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Sahoo SK, Ommi O, Maddipatla S, Singh P, Ahmad MN, Kaul G, Nanduri S, Dasgupta A, Chopra S, Yaddanapudi VM. Isoxazole carboxylic acid methyl ester-based urea and thiourea derivatives as promising antitubercular agents. Mol Divers 2023; 27:2037-2052. [PMID: 36282413 PMCID: PMC9592870 DOI: 10.1007/s11030-022-10543-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/28/2022] [Indexed: 11/01/2022]
Abstract
In our continued efforts to find potential chemotherapeutics active against drug-resistant (DR) Mycobacterium tuberculosis (Mtb), causative agent of Tuberculosis (TB) and to curb the current burdensome treatment regimen, herein we describe the synthesis and biological evaluation of urea and thiourea variants of 5-phenyl-3-isoxazolecarboxylic acid methyl esters as promising anti-TB agent. Majority of the tested compounds displayed potent in vitro activity not only against drug-susceptible (DS) Mtb H37Rv but also against drug-resistant (DR) Mtb. Cell viability test against Vero cells deemed these compounds devoid of significant toxicity. 3,4-Dichlorophenyl derivative (MIC 0.25 µg/mL) and 4-chlorophenyl congener (MIC 1 µg/mL) among urea and thiourea libraries respectively exhibited optimum potency. Lead optimization resulted in the identification of 1,4-linked analogue of 3,4-dichlorophenyl urea derivative demonstrating improved selectivity. Further, in silico study complemented with previously proposed prodrug like attributes of isoxazole esters. Taken together, this molecular hybridization approach presents a new chemotype having potential to be translated into an alternate anti-Mtb agent.
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Affiliation(s)
- Santosh Kumar Sahoo
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India
| | - Ojaswitha Ommi
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India
| | - Sarvan Maddipatla
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India
| | - Priti Singh
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India
| | - Mohammad Naiyaz Ahmad
- Division of Microbiology, CSIR-Central Drug Research Institute, Sitapur Road, Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India
- AcSIR: Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Grace Kaul
- Division of Microbiology, CSIR-Central Drug Research Institute, Sitapur Road, Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India
- AcSIR: Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Srinivas Nanduri
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India
| | - Arunava Dasgupta
- Division of Microbiology, CSIR-Central Drug Research Institute, Sitapur Road, Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India.
- AcSIR: Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Sidharth Chopra
- Division of Microbiology, CSIR-Central Drug Research Institute, Sitapur Road, Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India.
- AcSIR: Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Venkata Madhavi Yaddanapudi
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India.
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2
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Capela R, Félix R, Clariano M, Nunes D, Perry MDJ, Lopes F. Target Identification in Anti-Tuberculosis Drug Discovery. Int J Mol Sci 2023; 24:10482. [PMID: 37445660 DOI: 10.3390/ijms241310482] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the etiological agent of tuberculosis (TB), a disease that, although preventable and curable, remains a global epidemic due to the emergence of resistance and a latent form responsible for a long period of treatment. Drug discovery in TB is a challenging task due to the heterogeneity of the disease, the emergence of resistance, and uncomplete knowledge of the pathophysiology of the disease. The limited permeability of the cell wall and the presence of multiple efflux pumps remain a major barrier to achieve effective intracellular drug accumulation. While the complete genome sequence of Mtb has been determined and several potential protein targets have been validated, the lack of adequate models for in vitro and in vivo studies is a limiting factor in TB drug discovery programs. In current therapeutic regimens, less than 0.5% of bacterial proteins are targeted during the biosynthesis of the cell wall and the energetic metabolism of two of the most important processes exploited for TB chemotherapeutics. This review provides an overview on the current challenges in TB drug discovery and emerging Mtb druggable proteins, and explains how chemical probes for protein profiling enabled the identification of new targets and biomarkers, paving the way to disruptive therapeutic regimens and diagnostic tools.
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Affiliation(s)
- Rita Capela
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Rita Félix
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Marta Clariano
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Diogo Nunes
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Maria de Jesus Perry
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Francisca Lopes
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
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Dak M, Šlachtová V, Šebela M, Bazgier V, Berka K, Smiejkowska N, Oorts L, Cappoen D, Brulíková L. Novel heterocyclic hydroxamates as inhibitors of the mycobacterial zinc metalloprotease Zmp1 to probe its mechanism of function. Eur J Med Chem 2022; 244:114831. [DOI: 10.1016/j.ejmech.2022.114831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/20/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022]
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Fernandes GFS, Thompson AM, Castagnolo D, Denny WA, Dos Santos JL. Tuberculosis Drug Discovery: Challenges and New Horizons. J Med Chem 2022; 65:7489-7531. [PMID: 35612311 DOI: 10.1021/acs.jmedchem.2c00227] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Over the past 2000 years, tuberculosis (TB) has claimed more lives than any other infectious disease. In 2020 alone, TB was responsible for 1.5 million deaths worldwide, comparable to the 1.8 million deaths caused by COVID-19. The World Health Organization has stated that new TB drugs must be developed to end this pandemic. After decades of neglect in this field, a renaissance era of TB drug discovery has arrived, in which many novel candidates have entered clinical trials. However, while hundreds of molecules are reported annually as promising anti-TB agents, very few successfully progress to clinical development. In this Perspective, we critically review those anti-TB compounds published in the last 6 years that demonstrate good in vivo efficacy against Mycobacterium tuberculosis. Additionally, we highlight the main challenges and strategies for developing new TB drugs and the current global pipeline of drug candidates in clinical studies to foment fresh research perspectives.
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Affiliation(s)
- Guilherme F S Fernandes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Andrew M Thompson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Daniele Castagnolo
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - William A Denny
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jean L Dos Santos
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14800903, Brazil
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5
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Tuyiringire N, Taremwa Mugisha I, Tusubira D, Munyampundu JP, Mambo Muvunyi C, Vander Heyden Y. In vitro antimycobacterial activity of medicinal plants Lantana camara, Cryptolepis sanguinolenta, and Zanthoxylum leprieurii. J Clin Tuberc Other Mycobact Dis 2022; 27:100307. [PMID: 35284659 PMCID: PMC8904236 DOI: 10.1016/j.jctube.2022.100307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Imperative need exists to search for new anti-TB drugs that are safer, and more effective against drug-resistant strains. Medicinal plants have been the source of active ingredients for drug development. However, the slow growth and biosafety level requirements of M. tuberculosis culture are considerable challenges. M. smegmatis can be used as a surrogate for M. tuberculosis. In the current study, preliminary phytochemical screening and antimycobacterial activity evaluation of crude methanolic extracts of medicinal plants against M. smegmatis, and two M. tuberculosis strains, were conducted. Materials and Methods Crude methanolic extracts, obtained from the leaves of L. camara, roots of C. sanguinolenta, and stem barks of Z. leprieurii, were tested for antimycobacterial activity against M. smegmatis (mc2155), pan-sensitive (H37Rv), and rifampicin-resistant (TMC-331) M. tuberculosis, using visual Resazurin Microtiter Assay (REMA) on 96 well plates. Preliminary qualitative phytochemical screening tests were performed using standard chemical methods. Results The three methanolic extracts inhibited mycobacterial growth in vitro. They were more active against rifampicin-resistant strain with MICs of 176, 97, and 45 µg/mL for L. camara, C. sanguinolenta, and Z. leprieurii extracts, respectively. The lowest activity was observed against M. smegmatis with MICs of 574, 325, and 520 µg/mL, respectively. Against H37Rv, activity was intermediate to those of TMC-331 and mc2155. However, L. camara extract showed the same activity against H37Rv and M. smegmatis. Preliminary phytochemical analysis revealed alkaloids, flavonoids, phenolic compounds, saponins, tannins, and terpenoids. Conclusions Leaves of L. camara, roots of C. sanguinolenta, and stem barks of Z. leprieurii exhibit antimycobacterial activity against M. smegmatis, pan-sensitive, and rifampicin-resistant M. tuberculosis. This offers the possibilities for novel therapeutic opportunities against TB including multidrug-resistant TB. Further investigations on safety and mechanisms of action are required. These studies could be done using M. smegmatis as a surrogate for the highly pathogenic M. tuberculosis.
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Affiliation(s)
- Naasson Tuyiringire
- Pharm-BioTechnology and Traditional Medicine Centre (PHARMBIOTRAC), Department of Pharmacy, Mbarara University of Science & Technology, P. O. Box 1410, Mbarara, Uganda
- School of Nursing and Midwifery, College of Medicine and Health Sciences, University of Rwanda, KG11 Ave, 47St/P.O. Box 3286, Kigali, Rwanda
- Corresponding author.
| | - Ivan Taremwa Mugisha
- Institute of Applied Health Sciences, Clarke International University, P.O. Box 7782, Kampala, Uganda
| | - Deusdedit Tusubira
- Department of Biochemistry, Mbarara University of Science and Technology, P. O. Box 1410, Mbarara, Uganda
| | - Jean-Pierre Munyampundu
- School of Science, College of Science and Technology, University of Rwanda, KN 67 Street Nyarugenge, P.O. Box 3900, Kigali, Rwanda
| | - Claude Mambo Muvunyi
- College of Medicine and Health Sciences, University of Rwanda, KG11 Ave, 47St/P.O. Box 3286, Kigali, Rwanda
| | - Yvan Vander Heyden
- Department of Analytical Chemistry, Applied Chemometrics and Molecular Modelling, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, Belgium
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Perveen S, Kumari D, Singh K, Sharma R. Tuberculosis drug discovery: Progression and future interventions in the wake of emerging resistance. Eur J Med Chem 2022; 229:114066. [PMID: 34973508 DOI: 10.1016/j.ejmech.2021.114066] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/13/2021] [Accepted: 12/19/2021] [Indexed: 02/06/2023]
Abstract
The emergence of drug resistance continues to afflict TB control where drug resistant strains have become a global health concern. Contrary to drug-sensitive TB, the treatment of MDR/XDR-TB is more complicated requiring the administration of second-line drugs that are inefficient than the first line drugs and are associated with greater side effects. The emergence of drug resistant Mtb strains had coincided with an innovation void in the field of drug discovery of anti-mycobacterials. However, the approval of bedaquiline and delamanid recently for use in MDR/XDR-TB has given an impetus to the TB drug discovery. The review discusses the drug discovery efforts in the field of tuberculosis with a focus on the strategies adopted and challenges confronted by TB research community. Here, we discuss the diverse clinical candidates in the current TB drug discovery pipeline. There is an urgent need to combat the current TB menace through multidisciplinary approaches and strategies making use of the recent advances in understanding the molecular biology and pathogenesis of Mtb. The review highlights the recent advances in drug discovery, with the host directed therapeutics and nanoparticles-drug delivery coming up as important tools to fight tuberculosis in the future.
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Affiliation(s)
- Summaya Perveen
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Diksha Kumari
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Kuljit Singh
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rashmi Sharma
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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7
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In Vitro Profiling of Antitubercular Compounds by Rapid, Efficient, and Nondestructive Assays Using Autoluminescent Mycobacterium tuberculosis. Antimicrob Agents Chemother 2021; 65:e0028221. [PMID: 34097493 PMCID: PMC8284454 DOI: 10.1128/aac.00282-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anti-infective drug discovery is greatly facilitated by the availability of in vitro assays that are more proficient at predicting the preclinical success of screening hits. Tuberculosis (TB) drug discovery is hindered by the relatively slow growth rate of Mycobacterium tuberculosis and the use of whole-cell-based in vitro assays that are inherently time-consuming, and for these reasons, rapid, noninvasive bioluminescence-based assays have been widely used in anti-TB drug discovery and development. In this study, in vitro assays that employ autoluminescent M. tuberculosis were optimized to determine MIC, minimum bactericidal concentration (MBC), time-kill curves, activity against macrophage internalized M. tuberculosis (90% effective concentration [EC90]), and postantibiotic effect (PAE) to provide rapid and dynamic biological information. Standardization of the luminescence-based MIC, MBC, time-kill, EC90, and PAE assays was accomplished by comparing results of established TB drugs and two ClpC1-targeting TB leads, ecumicin and rufomycin, to those obtained from conventional assays and/or to previous studies. Cumulatively, the use of the various streamlined luminescence-based in vitro assays has reduced the time for comprehensive in vitro profiling (MIC, MBC, time-kill, EC90, and PAE) by 2 months. The luminescence-based in vitro MBC and EC90 assays yield time and concentration-dependent kill information that can be used for pharmacokinetic-pharmacodynamic (PK-PD) modeling. The MBC and EC90 time-kill graphs revealed a significantly more rapid bactericidal activity for ecumicin than rufomycin. The PAEs of both ecumicin and rufomycin were comparable to that of the first-line TB drug rifampin. The optimization of several nondestructive, luminescence-based TB assays facilitates the in vitro profiling of TB drug leads in an efficient manner.
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Subhash N, Sundaramurthy V. Advances in host-based screening for compounds with intracellular anti-mycobacterial activity. Cell Microbiol 2021; 23:e13337. [PMID: 33813790 DOI: 10.1111/cmi.13337] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/14/2022]
Abstract
Intracellular pathogens interact with host systems in intimate ways to sustain a pathogenic lifestyle. Consequently, these interactions can potentially be targets of host-directed interventions against infectious diseases. In case of tuberculosis (TB), caused by the bacterium Mycobacterium tuberculosis (Mtb), while effective anti-tubercular compounds are available, the long treatment duration and emerging drug resistance necessitate identification of new class of molecules with anti-TB activity, as well as new treatment strategies. A significant part of the effort in finding new anti-TB drugs is focused on bacterial targets in bacterial systems. However, the host environment plays a major role in pathogenesis mechanisms and must be considered actively in these efforts. On the one hand, the bacterial origin targets must be relevant and accessible in the host, while on the other hand, new host origin targets required for the bacterial survival can be targeted. Such targets are good candidates for host-directed therapeutics, a strategy gaining traction as an adjunct in TB treatment. In this review, we will summarise the screening platforms used to identify compounds with anti-tubercular activities inside different host environments and outline recent technical advances in these platforms. Finally, while the examples given are specific to mycobacteria, the methods and principles outlined are broadly applicable to most intracellular infections.
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Affiliation(s)
- Neeraja Subhash
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.,SASTRA University, Thanjavur, India
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9
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Singhvi N, Singh P, Prakash O, Gupta V, Lal S, Bechthold A, Singh Y, Singh RK, Lal R. Differential mass spectrometry-based proteome analyses unveil major regulatory hubs in rifamycin B production in Amycolatopsis mediterranei. J Proteomics 2021; 239:104168. [PMID: 33662614 DOI: 10.1016/j.jprot.2021.104168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 01/18/2023]
Abstract
Rifamycin B is produced by Amycolatopsis mediterranei S699 as a secondary metabolite. Its semi-synthetic derivatives have been used for curing tuberculosis caused by Mycobacterium tuberculosis. But the emergence of rifampicin-resistant strains required analogs of rifamycin B to be developed by rifamycin biosynthetic gene cluster manipulation. In 2014 genetic engineering of the rifamycin polyketide synthase gene cluster in S699 led to a mutant, A. mediterranei DCO#34, that produced 24-desmethylrifamycin B. Unfortunately, the productivity was strongly reduced to 20 mgL-1 as compared to 50 mgL-1 of rifamycin B. To understand the mechanisms leading to reduced productivity and rifamycin biosynthesis by A. mediterranei S699 during the early and late growth phase we performed a proteome study for wild type strain S699, mutant DCO#34, and the non-producer strain SCO2-2. Proteins identification and relative label-free quantification were performed by nLC-MS/MS. Data are available via ProteomeXchange with identifier PXD016416. Also, in-silico protein-protein interaction approach was used to determine the relationship between different structural and regulatory proteins involved in rifamycin biosynthesis. Our studies revealed RifA, RifK, RifL, Rif-Orf19 as the major regulatory hubs. Relative abundance expression values revealed that genes encoding RifC-RifI and the transporter RifP, down-regulated in DCO#34 and genes encoding RifR, RifZ, other regulatory proteins up-regulated. SIGNIFICANCE: The study is designed mainly to understand the underlying mechanisms of rifamycin biosynthesis in Amycolatopsis mediterranei. This resulted in the identification of regulatory hubs which play a crucial role in regulating secondary metabolism. It elucidates the complex mechanism of secondary metabolite biosynthesis and their conversion and extracellular transportation in temporal correlation with the different growth phases. The study also elucidated the mechanisms leading to reduced production of analog, 24-desmethylrifamycin B by the genetically modified strain DCO#34, derivatives of which have been found effective against rifampicin-resistant strains of Mycobacterium tuberculosis. These results can be useful while carrying out genetic manipulations to improve the strains of Amycolatopsis to produce better analogs/drugs and promote the eradication of TB. Thus, this study is contributing significantly to the growing knowledge in the field of the crucial drug, rifamycin B biosynthesis by an economically important bacterium Amycolatopsis mediterranei.
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Affiliation(s)
- Nirjara Singhvi
- Department of Zoology, University of Delhi, Delhi 110007, India
| | - Priya Singh
- Department of Zoology, University of Delhi, Delhi 110007, India
| | - Om Prakash
- National Centre for Microbial Resource-National Centre for Cell Sciences, Pune, Maharashtra 411007, India
| | - Vipin Gupta
- Department of Zoology, University of Delhi, Delhi 110007, India
| | - Sukanya Lal
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
| | - Andreas Bechthold
- Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, 79104 Freiburg, Germany
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi 110007, India
| | - Rakesh Kumar Singh
- Translational Science Laboratory, Florida State University, FL 32306, USA
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi 110007, India.
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Davis RL. Mechanism of Action and Target Identification: A Matter of Timing in Drug Discovery. iScience 2020; 23:101487. [PMID: 32891054 PMCID: PMC7479624 DOI: 10.1016/j.isci.2020.101487] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/11/2020] [Accepted: 08/18/2020] [Indexed: 01/14/2023] Open
Abstract
Two opposing viewpoints are held regarding the need for understanding a drug's molecular target and mechanism of action. One extreme viewpoint is that it is unnecessary, because, after all, there are many beneficial drugs in use for which the target and mechanism of action remain unknown. A second extreme viewpoint is that target identification and mechanism of action should be elucidated very early in the drug discovery process due to the tangible benefits provided by this knowledge. I offer an intermediate perspective that considers the complexity of the disease of interest, the existence of a standard-of-care treatment, and the resources available to the investigator.
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Affiliation(s)
- Ronald L Davis
- Department of Neuroscience, Scripps Research Institute Florida, Jupiter, FL 33458, USA.
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11
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Singhvi N, Gupta V, Singh P, Prakash O, Bechthold A, Singh Y, Lal R. Prediction of Transcription Factors and Their Involvement in Regulating Rifamycin Production in Amycolatopsis mediterranei S699. Indian J Microbiol 2020; 60:310-317. [PMID: 32655198 DOI: 10.1007/s12088-020-00868-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/03/2020] [Indexed: 12/16/2022] Open
Abstract
Amycolatopsis mediterranei S699 produces rifamycin B and successors of this strain are in use for the industrial production of rifamycin B. Semisynthetic derivatives of rifamycin B are used against Mycobacterium tuberculosis that causes tuberculosis. Although the rifamycin biosynthetic gene cluster was characterized two decades ago, the regulation of rifamycin B biosynthesis in Amycolatopsis mediterranei S699 is poorly understood. In this study, we analysed the genome and proteome of Amycolatopsis mediterranei S699 and identified 1102 transcription factors which comprise about 10% of the total genome. Using interactomics approaches we delineated 30 unique transcription factors directly involved in secondary metabolism that regulate rifamycin B biosynthesis. We also predict the role of RifN as hub in controlling the regulation of other genes involved in rifamycin biosynthesis. RifN is important for maintaining the integrity of the rifamycin-network. Thus, these transcription factor can be exploited to improve rifamycin B production in Amycolatopsis mediterranei S699.
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Affiliation(s)
- Nirjara Singhvi
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Vipin Gupta
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Priya Singh
- Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: Acharya Narendra Dev College, University of Delhi, New Delhi, 110019 India
| | - Om Prakash
- National Centre for Cell Sciences, Pune, Maharashtra 411007 India
| | - Andreas Bechthold
- Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, 79104 Freiburg, Germany
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Rup Lal
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, New Delhi, 110033 India
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12
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Parish T. In vitro drug discovery models for Mycobacterium tuberculosis relevant for host infection. Expert Opin Drug Discov 2020; 15:349-358. [PMID: 31899974 DOI: 10.1080/17460441.2020.1707801] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Introduction: Tuberculosis is the leading cause of death from infectious disease. Current drug therapy requires a combination of antibiotics taken over >6 months. An urgent need for new agents that can shorten therapy is required. In order to develop new drugs, simple in vitro assays are required that can identify efficacious compounds rapidly and predict in vivo activity in the human.Areas covered: This review focusses on the most relevant in vitro assays that can be utilized in a drug discovery program and which mimic different aspects of infection or disease. The focus is largely on assays used to test >1000s of compounds reliably and robustly. However, some assays used for 10s to 100s of compounds are included where the utility outweighs the low capacity. Literature searches for high throughput screening, models and in vitro assays were undertaken.Expert opinion: Drug discovery and development in tuberculosis is extremely challenging due to the requirement for predicting drug efficacy in a disease with complex pathology in which bacteria exist in heterogeneous states in inaccesible locations. A combination of assays can be used to determine profiles against replicating, non-replicating, intracellular and tolerant bacteria.
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Affiliation(s)
- Tanya Parish
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
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Rakhmawatie MD, Wibawa T, Lisdiyanti P, Pratiwi WR, Mustofa. Evaluation of crystal violet decolorization assay and resazurin microplate assay for antimycobacterial screening. Heliyon 2019; 5:e02263. [PMID: 31497667 PMCID: PMC6722264 DOI: 10.1016/j.heliyon.2019.e02263] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/28/2019] [Accepted: 08/06/2019] [Indexed: 11/29/2022] Open
Abstract
The main obstacle in antimycobacterial discovery is the extremely slow growth rates of pathogenic mycobacteria that lead to the long incubation times needed in antimycobacterial screening. Some in vitro testings has been developed and are currently available for antimycobacterial screening. The aim of the study was to compare Resazurin Microplate Assay (REMA) and Crystal Violet Decolorization Assay (CVDA) for testing mycobacteria susceptibility to isoniazid and rifampicin as well as for antimycobacterial screening of natural products (NP). Mycobacterium tuberculosis strain H37Rv and Mycobacterium smegmatis strain mc2 155 were used as tested mycobacteria. Serial two-fold dilutions from 0.0625 to 1.0 μg/mL for the isoniazid and rifampicin and from 6.25 to 100.0 μg/mL for the NP A and B were prepared. Tested mycobacteria were then incubated with tested drugs or NPs in each growth medium at 37 °C for 7 days for M. tuberculosis and 3 days for M. smegmatis. MIC values against M. tuberculosis were interpreted 24-48 h after adding resazurin or at least 72 h after adding crystal violet, whereas MIC values against M. smegmatis were interpreted 1 h after adding resazurin or 24 h after adding crystal violet. The MIC values against M. tuberculosis interpreted by REMA were 0.0625, 0.0625, 6.25, and >100 μg/mL for rifampicin, isoniazid, NP A, and NP B, respectively, and those interpreted by CVDA were 0.0625, 0.0625, 6.25, and >100 μg/mL for rifampicin, isoniazid, NP A, and NP B, respectively. Moreover, the MIC values against M. smegmatis interpreted by REMA were 0.0625, >1, 6.25, and 100 μg/mL for rifampicin, isoniazid, NP A, and NP B, respectively, and those interpreted by CVDA were 0.125, >1, 6.25, and >100 μg/mL for rifampicin, isoniazid, NP A, NP B respectively. In conclusion, REMA is faster and easier than CVDA to interpret MIC values, however CVDA produces higher MIC values than REMA for rifampicin and NP B in M. smegmatis susceptibility testing. Therefore, REMA and CVDA can be used for antimycobacterial screening.
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Affiliation(s)
- Maya Dian Rakhmawatie
- Doctoral Program in Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Muhammadiyah Semarang, Semarang, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Puspita Lisdiyanti
- Research Center for Biotechnology, Indonesian Institute of Sciences, Bogor, Indonesia
| | - Woro Rukmi Pratiwi
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mustofa
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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14
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Campaniço A, Carrasco MP, Njoroge M, Seldon R, Chibale K, Perdigão J, Portugal I, Warner DF, Moreira R, Lopes F. Azaaurones as Potent Antimycobacterial Agents Active against MDR- and XDR-TB. ChemMedChem 2019; 14:1537-1546. [PMID: 31294529 DOI: 10.1002/cmdc.201900289] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/19/2019] [Indexed: 12/31/2022]
Abstract
Herein we report the screening of a small library of aurones and their isosteric counterparts, azaaurones and N-acetylazaaurones, against Mycobacterium tuberculosis. Aurones were found to be inactive at 20 μm, whereas azaaurones and N-acetylazaaurones emerged as the most potent compounds, with nine derivatives displaying MIC99 values ranging from 0.4 to 2.0 μm. In addition, several N-acetylazaaurones were found to be active against multidrug-resistant (MDR) and extensively drug-resistant (XDR) clinical M. tuberculosis isolates. The antimycobacterial mechanism of action of these compounds remains to be determined; however, a preliminary mechanistic study confirmed that they do not inhibit the mycobacterial cytochrome bc1 complex. Additionally, microsomal metabolic stability and metabolite identification studies revealed that N-acetylazaaurones are deacetylated to their azaaurone counterparts. Overall, these results demonstrate that azaaurones and their N-acetyl counterparts represent a new entry in the toolbox of chemotypes capable of inhibiting M. tuberculosis growth.
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Affiliation(s)
- André Campaniço
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Marta P Carrasco
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Mathew Njoroge
- Division of Clinical Pharmacology, Department of Medicine, Drug Discovery and Development Centre (H3D), University of Cape Town, Observatory, 7925, South Africa
| | - Ronnett Seldon
- Department of Chemistry, South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch, 7701, South Africa
| | - Kelly Chibale
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa.,Department of Chemistry, South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch, 7701, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701, South Africa
| | - João Perdigão
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Isabel Portugal
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Digby F Warner
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701, South Africa.,Department of Pathology, SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, University of Cape Town, Rondebosch, 7701, South Africa.,Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Rondebosch, 7701, South Africa
| | - Rui Moreira
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Francisca Lopes
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
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15
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Identification of cyclic hexapeptides natural products with inhibitory potency against Mycobacterium tuberculosis. BMC Res Notes 2018; 11:416. [PMID: 29954459 PMCID: PMC6022709 DOI: 10.1186/s13104-018-3526-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/20/2018] [Indexed: 11/26/2022] Open
Abstract
Objective Our aim was to identify natural products with anti-tubercular activity. Results A set of ~ 500 purified natural product compounds was screened for inhibition against the human pathogen Mycobacterium tuberculosis. A series of cyclic hexapeptides with anti-tubercular activity was identified. Five analogs from a set of sixteen closely related compounds were active, with minimum inhibitory concentrations ranging from 2.3 to 8.9 μM. Eleven structural analogs had no significant activity (MIC > 20 μM) demonstrating structure activity relationship. Sequencing of resistant mutant isolates failed to identify changes accounting for the resistance phenotype.
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16
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van den Brink WJ, Hankemeier T, van der Graaf PH, de Lange ECM. Bundling arrows: improving translational CNS drug development by integrated PK/PD-metabolomics. Expert Opin Drug Discov 2018. [DOI: 10.1080/17460441.2018.1446935] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- W. J. van den Brink
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - T. Hankemeier
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - P. H. van der Graaf
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
- Certara QSP, Canterbury Innovation House, Canterbury, United Kingdom
| | - E. C. M. de Lange
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
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17
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de Carvalho NC, Neves SP, Dias RB, Valverde LDF, Sales CBS, Rocha CAG, Soares MBP, Dos Santos ER, Oliveira RMM, Carlos RM, Nogueira PCL, Bezerra DP. A novel ruthenium complex with xanthoxylin induces S-phase arrest and causes ERK1/2-mediated apoptosis in HepG2 cells through a p53-independent pathway. Cell Death Dis 2018; 9:79. [PMID: 29362398 PMCID: PMC5833756 DOI: 10.1038/s41419-017-0104-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/02/2017] [Accepted: 10/30/2017] [Indexed: 12/13/2022]
Abstract
Ruthenium-based compounds have gained great interest due to their potent cytotoxicity in cancer cells; however, much of their potential applications remain unexplored. In this paper, we report the synthesis of a novel ruthenium complex with xanthoxylin (RCX) and the investigation of its cellular and molecular action in human hepatocellular carcinoma HepG2 cells. We found that RCX exhibited a potent cytotoxic effect in a panel of cancer cell lines in monolayer cultures and in a 3D model of multicellular cancer spheroids formed from HepG2 cells. This compound is detected at a high concentration in the cell nuclei, induces DNA intercalation and inhibits DNA synthesis, arresting the cell cycle in the S-phase, which is followed by the activation of the caspase-mediated apoptosis pathway in HepG2 cells. Gene expression analysis revealed changes in the expression of genes related to cell cycle control, apoptosis and the MAPK pathway. In addition, RCX induced the phosphorylation of ERK1/2, and pretreatment with U-0126, an MEK inhibitor known to inhibit the activation of ERK1/2, prevented RCX-induced apoptosis. In contrast, pretreatment with a p53 inhibitor (cyclic pifithrin-α) did not prevent RCX-induced apoptosis, indicating the activation of a p53-independent apoptosis pathway. RCX also presented a potent in vivo antitumor effect in C.B-17 SCID mice engrafted with HepG2 cells. Altogether, these results indicate that RCX is a novel anticancer drug candidate.
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Affiliation(s)
- Nanashara C de Carvalho
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Bahia, 40296-710, Brazil
| | - Sara P Neves
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Bahia, 40296-710, Brazil
| | - Rosane B Dias
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Bahia, 40296-710, Brazil
| | - Ludmila de F Valverde
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Bahia, 40296-710, Brazil
| | - Caroline B S Sales
- Department of Biomorphology, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, 40110-902, Brazil
| | - Clarissa A G Rocha
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Bahia, 40296-710, Brazil
| | - Milena B P Soares
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Bahia, 40296-710, Brazil.,Center of Biotechnology and Cell therapy, Hospital São Rafael, Salvador, Bahia, 41253-190, Brazil
| | - Edjane R Dos Santos
- Department of Chemistry, Federal University of São Carlos, São Carlos, São Paulo, 13561-901, Brazil
| | - Regina M M Oliveira
- Department of Chemistry, Federal University of São Carlos, São Carlos, São Paulo, 13561-901, Brazil
| | - Rose M Carlos
- Department of Chemistry, Federal University of São Carlos, São Carlos, São Paulo, 13561-901, Brazil
| | - Paulo C L Nogueira
- Department of Chemistry, Federal University of Sergipe, São Cristóvão, Sergipe, 49100-000, Brazil
| | - Daniel P Bezerra
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Bahia, 40296-710, Brazil.
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18
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Torfs E, Vajs J, de Macedo MB, Cools F, Vanhoutte B, Gorbanev Y, Bogaerts A, Verschaeve L, Caljon G, Maes L, Delputte P, Cos P, Košmrlj J, Cappoen D. Synthesis and in vitro investigation of halogenated 1,3-bis(4-nitrophenyl)triazenide salts as antitubercular compounds. Chem Biol Drug Des 2017; 91:631-640. [DOI: 10.1111/cbdd.13087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 06/06/2017] [Accepted: 07/27/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Eveline Torfs
- Laboratory of Microbiology; Parasitology and Hygiene (LMPH); S7; Faculty of Pharmaceutical; Biomedical and Veterinary Sciences; University of Antwerp; Wilrijk Belgium
| | - Jure Vajs
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Ljubljana Slovenia
| | - Maíra Bidart de Macedo
- Laboratory of Microbiology; Parasitology and Hygiene (LMPH); S7; Faculty of Pharmaceutical; Biomedical and Veterinary Sciences; University of Antwerp; Wilrijk Belgium
| | - Freya Cools
- Laboratory of Microbiology; Parasitology and Hygiene (LMPH); S7; Faculty of Pharmaceutical; Biomedical and Veterinary Sciences; University of Antwerp; Wilrijk Belgium
| | - Bieke Vanhoutte
- Laboratory of Microbiology; Parasitology and Hygiene (LMPH); S7; Faculty of Pharmaceutical; Biomedical and Veterinary Sciences; University of Antwerp; Wilrijk Belgium
| | - Yury Gorbanev
- Research Group PLASMANT; Department of Chemistry; University of Antwerp; Wilrijk Belgium
| | - Annemie Bogaerts
- Research Group PLASMANT; Department of Chemistry; University of Antwerp; Wilrijk Belgium
| | - Luc Verschaeve
- Program Toxicology; O.D. Public Health and Surveillance; Scientific Institute of Public Health (Site Elsene); Brussels Belgium
- Department of Biomedical Sciences; University of Antwerp; Wilrijk Belgium
| | - Guy Caljon
- Laboratory of Microbiology; Parasitology and Hygiene (LMPH); S7; Faculty of Pharmaceutical; Biomedical and Veterinary Sciences; University of Antwerp; Wilrijk Belgium
| | - Louis Maes
- Laboratory of Microbiology; Parasitology and Hygiene (LMPH); S7; Faculty of Pharmaceutical; Biomedical and Veterinary Sciences; University of Antwerp; Wilrijk Belgium
| | - Peter Delputte
- Laboratory of Microbiology; Parasitology and Hygiene (LMPH); S7; Faculty of Pharmaceutical; Biomedical and Veterinary Sciences; University of Antwerp; Wilrijk Belgium
| | - Paul Cos
- Laboratory of Microbiology; Parasitology and Hygiene (LMPH); S7; Faculty of Pharmaceutical; Biomedical and Veterinary Sciences; University of Antwerp; Wilrijk Belgium
| | - Janez Košmrlj
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Ljubljana Slovenia
| | - Davie Cappoen
- Laboratory of Microbiology; Parasitology and Hygiene (LMPH); S7; Faculty of Pharmaceutical; Biomedical and Veterinary Sciences; University of Antwerp; Wilrijk Belgium
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