential leads is to screen in vitro small molecules against Mycobacterium tuberculosis (Mtb). Until recently there was no central repository to collect information on compounds screened. Consequently, it has been difficult to analyze molecular properties of compounds that inhibit the growth of Mtb in vitro. We have collected data from publically available sources on over 300 000 small molecules deposited in the Collaborative Drug Discovery TB Database. A cheminformatics analysis on these compounds indicates that inhibitors of the growth of Mtb have statistically higher mean logP, rule of 5 alerts, while also having lower HBD count, atom count and lower PSA (ChemAxon descriptors), compared to compounds that are classed as inactive. Additionally, Bayesian models for selecting Mtb active compounds were evaluated with over 100 000 compounds and, they demonstrated 10 fold enrichment over random for the top ranked 600 compounds. This represents a promising approach for finding compounds active against Mtb in whole cells screened under the same in vitro conditions. Various sets of Mtb hit molecules were also examined by various filtering rules used widely in the pharmaceutical industry to identify compounds with potentially reactive moieties. We found differences between the number of compounds flagged by these rules in Mtb datasets, malaria hits, FDA approved drugs and antibiotics. Combining these approaches may enable selection of compounds with increased probability of inhibition of whole cell Mtb activity.
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Affiliation(s)
- Sean Ekins
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010. and Collaborations In Chemistry, 601 Runnymede Avenue, Jenkintown, PA 19046, USA and Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, USA and Department of Pharmacology, Robert Wood Johnson Medical School, University of Medicine & Dentistry of New Jersey, Piscataway, New Jersey 08854, USA
| | - Takushi Kaneko
- Global Alliance for TB Drug Development, 40 Wall Street, 24th floor, New York, NY 10005, USA
| | | | - Justin Bradford
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010.
| | - Krishna Dole
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010.
| | - Anna Spektor
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010.
| | - Kellan Gregory
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010.
| | - David Blondeau
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010.
| | - Sylvia Ernst
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010.
| | - Jeremy Yang
- Division of Biocomputing, University of New Mexico, Albuquerque, NM 87131
| | - Nicko Goncharoff
- SureChem, The Macmillan Building, 4 Crinan Street, London, UKN1 9XW
| | - Moses M Hohman
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010.
| | - Barry A Bunin
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010.
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Moraski GC, Chang M, Villegas-Estrada A, Franzblau SG, Möllmann U, Miller MJ. Structure–activity relationship of new anti-tuberculosis agents derived from oxazoline and oxazole benzyl esters. Eur J Med Chem 2010. [DOI: 10.1016/j.ejmech.2009.12.074 pmid: 20116900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Moraski GC, Chang M, Villegas-Estrada A, Franzblau SG, Möllmann U, Miller MJ. Structure-activity relationship of new anti-tuberculosis agents derived from oxazoline and oxazole benzyl esters. Eur J Med Chem 2010; 45:1703-16. [PMID: 20116900 PMCID: PMC2843756 DOI: 10.1016/j.ejmech.2009.12.074] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 12/21/2009] [Accepted: 12/23/2009] [Indexed: 11/29/2022]
Abstract
During the syntheses and studies of natural iron chelators (mycobactins), we serendipitously discovered that a simple, small molecule, oxazoline-containing intermediate 3 displayed surprising anti-tuberculosis activity (MIC of 7.7 microM, average). Herein we report elaboration of SAR around this hit as well as the syntheses and evaluation of a hundred oxazoline- and oxazole-containing compounds derived from an efficient three step process: 1) formation of beta-hydroxy amides with serine or threonine; 2) cyclization to afford oxazolines; and 3) dehydration to give the corresponding oxazoles. A number of compounds prepared by this method were shown to possess impressive activity against Mycobacterium tuberculosis, extremely low toxicity and therefore high therapeutic indexes, as well as activity against even the more recalcitrant non-replicating form of M. tuberculosis. The uniqueness of their structures and their simplicity should allow them to be further optimized to meet ADME (absorption, distribution, metabolism, excretion) requirements. The syntheses of eight of the most potent in vitro compounds were scaled up and the compounds were tested in an in vivo mouse infection model to evaluate their efficacy before engaging upon more elaborate compound design and optimization.
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Affiliation(s)
- Garrett C. Moraski
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46656
| | - Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46656
| | - Adriel Villegas-Estrada
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46656
| | - Scott G. Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612
| | - Ute Möllmann
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Marvin J. Miller
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46656
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Ekins S, Bradford J, Dole K, Spektor A, Gregory K, Blondeau D, Hohman M, Bunin BA. A collaborative database and computational models for tuberculosis drug discovery. Mol Biosyst 2010; 6:840-51. [PMID: 20567770 DOI: 10.1039/b917766c] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The search for molecules with activity against Mycobacterium tuberculosis (Mtb) is employing many approaches in parallel including high throughput screening and computational methods. We have developed a database (CDD TB) to capture public and private Mtb data while enabling data mining and collaborations with other researchers. We have used the public data along with several cheminformatics approaches to produce models that describe active and inactive compounds. We have compared these datasets to those for known FDA approved drugs and between Mtb active and inactive compounds. The distribution of polar surface area and pK(a) of active compounds was found to be a statistically significant determinant of activity against Mtb. Hydrophobicity was not always statistically significant. Bayesian classification models for 220, 463 molecules were generated and tested with external molecules, and enabled the discrimination of active or inactive substructures from other datasets in the CDD TB. Computational pharmacophores based on known Mtb drugs were able to map to and retrieve a small subset of some of the Mtb datasets, including a high percentage of Mtb actives. The combination of the database, dataset analysis, Bayesian and pharmacophore models provides new insights into molecular properties and features that are determinants of activity in whole cells. This study provides novel insights into the key 1D molecular descriptors, 2D chemical substructures and 3D pharmacophores which can be used to mine the chemistry space, prioritizing those molecules with a higher probability of activity against Mtb.
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Affiliation(s)
- Sean Ekins
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94403, USA.
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Pavan FR, Poelhsitz GV, do Nascimento FB, Leite SR, Batista AA, Deflon VM, Sato DN, Franzblau SG, Leite CQ. Ruthenium (II) phosphine/picolinate complexes as antimycobacterial agents. Eur J Med Chem 2010; 45:598-601. [DOI: 10.1016/j.ejmech.2009.10.049] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 08/11/2009] [Accepted: 10/29/2009] [Indexed: 11/21/2022]
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Saikia D, Parihar S, Chanda D, Ojha S, Kumar J, Chanotiya C, Shanker K, Negi AS. Antitubercular potential of some semisynthetic analogues of phytol. Bioorg Med Chem Lett 2010; 20:508-12. [DOI: 10.1016/j.bmcl.2009.11.107] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Revised: 10/30/2009] [Accepted: 11/20/2009] [Indexed: 11/20/2022]
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Kumar RS, Perumal S, Shetty KA, Yogeeswari P, Sriram D. 1,3-Dipolar cycloaddition of C-aryl-N-phenylnitrones to (R)-1-(1-phenylethyl)-3-[(E)-arylmethylidene]tetrahydro-4(1H)-pyridinones: Synthesis and antimycobacterial evaluation of enantiomerically pure spiroisoxazolidines. Eur J Med Chem 2010; 45:124-33. [DOI: 10.1016/j.ejmech.2009.09.034] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 09/10/2009] [Accepted: 09/22/2009] [Indexed: 11/30/2022]
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Jaju S, Palkar M, Maddi V, Ronad P, Mamledesai S, Satyanarayana D, Ghatole M. Synthesis and Antimycobacterial Activity of a Novel Series of Isonicotinylhydrazide Derivatives. Arch Pharm (Weinheim) 2009; 342:723-31. [DOI: 10.1002/ardp.200900001] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Christophe T, Jackson M, Jeon HK, Fenistein D, Contreras-Dominguez M, Kim J, Genovesio A, Carralot JP, Ewann F, Kim EH, Lee SY, Kang S, Seo MJ, Park EJ, Škovierová H, Pham H, Riccardi G, Nam JY, Marsollier L, Kempf M, Joly-Guillou ML, Oh T, Shin WK, No Z, Nehrbass U, Brosch R, Cole ST, Brodin P. High content screening identifies decaprenyl-phosphoribose 2' epimerase as a target for intracellular antimycobacterial inhibitors. PLoS Pathog 2009; 5:e1000645. [PMID: 19876393 PMCID: PMC2763345 DOI: 10.1371/journal.ppat.1000645] [Citation(s) in RCA: 235] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 10/05/2009] [Indexed: 12/04/2022] Open
Abstract
A critical feature of Mycobacterium tuberculosis, the causative agent of human tuberculosis (TB), is its ability to survive and multiply within macrophages, making these host cells an ideal niche for persisting microbes. Killing the intracellular tubercle bacilli is a key requirement for efficient tuberculosis treatment, yet identifying potent inhibitors has been hampered by labor-intensive techniques and lack of validated targets. Here, we present the development of a phenotypic cell-based assay that uses automated confocal fluorescence microscopy for high throughput screening of chemicals that interfere with the replication of M. tuberculosis within macrophages. Screening a library of 57,000 small molecules led to the identification of 135 active compounds with potent intracellular anti-mycobacterial efficacy and no host cell toxicity. Among these, the dinitrobenzamide derivatives (DNB) showed high activity against M. tuberculosis, including extensively drug resistant (XDR) strains. More importantly, we demonstrate that incubation of M. tuberculosis with DNB inhibited the formation of both lipoarabinomannan and arabinogalactan, attributable to the inhibition of decaprenyl-phospho-arabinose synthesis catalyzed by the decaprenyl-phosphoribose 2′ epimerase DprE1/DprE2. Inhibition of this new target will likely contribute to new therapeutic solutions against emerging XDR-TB. Beyond validating the high throughput/content screening approach, our results open new avenues for finding the next generation of antimicrobials. Tuberculosis is still a major threat to global health. The disease in humans is caused by a bacterium, Mycobacterium tuberculosis, and treatment of an infected individual requires more than six months of chemotherapy. Because such a long course of treatment is required, compliance is low, which can result in the development of multidrug resistant strains (MDR-TB) and even extremely resistant strains (XDR-TB). Identifying new drug targets and potential lead therapeutic compounds are needed to combat MDR-XDR-TB. We developed a new type of assay based on the visualization of mycobacterium replication within host cells and applied it for the search of compounds that are able to chase the pathogen from its hideout. As a result, we found 20 new series of drug candidates that are effective against the bacilli in its hiding place, potentially addressing a crucial aspect in the resilience of the disease. We also showed that one series of compounds acts by inhibiting a key enzyme required for the synthesis of an essential component from the mycobacterial cell wall that is not targeted by any of the commercially available antituberculosis drugs. Altogether, our results pave the way for development of the next generation of antibacterial agents.
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Affiliation(s)
- Thierry Christophe
- Screening Technologies and Pharmacology, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Hee Kyoung Jeon
- Screening Technologies and Pharmacology, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Denis Fenistein
- Image Mining, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Monica Contreras-Dominguez
- Biology of Intracellular Pathogens Inserm Avenir Group, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Jaeseung Kim
- Medicinal Chemistry, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Auguste Genovesio
- Image Mining, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Jean-Philippe Carralot
- Biology of Intracellular Pathogens Inserm Avenir Group, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Fanny Ewann
- Biology of Intracellular Pathogens Inserm Avenir Group, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Eun Hye Kim
- Biology of Intracellular Pathogens Inserm Avenir Group, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Sae Yeon Lee
- Medicinal Chemistry, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Sunhee Kang
- Medicinal Chemistry, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Min Jung Seo
- Medicinal Chemistry, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Eun Jung Park
- Medicinal Chemistry, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Henrieta Škovierová
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Ha Pham
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Giovanna Riccardi
- Dipartimento di Genetica e Microbiologia, Università degli Studi di Pavia, Pavia, Italy
| | - Ji Youn Nam
- Screening Technologies and Pharmacology, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Laurent Marsollier
- Groupe d'Etude des Interactions Hôte Pathogène, Université d'Angers, Angers, France
| | - Marie Kempf
- Groupe d'Etude des Interactions Hôte Pathogène, Université d'Angers, Angers, France
| | | | - Taegwon Oh
- International Tuberculosis Research Center, Masan, Korea
| | - Won Kyung Shin
- International Tuberculosis Research Center, Masan, Korea
| | - Zaesung No
- Medicinal Chemistry, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Ulf Nehrbass
- Screening Technologies and Pharmacology, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Roland Brosch
- Institut Pasteur, Integrated Mycobacterial Pathogenomics, Paris, France
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Priscille Brodin
- Biology of Intracellular Pathogens Inserm Avenir Group, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea
- Institut Pasteur, Integrated Mycobacterial Pathogenomics, Paris, France
- * E-mail:
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Ananthan S, Faaleolea ER, Goldman RC, Hobrath JV, Kwong CD, Laughon BE, Maddry JA, Mehta A, Rasmussen L, Reynolds RC, Secrist JA, Shindo N, Showe DN, Sosa MI, Suling WJ, White EL. High-throughput screening for inhibitors of Mycobacterium tuberculosis H37Rv. Tuberculosis (Edinb) 2009; 89:334-53. [PMID: 19758845 DOI: 10.1016/j.tube.2009.05.008] [Citation(s) in RCA: 221] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 05/20/2009] [Accepted: 05/27/2009] [Indexed: 10/20/2022]
Abstract
There is an urgent need for the discovery and development of new antitubercular agents that target new biochemical pathways and treat drug resistant forms of the disease. One approach to addressing this need is through high-throughput screening of medicinally relevant libraries against the whole bacterium in order to discover a variety of new, active scaffolds that will stimulate new biological research and drug discovery. Through the Tuberculosis Antimicrobial Acquisition and Coordinating Facility (www.taacf.org), a large, medicinally relevant chemical library was screened against M. tuberculosis strain H37Rv. The screening methods and a medicinal chemistry analysis of the results are reported herein.
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Affiliation(s)
- Subramaniam Ananthan
- Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205, USA.
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Figueiredo R, Moiteiro C, Medeiros MA, Silva PAD, Ramos D, Spies F, Ribeiro M, Lourenço MCS, Júnior I, Gaspar MM, Cruz MEM, Curto MJM, Franzblau S, Orozco H, Aguilar D, Hernandez-Pando R, Costa MC. Synthesis and evaluation of rifabutin analogs against Mycobacterium avium and H37Rv, MDR and NRP Mycobacterium tuberculosis. Bioorg Med Chem 2009; 17:503-11. [DOI: 10.1016/j.bmc.2008.12.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 11/30/2008] [Accepted: 12/02/2008] [Indexed: 11/15/2022]
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Slayden RA, Belisle JT. Morphological features and signature gene response elicited by inactivation of FtsI in Mycobacterium tuberculosis. J Antimicrob Chemother 2008; 63:451-7. [PMID: 19109339 DOI: 10.1093/jac/dkn507] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Universally conserved events in cell division provide the opportunity for the development of novel chemotherapeutics against Mycobacterium tuberculosis. The aim of this study was to use the beta-lactam antimicrobials cefalexin and piperacillin to inhibit FtsI and characterize the morphological changes and global transcriptional activities of genes to identify a signature response to FtsI inactivation. METHODS Cefalexin and piperacillin were used to block cell division, and microscopy was used to evaluate the effects on bacterial morphology and ultrastructure. Global transcriptional analysis was performed to determine the impact of FtsI inhibition on cell cycle processes and to identify molecular markers. RESULTS Inhibition of FtsI with cefalexin and piperacillin resulted in filamentous cells with multiple concentric rings and occasional branching as visualized by light and electron microscopy. Whole genome microarray-based transcriptional profiling and transcriptional mapping allowed the evaluation of cell cycle processes in response to inhibition of FtsI and characterization of transcriptional response and cell cycle processes. CONCLUSIONS This study substantiated that FtsZ-ring constriction and septal resolution require the transpeptidase activity of FtsI, making FtsI essential for cell division in M. tuberculosis. Therefore, FtsI is a target for drug discovery, and these studies provided a molecular signature of FtsI inactivation that can be applied to screening strategies for novel FtsI inhibitors.
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Affiliation(s)
- Richard A Slayden
- Department of Microbiology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO 80523, USA.
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van den Boogaard J, Kibiki GS, Kisanga ER, Boeree MJ, Aarnoutse RE. New drugs against tuberculosis: problems, progress, and evaluation of agents in clinical development. Antimicrob Agents Chemother 2009; 53:849-62. [PMID: 19075046 DOI: 10.1128/AAC.00749-08] [Citation(s) in RCA: 167] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Cho Y, Ioerger TR, Sacchettini JC. Discovery of novel nitrobenzothiazole inhibitors for Mycobacterium tuberculosis ATP phosphoribosyl transferase (HisG) through virtual screening. J Med Chem 2008; 51:5984-92. [PMID: 18778048 PMCID: PMC2610488 DOI: 10.1021/jm800328v] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
HisG is an ATP-phosphoribosyl transferase (ATPPRTase) that catalyzes the first step in the biosynthetic pathway for histidine. Among the enzymes in this pathway, only HisG represents a potential drug target for tuberculosis. Only a few inhibitors with limited potency for HisG are currently known. To discover more potent and diverse inhibitors, virtual screening was performed. The crystal structure of M. tuberculosis HisG has been solved and reveals a large, solvent-exposed active site with subsites for ATP and PRPP substrates. Two docking algorithms, GOLD and FLEXX, were used to screen two large libraries, Chembridge and NCI, containing over 500000 compounds combined. An initial subset of top-ranked compounds were selected and assayed, and seven were found to have enzyme inhibition activity at micromolar concentrations. Several of the hits contained a nitrobenzothiazole fragment, which was predicted to dock into the monophosphate-binding loop, and this binding mode was confirmed by crystallographic evidence. A secondary screen was performed to identify compounds with similar structures. Several of these also exhibited micromolar inhibition. Furthermore, two of the compounds showed bacteriocidal activity in a whole-cell assay against Mycobacterium smegmatis.
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Affiliation(s)
- Yoonsang Cho
- Department of Pharmacology, Yale University School of Medicine
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Respicio L, Nair PA, Huang Q, Anil B, Tracz S, Truglio JJ, Kisker C, Raleigh DP, Ojima I, Knudson DL, Tonge PJ, Slayden RA. Characterizing septum inhibition in Mycobacterium tuberculosis for novel drug discovery. Tuberculosis (Edinb) 2008; 88:420-9. [PMID: 18479968 DOI: 10.1016/j.tube.2008.03.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Revised: 03/04/2008] [Accepted: 03/08/2008] [Indexed: 11/23/2022]
Abstract
A temperature sensitive mutation in the cell division protein FtsZ was used in combination with transcriptional analysis to identify biomarkers for inhibition of septum formation. Crystallography and modeling revealed that the glycine for aspartate substitution at amino acid 210 was located in helix 8 of the protein, adjacent to the T7 synergy loop. To verify the molecular behavior of FtsZ D210G, the in vitro activity and structural stability were evaluated as a function of temperature. These analyses confirmed that the FtsZ D210G mutant had reduced GTPase and polymerization activity compared to wild-type FtsZ, and CD spectroscopy demonstrated that both FtsZ D210G and wild-type FtsZ had similar structure and stability. Significantly, the FtsZ D210G merodiploid strain of M. tuberculosis had compromised growth at 37 degrees C, substantiating the suitability of FtsZ D210G as a molecular tool for global analysis in response to improper FtsZ polymerization and septum inhibition. Advanced model-based bioinformatics and transcriptional mapping were used to identify high-content multiple features that provide biomarkers for the development of a rational drug screening platform for discovering novel chemotherapeutics that target cell division.
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Boyne ME, Sullivan TJ, amEnde CW, Lu H, Gruppo V, Heaslip D, Amin AG, Chatterjee D, Lenaerts A, Tonge PJ, Slayden RA. Targeting fatty acid biosynthesis for the development of novel chemotherapeutics against Mycobacterium tuberculosis: evaluation of A-ring-modified diphenyl ethers as high-affinity InhA inhibitors. Antimicrob Agents Chemother 2007; 51:3562-7. [PMID: 17664324 PMCID: PMC2043287 DOI: 10.1128/aac.00383-07] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Structure-based design was used to develop a focused library of A-ring-modified diphenyl ether InhA inhibitors. From this library of analogs, two high-affinity alkyl-substituted diphenyl ethers, 6PP and 8PP, were selected for advanced study into their in vitro activity against Mycobacterium tuberculosis clinical isolates, their in vivo properties, and their signature response mode of action. 6PP and 8PP demonstrated enhanced activity against whole bacteria and showed activity in a rapid macrophage model of infection. In addition, transcriptional profiling revealed that the A-ring modifications of 6PP and 8PP increased the specificity of each analog for InhA. Both analogs had substantially longer half-lives in serum than did the parent compound, exhibited a fivefold reduction in cytotoxicity compared to the parent compound, and were well tolerated when administered orally at 300 mg/kg of body weight in animal models. Thus, the A-ring modifications increased the affinity and whole-cell specificity of the compounds for InhA and increased their bioavailability. The next step in optimization of the pharmacophore for preclinical evaluation is modification of the B ring to increase the bioavailability to that required for oral delivery.
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Affiliation(s)
- Melissa E Boyne
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
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Abstract
Tuberculosis is today amongst the worldwide health threats. As resistant strains of Mycobacterium tuberculosis have slowly emerged, treatment failure is too often a fact, especially in countries lacking the necessary health care organisation to provide the long and costly treatment adapted to patients. Because of lack of treatment or lack of adapted treatment, at least two million people will die of tuberculosis this year. Due to this concern, this infectious disease was the focus of renewed scientific interest in the last decade. Regimens were optimized and much was learnt on the mechanisms of action of the antituberculosis drugs used. Moreover, the quest for original drugs overcoming some of the problems of current regimens also became the focus of research programmes and many new series of M. tuberculosis growth inhibitors were reported. This review presents the drugs currently used in antituberculosis treatments and the most advanced compounds undergoing clinical trials. We then provide a description of their mechanism of action along with other series of inhibitors known to act on related biochemical targets. This is followed by other inhibitors of M. tuberculosis growth, including recently reported compounds devoid of a reported mechanism of action.
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Affiliation(s)
- Yves L Janin
- URA 2128 CNRS-Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
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