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Chowdhuri SP, Dhiman S, Das SK, Meena N, Das S, Kumar A, Das BB. Novel Pyrido[2',1':2,3]imidazo[4,5- c]quinoline Derivative Selectively Poisons Leishmania donovani Bisubunit Topoisomerase 1 to Inhibit the Antimony-Resistant Leishmania Infection in Vivo. J Med Chem 2023; 66:3411-3430. [PMID: 36823782 DOI: 10.1021/acs.jmedchem.2c01932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The unique bisubunit structure of Leishmania donovani topoisomerase 1B (LdTop1) is a potential drug target in the parasites unlike the monomeric Top1 from its human host counterpart. Here, we report the design, synthesis, and validation of a chimeric pyrido[2',1':2,3]imidazo[4,5-c]quinoline derivative (C17) as a novel antileishmanial agent that poisons topoisomerase 1-DNA covalent complexes (LdTop1cc) inside the parasites and inhibits Top1 religation activity both in the drug sensitive and antimony-resistant L. donovani clinical isolates. Importantly, the human Top1 is not sensitive to C17. Further, C17 overcomes the chemical instability of camptothecin (CPT) by generating persistent LdTop1cc-induced DNA breaks inside the parasites even after 12 h of drug removal. Intraperitoneal administration of C17 results in marked reduction of the Leishmania amastigotes from the infected spleen and liver of BALB/c mice. C17 confers a host protective immune-response up-regulating the Th1 cytokines facilitating parasite clearance which can be exploited for treating drug-resistant leishmaniasis.
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Affiliation(s)
- Srijita Paul Chowdhuri
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Shiv Dhiman
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333 031 Rajasthan, India
| | - Subhendu K Das
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Neha Meena
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333 031 Rajasthan, India
| | - Sonali Das
- Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Anil Kumar
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333 031 Rajasthan, India
| | - Benu Brata Das
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
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Lamba S, Roy A. Demystifying the potential of inhibitors targeting DNA topoisomerases in unicellular protozoan parasites. Drug Discov Today 2023; 28:103574. [PMID: 37003515 DOI: 10.1016/j.drudis.2023.103574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/09/2023] [Accepted: 03/25/2023] [Indexed: 04/01/2023]
Abstract
DNA topoisomerases are a group of enzymes omnipresent in all organisms. They maintain the DNA topology during replication, repair, recombination, and transcription. However, the structure of topoisomerase in protozoan parasites differs significantly from that of human topoisomerases; thus, this enzyme acts as a crucial target in drug development against parasitic diseases. Although the therapeutic potential of drugs targeting the parasitic topoisomerase is well known, to manage the shortcomings of currently available therapeutics and the emergence of drug resistance, the discovery of novel antiparasitic molecules is an urgent need. In this review, we describe various investigational and repurposed topoisomerase inhibitors developed against protozoan parasites over the past few years. Teaser: Fatal parasitic diseases are an increasing cause for concern; here, we provide a compilation of different inhibitors targeting DNA topoisomerases, enzymes that are essential for, and unique to, protozoan parasites; therefore, inhibitors are efficient and have few adverse effects.
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Affiliation(s)
- Swati Lamba
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, India
| | - Amit Roy
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, India.
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Goel N, Gupta VK, Garg A, Bhoumik A, Biswas R, Natarajan R, Majumder HK, Jaisankar P. Holanamine, a Steroidal Alkaloid from the Bark of Holarrhena pubescens Wall. ex G. Don Inhibits the Growth of Leishmania donovani by Targeting DNA Topoisomerase 1B. ACS Infect Dis 2023; 9:162-177. [PMID: 36417798 DOI: 10.1021/acsinfecdis.2c00562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Leishmaniasis is a group of neglected tropical diseases (NTDs) caused by about 20 species of obligate intracellular protozoan parasites of the genus Leishmania, which occurs in cutaneous, mucocutaneous, and visceral forms. Many researchers have sought to utilize natural products for novel and effective treatments to combat many infectious diseases, including leishmaniasis. Holarrhena pubescens Wall. ex G. Don (Apocynaceae) bark is a rich source of bioactive steroidal alkaloids. The total alkaloidal extract (IC50 6.12 ± 0.117 μg/mL), and the isolated alkaloid, holanamine, showed significant antileishmanial activity (IC50 2.66 ± 0.112 μM against AG83 and 3.80 ± 0.126 μM against BHU-575) against the Leishmania donovani parasite, better than miltefosine (IC50 19.61 ± 0.093 μM against AG83 and 23.20 ± 0.094 μM against BHU-575). Holanamine inhibited the L. donovani topoisomerase 1B (LdToP1B) in a non-competitive manner (IC50 2.81 ± 0.105 μM), indicating that it interacts with the free enzyme and enzyme-DNA complex without inhibiting human topoisomerase. Hydrogen bonding and hydrophobic interactions of holanamine with the N-terminal and hinge region of the large subunit of LTop1B is responsible for its potent antileishmanial activity, as shown by docking studies. Treatment with holanamine causes apoptotic-like cell death by generating cellular and mitochondrial reactive oxygen species, disrupting the mitochondrial membrane potential and inducing ultrastructural alterations in the promastigotes. Holanamine effectively clears intracellular amastigotes but minimally affects host macrophages with no significant cytotoxicity in HEK 293 and L929 cell lines. Thus, our studies show that holanamine can further be used to develop effective antileishmanial agents against evolving drug-resistant parasites.
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Affiliation(s)
- Narender Goel
- Department of Natural Products, National Institute of Pharmaceutical Education and Research (NIPER), Chunilal Bhawan, 168, Maniktala Main Road, Kolkata700054, India.,Laboratory of Catalysis and Chemical Biology, Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Vivek Kumar Gupta
- Laboratory of Catalysis and Chemical Biology, Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Aakriti Garg
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Chunilal Bhawan, 168, Maniktala Main Road, Kolkata700054, India
| | - Arpita Bhoumik
- Laboratory of Molecular Parasitology, Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Raju Biswas
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Ramalingam Natarajan
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Hemanta K Majumder
- Laboratory of Molecular Parasitology, Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Parasuraman Jaisankar
- Laboratory of Catalysis and Chemical Biology, Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
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4
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Gouri V, Upreti S, Samant M. Evaluation of target-specific natural compounds for drug discovery against Leishmaniasis. Parasitol Int 2022; 91:102622. [DOI: 10.1016/j.parint.2022.102622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/07/2022] [Accepted: 06/30/2022] [Indexed: 11/28/2022]
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Reguera RM, Elmahallawy EK, García-Estrada C, Carbajo-Andrés R, Balaña-Fouce R. DNA Topoisomerases of Leishmania Parasites; Druggable Targets for Drug Discovery. Curr Med Chem 2019; 26:5900-5923. [DOI: 10.2174/0929867325666180518074959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/15/2018] [Accepted: 05/14/2018] [Indexed: 12/13/2022]
Abstract
DNA topoisomerases (Top) are a group of isomerase enzymes responsible for controlling the topological problems caused by DNA double helix in the cell during the processes of replication, transcription and recombination. Interestingly, these enzymes have been known since long to be key molecular machines in several cellular processes through overwinding or underwinding of DNA in all living organisms. Leishmania, a trypanosomatid parasite responsible for causing fatal diseases mostly in impoverished populations of low-income countries, has a set of six classes of Top enzymes. These are placed in the nucleus and the single mitochondrion and can be deadly targets of suitable drugs. Given the fact that there are clear differences in structure and expression between parasite and host enzymes, numerous studies have reported the therapeutic potential of Top inhibitors as antileishmanial drugs. In this regard, numerous compounds have been described as Top type IB and Top type II inhibitors in Leishmania parasites, such as camptothecin derivatives, indenoisoquinolines, indeno-1,5- naphthyridines, fluoroquinolones, anthracyclines and podophyllotoxins. The aim of this review is to highlight several facts about Top and Top inhibitors as potential antileishmanial drugs, which may represent a promising strategy for the control of this disease of public health importance.
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Affiliation(s)
- Rosa M. Reguera
- Department of Biomedical Sciences, University of Leon (ULE), Leon, Spain
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Kundu B, Das SK, Paul Chowdhuri S, Pal S, Sarkar D, Ghosh A, Mukherjee A, Bhattacharya D, Das BB, Talukdar A. Discovery and Mechanistic Study of Tailor-Made Quinoline Derivatives as Topoisomerase 1 Poison with Potent Anticancer Activity. J Med Chem 2019; 62:3428-3446. [PMID: 30897325 DOI: 10.1021/acs.jmedchem.8b01938] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To overcome chemical limitations of camptothecin (CPT), we report design, synthesis, and validation of a quinoline-based novel class of topoisomerase 1 (Top1) inhibitors and establish that compound 28 ( N-(3-(1 H-imidazol-1-yl)propyl)-6-(4-methoxyphenyl)-3-(1,3,4-oxadiazol-2-yl)quinolin-4-amine) exhibits the highest potency in inhibiting human Top1 activity with an IC50 value of 29 ± 0.04 nM. Compound 28 traps Top1-DNA cleavage complexes (Top1ccs) both in the in vitro cleavage assays and in live cells. Point mutation of Top1-N722S fails to trap compound 28-induced Top1cc because of its inability to form a hydrogen bond with compound 28. Unlike CPT, compound 28 shows excellent plasma serum stability and is not a substrate of P-glycoprotein 1 (permeability glycoprotein) advancing its potential anticancer activity. Finally, we provide evidence that compound 28 overcomes the chemical instability of CPT in human breast adenocarcinoma cells through generation of persistent and less reversible Top1cc-induced DNA double-strand breaks as detected by γH2AX foci immunostaining after 5 h of drug removal.
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Affiliation(s)
- Biswajit Kundu
- Department of Organic and Medicinal Chemistry , CSIR-Indian Institute of Chemical Biology , 4 Raja S. C. Mullick Road , Kolkata 700032 , West Bengal , India
| | - Subhendu K Das
- Laboratory of Molecular Biology, School of Biological Sciences ; Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road , Kolkata , 700032 West Bengal , India
| | - Srijita Paul Chowdhuri
- Laboratory of Molecular Biology, School of Biological Sciences ; Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road , Kolkata , 700032 West Bengal , India
| | - Sourav Pal
- Department of Organic and Medicinal Chemistry , CSIR-Indian Institute of Chemical Biology , 4 Raja S. C. Mullick Road , Kolkata 700032 , West Bengal , India.,Academy of Scientific and Innovative Research , Kolkata 700032 , West Bengal , India
| | - Dipayan Sarkar
- Department of Organic and Medicinal Chemistry , CSIR-Indian Institute of Chemical Biology , 4 Raja S. C. Mullick Road , Kolkata 700032 , West Bengal , India.,Academy of Scientific and Innovative Research , Kolkata 700032 , West Bengal , India
| | - Arijit Ghosh
- Laboratory of Molecular Biology, School of Biological Sciences ; Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road , Kolkata , 700032 West Bengal , India
| | - Ayan Mukherjee
- Department of Organic and Medicinal Chemistry , CSIR-Indian Institute of Chemical Biology , 4 Raja S. C. Mullick Road , Kolkata 700032 , West Bengal , India.,Academy of Scientific and Innovative Research , Kolkata 700032 , West Bengal , India
| | - Debomita Bhattacharya
- Department of Organic and Medicinal Chemistry , CSIR-Indian Institute of Chemical Biology , 4 Raja S. C. Mullick Road , Kolkata 700032 , West Bengal , India
| | - Benu Brata Das
- Laboratory of Molecular Biology, School of Biological Sciences ; Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road , Kolkata , 700032 West Bengal , India
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry , CSIR-Indian Institute of Chemical Biology , 4 Raja S. C. Mullick Road , Kolkata 700032 , West Bengal , India
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Chowdhury SR, Majumder HK. DNA Topoisomerases in Unicellular Pathogens: Structure, Function, and Druggability. Trends Biochem Sci 2019; 44:415-432. [PMID: 30609953 DOI: 10.1016/j.tibs.2018.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/20/2018] [Accepted: 12/03/2018] [Indexed: 02/06/2023]
Abstract
All organisms, including unicellular pathogens, compulsorily possess DNA topoisomerases for successful nucleic acid metabolism. But particular subtypes of topoisomerases exist, in all prokaryotes and in some unicellular eukaryotes, that are absent in higher eukaryotes. Moreover, topoisomerases from pathogenic members of a niche possess some unique molecular architecture and functionalities completely distinct from their nonpathogenic colleagues. This review will highlight the unique attributes associated with the structures and functions of topoisomerases from the unicellular pathogens, with special reference to bacteria and protozoan parasites. It will also summarise the progress made in the domain pertaining to the druggability of these topoisomerases, upon which a future platform for therapeutic development can be successfully constructed.
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Affiliation(s)
- Somenath Roy Chowdhury
- Laboratory of Molecular Parasitology, Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Hemanta K Majumder
- Laboratory of Molecular Parasitology, Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
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Das SK, Ghosh A, Paul Chowdhuri S, Halder N, Rehman I, Sengupta S, Sahoo KC, Rath H, Das BB. Neutral Porphyrin Derivative Exerts Anticancer Activity by Targeting Cellular Topoisomerase I (Top1) and Promotes Apoptotic Cell Death without Stabilizing Top1-DNA Cleavage Complexes. J Med Chem 2018; 61:804-817. [PMID: 29290109 PMCID: PMC5808360 DOI: 10.1021/acs.jmedchem.7b01297] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Camptothecin (CPT) selectively traps
topoisomerase 1-DNA cleavable
complexes (Top1cc) to promote anticancer activity. Here, we report
the design and synthesis of a new class of neutral porphyrin derivative
5,10-bis(4-carboxyphenyl)-15, 20-bis(4-dimethylaminophenyl)porphyrin
(compound 8) as a potent catalytic inhibitor of human
Top1. In contrast to CPT, compound 8 reversibly binds
with the free enzyme and inhibits the formation of Top1cc and promotes
reversal of the preformed Top1cc with CPT. Compound 8 induced inhibition of Top1cc formation in live cells was substantiated
by fluorescence recovery after photobleaching (FRAP) assays. We established
that MCF7 cells treated with compound 8 trigger proteasome-mediated
Top1 degradation, accumulate higher levels of reactive oxygen species
(ROS), PARP1 cleavage, oxidative DNA fragmentation, and stimulate
apoptotic cell death without stabilizing apoptotic Top1-DNA cleavage
complexes. Finally, compound 8 shows anticancer activity
by targeting cellular Top1 and preventing the enzyme from directly
participating in the apoptotic process.
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Affiliation(s)
| | | | | | | | | | - Souvik Sengupta
- Division of Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University , Central Campus, Navrangpura, Ahmedabad, Gujarat 380009, India
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Zhang P, Zhang L, Zhang Y, Mao L, Jiang H. Substitutions in Spodoptera exigua topoisomerase I modulate its relaxation activity and camptothecin sensitivity. PEST MANAGEMENT SCIENCE 2017; 73:1179-1186. [PMID: 27643798 DOI: 10.1002/ps.4440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/25/2016] [Accepted: 09/12/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Topoisomerase I (Top I) is referred as the cellular target of the camptothecins (CPTs) which are now being explored as potential pesticides for insect control. Three amino acid substitutions, including L530P, A653T and S729T, in Top Is of insects were found in our previous studies. In order to investigate the effect of these three substitutions, a comparative analysis was conducted between the wild-type and mutant Top Is in Spodoptera exigua Hübner. RESULTS The optimal salt concentration of A653T and S729T was 150 mm, which is consistent with that of the wild-type Top I, while the mutant L530P showed maximum relaxation activity at a lower KCl concentration (100 mm). The mutated L530P and A653T Top Is showed a higher relaxation efficiency owing to an increased relaxation velocity toward the negatively supercoiled plasmid pBR322 DNA, which rendered L530P and A653T resistant to CPTs, whereas mutant S729T exhibited sensitivity to CPTs as a result of a decreased relaxation activity toward plasmid pBR322 DNA. CONCLUSIONS These results suggested that the polymorphism in Top I of insects was related to the biological activity of CPTs, which provided the basic information for reasonable usage of CPTs to control insect pests. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Pei Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanning Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liangang Mao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongyun Jiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Copper salisylaldoxime (CuSAL) imparts protective efficacy against visceral leishmaniasis by targeting Leishmania donovani topoisomerase IB. Exp Parasitol 2017; 175:8-20. [DOI: 10.1016/j.exppara.2017.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 01/11/2017] [Accepted: 02/03/2017] [Indexed: 10/20/2022]
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Antileishmanial Mechanism of Diamidines Involves Targeting Kinetoplasts. Antimicrob Agents Chemother 2016; 60:6828-6836. [PMID: 27600039 DOI: 10.1128/aac.01129-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/28/2016] [Indexed: 02/08/2023] Open
Abstract
Leishmaniasis is a disease caused by pathogenic Leishmania parasites; current treatments are toxic and expensive, and drug resistance has emerged. While pentamidine, a diamidine-type compound, is one of the treatments, its antileishmanial mechanism of action has not been investigated in depth. Here we tested several diamidines, including pentamidine and its analog DB75, against Leishmania donovani and elucidated their antileishmanial mechanisms. We identified three promising new antileishmanial diamidine compounds with 50% effective concentrations (EC50s) of 3.2, 3.4, and 4.5 μM, while pentamidine and DB75 exhibited EC50s of 1.46 and 20 μM, respectively. The most potent antileishmanial inhibitor, compound 1, showed strong DNA binding properties, with a shift in the melting temperature (ΔTm) of 24.2°C, whereas pentamidine had a ΔTm value of 2.1°C, and DB75 had a ΔTm value of 7.7°C. Additionally, DB75 localized in L. donovani kinetoplast DNA (kDNA) and mitochondria but not in nuclear DNA (nDNA). For 2 new diamidines, strong localization signals were observed in kDNA at 1 μM, and at higher concentrations, the signals also appeared in nuclei. All tested diamidines showed selective and dose-dependent inhibition of kDNA, but not nDNA, replication, likely by inhibiting L. donovani topoisomerase IB. Overall, these results suggest that diamidine antileishmanial compounds exert activity by accumulating toward and blocking replication of parasite kDNA.
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A Novel Spirooxindole Derivative Inhibits the Growth of Leishmania donovani Parasites both In Vitro and In Vivo by Targeting Type IB Topoisomerase. Antimicrob Agents Chemother 2016; 60:6281-93. [PMID: 27503653 DOI: 10.1128/aac.00352-16] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 08/02/2016] [Indexed: 11/20/2022] Open
Abstract
Visceral leishmaniasis is a fatal parasitic disease, and there is an emergent need for development of effective drugs against this neglected tropical disease. We report here the development of a novel spirooxindole derivative, N-benzyl-2,2'α-3,3',5',6',7',7α,α'-octahydro-2methoxycarbonyl-spiro[indole-3,3'-pyrrolizidine]-2-one (compound 4c), which inhibits Leishmania donovani topoisomerase IB (LdTopIB) and kills the wild type as well as drug-resistant parasite strains. This compound inhibits catalytic activity of LdTopIB in a competitive manner. Unlike camptothecin (CPT), the compound does not stabilize the DNA-topoisomerase IB cleavage complex; rather, it hinders drug-DNA-enzyme covalent complex formation. Fluorescence studies show that the stoichiometry of this compound binding to LdTopIB is 2:1 (mole/mole), with a dissociation constant of 6.65 μM. Molecular docking with LdTopIB using the stereoisomers of compound 4c produced two probable hits for the binding site, one in the small subunit and the other in the hinge region of the large subunit of LdTopIB. This spirooxindole is highly cytotoxic to promastigotes of L. donovani and also induces apoptosis-like cell death in the parasite. Treatment with compound 4c causes depolarization of mitochondrial membrane potential, formation of reactive oxygen species inside parasites, and ultimately fragmentation of nuclear DNA. Compound 4c also effectively clears amastigote forms of wild-type and drug-resistant parasites from infected mouse peritoneal macrophages but has less of an effect on host macrophages. Moreover, compound 4c showed strong antileishmanial efficacies in the BALB/c mouse model of leishmaniasis. This compound potentially can be used as a lead for developing excellent antileishmanial agents against emerging drug-resistant strains of the parasite.
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13
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Das SK, Rehman I, Ghosh A, Sengupta S, Majumdar P, Jana B, Das BB. Poly(ADP-ribose) polymers regulate DNA topoisomerase I (Top1) nuclear dynamics and camptothecin sensitivity in living cells. Nucleic Acids Res 2016; 44:8363-75. [PMID: 27466387 PMCID: PMC5041477 DOI: 10.1093/nar/gkw665] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/13/2016] [Indexed: 01/19/2023] Open
Abstract
Topoisomerase 1 (Top1) is essential for removing the DNA supercoiling generated during replication and transcription. Anticancer drugs like camptothecin (CPT) and its clinical derivatives exert their cytotoxicity by reversibly trapping Top1 in covalent complexes on the DNA (Top1cc). Poly(ADP-ribose) polymerase (PARP) catalyses the addition of ADP-ribose polymers (PAR) onto itself and Top1. PARP inhibitors enhance the cytotoxicity of CPT in the clinical trials. However, the molecular mechanism by which PARylation regulates Top1 nuclear dynamics is not fully understood. Using live-cell imaging of enhanced green fluorescence tagged-human Top1, we show that PARP inhibitors (Veliparib, ABT-888) delocalize Top1 from the nucleolus to the nucleoplasm, which is independent of Top1–PARP1 interaction. Using fluorescence recovery after photobleaching and subsequent fitting of the data employing kinetic modelling we demonstrate that ABT-888 markedly increase CPT-induced bound/immobile fraction of Top1 (Top1cc) across the nuclear genome, suggesting Top1-PARylation counteracts CPT-induced stabilization of Top1cc. We further show Trp205 and Asn722 of Top1 are critical for subnuclear dynamics. Top1 mutant (N722S) was restricted to the nucleolus in the presence of CPT due to its deficiency in the accumulation of CPT-induced Top1-PARylation and Top1cc formation. This work identifies ADP-ribose polymers as key determinant for regulating Top1 subnuclear dynamics.
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Affiliation(s)
- Subhendu K Das
- Laboratory of Molecular Biology, Department of Physical Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Ishita Rehman
- Laboratory of Molecular Biology, Department of Physical Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Arijit Ghosh
- Laboratory of Molecular Biology, Department of Physical Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Souvik Sengupta
- Laboratory of Molecular Biology, Department of Physical Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Papiya Majumdar
- Laboratory of Molecular Biology, Department of Physical Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Biman Jana
- Physical Chemistry Department, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Benu Brata Das
- Laboratory of Molecular Biology, Department of Physical Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
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14
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Majumdar P, Bathula C, Basu SM, Das SK, Agarwal R, Hati S, Singh A, Sen S, Das BB. Design, synthesis and evaluation of thiohydantoin derivatives as potent topoisomerase I (Top1) inhibitors with anticancer activity. Eur J Med Chem 2015; 102:540-51. [DOI: 10.1016/j.ejmech.2015.08.032] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 08/14/2015] [Accepted: 08/15/2015] [Indexed: 11/30/2022]
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15
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Hussain H, Al-Harrasi A, Al-Rawahi A, Green IR, Gibbons S. Fruitful decade for antileishmanial compounds from 2002 to late 2011. Chem Rev 2014; 114:10369-428. [PMID: 25253511 DOI: 10.1021/cr400552x] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hidayat Hussain
- UoN Chair of Oman's Medicinal Plants and Marine Natural Products, University of Nizwa , P.O. Box 33, Birkat Al Mauz, Nizwa 616, Sultanate of Oman
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16
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Kumar A, Chowdhury SR, Chakrabarti T, Majumdar HK, Jha T, Mukhopadhyay S. A New Ellagic Acid Glycoside and DNA Topoisomerase IB Inhibitory Activity of Saponins from Putranjiva roxburghii. Nat Prod Commun 2014. [DOI: 10.1177/1934578x1400900523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Chemical investigation of the stem bark and leaves of Putranjiva roxburghii has resulted in the isolation of a new ellagic acid glycoside (5) along with four saponins (1-4). The structures of the isolated compounds were established by detailed spectral analysis. Incidentally putranoside-A methyl ester (4) has been isolated for the first time from this species and the saponins (1-4) exhibited potent DNA topoisomerase IB inhibitory activity.
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Affiliation(s)
- Ashish Kumar
- Chemistry Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata- 700032, India
| | - Somenath Roy Chowdhury
- Molecular Parasitology Laboratory, Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata -700032, India
| | - Tulika Chakrabarti
- Chemistry Division, Sir Padampat Singhania University, Udaipur-313601, Rajasthan, India
| | - Hemanta K Majumdar
- Molecular Parasitology Laboratory, Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata -700032, India
| | - Tarun Jha
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata- 700032, India
| | - Sibabrata Mukhopadhyay
- Chemistry Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata- 700032, India
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17
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Das BB, Huang SYN, Murai J, Rehman I, Amé JC, Sengupta S, Das SK, Majumdar P, Zhang H, Biard D, Majumder HK, Schreiber V, Pommier Y. PARP1-TDP1 coupling for the repair of topoisomerase I-induced DNA damage. Nucleic Acids Res 2014; 42:4435-49. [PMID: 24493735 PMCID: PMC3985661 DOI: 10.1093/nar/gku088] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Poly(ADP-ribose) polymerases (PARP) attach poly(ADP-ribose) (PAR) chains to various proteins including themselves and chromatin. Topoisomerase I (Top1) regulates DNA supercoiling and is the target of camptothecin and indenoisoquinoline anticancer drugs, as it forms Top1 cleavage complexes (Top1cc) that are trapped by the drugs. Endogenous and carcinogenic DNA lesions can also trap Top1cc. Tyrosyl-DNA phosphodiesterase 1 (TDP1), a key repair enzyme for trapped Top1cc, hydrolyzes the phosphodiester bond between the DNA 3'-end and the Top1 tyrosyl moiety. Alternative repair pathways for Top1cc involve endonuclease cleavage. However, it is unknown what determines the choice between TDP1 and the endonuclease repair pathways. Here we show that PARP1 plays a critical role in this process. By generating TDP1 and PARP1 double-knockout lymphoma chicken DT40 cells, we demonstrate that TDP1 and PARP1 are epistatic for the repair of Top1cc. The N-terminal domain of TDP1 directly binds the C-terminal domain of PARP1, and TDP1 is PARylated by PARP1. PARylation stabilizes TDP1 together with SUMOylation of TDP1. TDP1 PARylation enhances its recruitment to DNA damage sites without interfering with TDP1 catalytic activity. TDP1-PARP1 complexes, in turn recruit X-ray repair cross-complementing protein 1 (XRCC1). This work identifies PARP1 as a key component driving the repair of trapped Top1cc by TDP1.
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Affiliation(s)
- Benu Brata Das
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA, Laboratory of Molecular Biology, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India, Biotechnology and Cell Signaling, UMR7242 CNRS, Université de Strasbourg, Laboratory of Excellence Medalis, ESBS, Blvd Sébastien Brant, CS 10413, 67412 Illkirch, France, CEA-DSV-iMETI-SEPIA, BP6, 92265 Fontenay-aux-Roses cedex, France and Laboratory of Molecular Parasitology, Indian Institute of Chemical Biology, Kolkata 700032, India
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Saha S, Mukherjee T, Chowdhury S, Mishra A, Chowdhury SR, Jaisankar P, Mukhopadhyay S, Majumder HK. The lignan glycosides lyoniside and saracoside poison the unusual type IB topoisomerase of Leishmania donovani and kill the parasite both in vitro and in vivo. Biochem Pharmacol 2013; 86:1673-87. [PMID: 24134912 DOI: 10.1016/j.bcp.2013.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/04/2013] [Accepted: 10/07/2013] [Indexed: 10/26/2022]
Abstract
Lignans are diphenyl propanoids with vast range of biological activities. The present study provides an important insight into the anti-leishmanial activities of two lignan glycosides, viz. lyoniside and saracoside. These compounds inhibit catalytic activities of topoisomerase IB (LdTopIB) of Leishmania donovani in non-competitive manner and stabilize the LdTopIB mediated cleavage complex formation both in vitro and in Leishmania promastigotes and subsequently inhibit the religation of cleaved strand. These two compounds not only poison LdTopIB but also can interact with the free enzyme LdTopIB. We have also shown that lyoniside and saracoside are cytotoxic to promastigotes and intracellular amastigotes. The protein-DNA complex formation leads to double strand breaks in DNA which ultimately triggers apoptosis-like cell death in the parasite. Along with their cytotoxicity towards sodium antimony gluconate (SAG) sensitive AG83 strain, their ability to kill SAG resistant GE1 strain makes these two compounds potential anti-leishmanial candidates. Not only they effectively kill L. donovani amastigotes inside macrophages in vitro, lyoniside and saracoside demonstrated strong anti-leishmanial efficacies in BALB/c mice model of leishmaniasis. Treatment with these lignan glycosides produce nitric oxide and reactive oxygen species which result in almost complete clearance of the liver and splenic parasite burden. These compounds do not inhibit human topoisomerase IB upto 200μM concentrations and had poor cytotoxic effect on uninfected cultured murine peritoneal macrophages upto 100μM concentrations. Taken together it can be concluded that these compounds can be developed into excellent therapeutic agent against deadly disease leishmaniasis.
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Affiliation(s)
- Sourav Saha
- Molecular Parasitology Laboratory (S.S., S.C., A.M., S.R.C., H.K.M.), Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
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19
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Mukherjee T, Chowdhury S, Kumar A, Majumder HK, Jaisankar P, Mukhopadhyay S. Saracoside: A New Lignan Glycoside from Saraca indica, a Potential Inhibitor of DNA Topoisomerase IB. Nat Prod Commun 2012. [DOI: 10.1177/1934578x1200700619] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Chemical investigation of the stem bark of Saraca indica has resulted in the isolation of a new lignan glycoside, saracoside, along with four known lignan glycosides lyoniside, icariside E3, (+)5′methoxyisolarciresinol-9′- O-β-D-glucopyranoside and nudiposide, and a phenolic glucopyranoside, 3,4,5– trimethoxyphenyl-β-D-glucopyranoside, which has been isolated for the first time from this species. The isolated lignan glycosides exhibit potent DNA topoisomerase IB inhibitory activity.
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Affiliation(s)
- Tulika Mukherjee
- Chemistry Division, Indian Institute of Chemical Biology, Jadavpur, Kolkata -700032, India
| | - Sayan Chowdhury
- Molecular Parasitology Laboratory, Indian Institute of Chemical Biology, Jadavpur, Kolkata -700032, India
| | - Ashish Kumar
- Chemistry Division, Indian Institute of Chemical Biology, Jadavpur, Kolkata -700032, India
| | - Hemanta K Majumder
- Molecular Parasitology Laboratory, Indian Institute of Chemical Biology, Jadavpur, Kolkata -700032, India
| | - Parasuraman Jaisankar
- Chemistry Division, Indian Institute of Chemical Biology, Jadavpur, Kolkata -700032, India
| | - Sibabrata Mukhopadhyay
- Chemistry Division, Indian Institute of Chemical Biology, Jadavpur, Kolkata -700032, India
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20
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Chowdhury S, Mukherjee T, Sengupta S, Chowdhury SR, Mukhopadhyay S, Majumder HK. Novel Betulin Derivatives as Antileishmanial Agents with Mode of Action Targeting Type IB DNA Topoisomerase. Mol Pharmacol 2011; 80:694-703. [DOI: 10.1124/mol.111.072785] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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21
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Sengupta S, Ganguly A, Roy A, Bosedasgupta S, D'Annessa I, Desideri A, Majumder HK. ATP independent type IB topoisomerase of Leishmania donovani is stimulated by ATP: an insight into the functional mechanism. Nucleic Acids Res 2010; 39:3295-309. [PMID: 21186185 PMCID: PMC3082896 DOI: 10.1093/nar/gkq1284] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most type IB topoisomerases do not require ATP and Mg(2+) for activity. However, as shown previously for vaccinia topoisomerase I, we demonstrate that ATP stimulates the relaxation activity of the unusual heterodimeric type IB topoisomerase from Leishmania donovani (LdTOP1L/S) in the absence of Mg(2+). The stimulation is independent of ATP hydrolysis but requires salt as a co-activator. ATP binds to LdTOP1L/S and increases its rate of strand rotation. Docking studies indicate that the amino acid residues His93, Tyr95, Arg188 and Arg190 of the large subunit may be involved in ATP binding. Site directed mutagenesis of these four residues individually to alanine and subsequent relaxation assays reveal that the R190A mutant topoisomerase is unable to exhibit ATP-mediated stimulation in the absence of Mg(2+). However, the ATP-independent relaxation activities of all the four mutant enzymes remain unaffected. Additionally, we provide evidence that ATP binds LdTOP1L/S and modulates the activity of the otherwise ATP-independent enzyme. This study establishes ATP as an activator of LdTOP1L/S in the absence of Mg(2+).
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Affiliation(s)
- Souvik Sengupta
- Molecular Parasitology Laboratory, Indian Institute of Chemical Biology, 4 Raja S C Mullick Road, Kolkata 700032, India
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22
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Castelli S, Campagna A, Vassallo O, Tesauro C, Fiorani P, Tagliatesta P, Oteri F, Falconi M, Majumder HK, Desideri A. Conjugated eicosapentaenoic acid inhibits human topoisomerase IB with a mechanism different from camptothecin. Arch Biochem Biophys 2009; 486:103-10. [PMID: 19397888 DOI: 10.1016/j.abb.2009.04.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Revised: 04/17/2009] [Accepted: 04/19/2009] [Indexed: 01/08/2023]
Abstract
Conjugated eicosapentaenoic acid (cEPA) has been found to have antitumor effects which has been ascribed to their ability to inhibit DNA topoisomerases and DNA polymerases. We here show that cEPA inhibits the catalytic activity of human topoisomerase I, but unlike camptothecin it does not stabilize the cleavable complex, indicating a different mechanism of action. cEPA inhibits topoisomerase by impeding the catalytic cleavage of the DNA substrate as demonstrated using specific oligonucleotide substrates, and prevents the stabilization of the cleavable complex by camptothecin. Preincubation of the inhibitor with the enzyme is required to obtain complete inhibition. Molecular docking simulations indicate that the preferred cEPA binding site is proximal to the active site with the carboxylic group strongly interacting with the positively charged K443 and K587. Taken together the results indicate that cEPA inhibitor does not prevent DNA binding but inhibits DNA cleavage, binding in a region close to the topoisomerase active site.
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Affiliation(s)
- Silvia Castelli
- Department of Biology, University of Rome Tor Vergata, Italy
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Mutational studies reveal lysine 352 on the large subunit is indispensable for catalytic activity of bi-subunit topoisomerase I from Leishmania donovani. Mol Biochem Parasitol 2009; 165:57-66. [PMID: 19393162 DOI: 10.1016/j.molbiopara.2009.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Revised: 12/31/2008] [Accepted: 01/08/2009] [Indexed: 11/22/2022]
Abstract
From the vanadate complex crystal structure of Leishmania donovani topoisomerase I, several amino acid residues have been implicated to be involved in the catalytic reaction. Although several predictions and propositions have been made, the exact role of these amino acids has not yet been clearly demonstrated in vitro. Among these residues, lysine 352 and arginine 314 stand as potential candidates for playing the role of a general acid during the cleavage step. In this study, we have characterized the role of lysine 352 on the large subunit, by site-directed mutagenesis and have tried to identify the general acid that can protonate the 5?-O atom of the leaving strand. Studies with the mutant enzymes reveal that, relaxation activity was severely affected when Lys352 was mutated to arginine or alanine (K352R or K352A). Mutation of Arg314 to Lys (R314K) has very little effect on the relaxation activity. Detailed study reveals that, both cleavage and religation steps are severely affected in case of K352R and K352A and the cleavage religation equilibrium is shifted towards the cleavage. On the contrary, the R314K mutant exhibits only a slightly slower rate of cleavage compared to wild-type enzyme. Cleavage assays with an oligonucleotide containing 5?-bridging phosphorothiolate indicate that Lys352 acts as a general acid in the cleavage step. Altogether, this study establishes the indispensable role of lysine 352 in the catalytic reaction of L. donovani topoisomerase I.
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Das BB, Ganguly A, Majumder HK. DNA Topoisomerases of Leishmania: The Potential Targets for Anti-Leishmanial Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 625:103-15. [DOI: 10.1007/978-0-387-77570-8_9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Amino acids 39-456 of the large subunit and 210-262 of the small subunit constitute the minimal functionally interacting fragments of the unusual heterodimeric topoisomerase IB of Leishmania. Biochem J 2008; 409:481-9. [PMID: 17924857 DOI: 10.1042/bj20071358] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The unusual, heterodimeric topoisomerase IB of Leishmania shows functional activity upon reconstitution of the DNA-binding large subunit (LdTOPIL; or L) and the catalytic small subunit (LdTOPIS; or S). In the present study, we generated N- and C-terminal-truncated deletion constructs of either subunit and identified proteins LdTOPIL(39-456) (lacking amino acids 1-39 and 457-635) and LdTOPIS(210-262) (lacking amino acids 1-210) as the minimal interacting fragments. The interacting region of LdTOPIL lies between residues 40-99 and 435-456, while for LdTOPIS it lies between residues 210-215 and 245-262. The heterodimerization between the two fragments is weak and therefore co-purified fragments showed reduced DNA binding, cleavage and relaxation properties compared with the wild-type enzyme. The minimal fragments could complement their respective wild-type subunits inside parasites when the respective subunits were down-regulated by transfection with conditional antisense constructs. Site-directed mutagenesis studies identify Lys455 of LdTOPIL and Asp261 of LdTOPIS as two residues involved in subunit interaction. Taken together, the present study provides crucial insights into the mechanistic details for understanding the unusual structure and inter-subunit co-operativity of this heterodimeric enzyme.
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An insight into the mechanism of inhibition of unusual bi-subunit topoisomerase I from Leishmania donovani by 3,3′-di-indolylmethane, a novel DNA topoisomerase I poison with a strong binding affinity to the enzyme. Biochem J 2007; 409:611-22. [DOI: 10.1042/bj20071286] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DIM (3,3′-di-indolylmethane), an abundant dietary component of cruciferous vegetables, exhibits a wide spectrum of pharmacological properties. In the present study, we show that DIM is a potent inhibitor of Leishmania donovani topoisomerase I with an IC50 of 1.2 μM. Equilibrium dialysis shows that DIM binds strongly to the free enzyme with a binding constant of 9.73×10−9 M. The binding affinity of DIM to the small subunit is 8.6-fold more than that of the large subunit of unusual LdTOP1LS (bi-subunit L. donovani topoisomerase I). DIM stabilizes topoisomerase I–DNA cleavage complexes in vitro and also in vivo. Like CPT (camptothecin), DIM inhibits the religation step when the drug was added to preformed topoisomerase I–DNA binary complex. Hence, DIM is similar to CPT with respect to its ability to form the topoisomerase I-mediated ‘cleavable complexes’ in vitro and in vivo. But unlike CPT, DIM interacts with both free enzyme and substrate DNA. Therefore DIM is a non-competitive class I inhibitor of topoisomerase I. DIM also inhibits the relaxation activity of the CPT-resistant mutant enzyme LdTOP1Δ39LS (N-terminal deletion of amino acids 1–39 of LdTOP1LS). The IC50 values of DIM in simultaneous and enzyme pre-incubation relaxation assays were 3.6 and 2.9 μM respectively, which are higher than that of wild-type topoisomerase I (LdTOP1LS), indicating that the affinity of DIM to LdTOP1Δ39LS is less than that for LdTOP1LS. This is the first report on DIM as an L. donovani topoisomerase I poison. Our study illuminates a new mode of action of enzyme inhibition by DIM that might be exploited for rational drug design in human leishmaniasis.
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BoseDasgupta S, Ganguly A, Das BB, Roy A, Khalkho NVM, Majumder HK. The large subunit of Leishmania topoisomerase I functions as the 'molecular steer' in type IB topoisomerase. Mol Microbiol 2007; 67:31-46. [PMID: 18036140 DOI: 10.1111/j.1365-2958.2007.06002.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kinetoplastid topoisomerase IB is an unusual bisubunit enzyme where reconstitution of the large (LdTOPIL or L) and small (LdTOPIS or S) subunits shows functional activity. It is yet to be deciphered whether one subunit or both navigate the heterodimer to its cellular DNA targets. Tethering a specific DNA-binding protein to topoisomerase I alters its site specificity. The chimeric constructs UMSBP-LdTOPIL/S or U-L/S (fusion of UMSBP to the N-terminus of L and reconstituted with S) and LdTOPIL/UMSBP-LdTOPIS or L/U-S (fusion of UMSBP to the N-terminus of S and reconstituted with L) exhibit relaxation activity. Only U-L/S shows altered site specificity and enhanced DNA-binding affinity for the universal minicircle sequence (UMS) containing substrate. This proves that L alone serves as the 'molecular steer' for this heterodimer. Reconstituted U-L/S also induces cleavage close to UMS and causes minicircle linearization. The differential properties of the reconstituted chimeras U-L/S and L/U-S reveal the structural and functional asymmetry between the heterodimer. Therefore this study helps in a better understanding of the mechanistic details underlying topoisomerization by this bi-subunit enzyme.
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Affiliation(s)
- Somdeb BoseDasgupta
- Department of Molecular Parasitology, Indian Institute of Chemical Biology, Kolkata-700032, India
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Das BB, Bose Dasgupta S, Ganguly A, Mazumder S, Roy A, Majumder HK. Leishmania donovanibisubunit topoisomerase I gene fusion leads to an active enzyme with conserved type IB enzyme function. FEBS J 2006; 274:150-63. [PMID: 17222179 DOI: 10.1111/j.1742-4658.2006.05572.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
All eukaryotic topoisomerase I enzymes are monomeric enzymes, whereas the kinetoplastid family (Trypanosoma and Leishmania) possess an unusual bisubunit topoisomerase I. To determine what happens to the enzyme architecture and catalytic property if the two subunits are fused, and to explore the functional relationship between the two subunits, we describe here in vitro gene fusion of Leishmania bisubunit topoisomerase I into a single ORF encoding a new monomeric topoisomerase I (LdTOPIL-fus-S). It was found that LdTOPIL-fus-S is active. Gene fusion leads to a significant modulation of in vitro topoisomerase I activity compared to the wild-type heterodimeric enzyme (LdTOPILS). Interestingly, an N-terminal truncation mutant (1-210 amino acids) of the small subunit, when fused to the intact large subunit [LdTOPIL-fus-Delta(1-210)S], showed reduced topoisomerase I activity and camptothecin sensitivity in comparison to LdTOPIL-fus-S. Investigation of the reduction in enzyme activity indicated that the nonconserved 1-210 residues of LdTOPIS probably act as a 'pseudolinker' domain between the core and catalytic domain of the fused Leishmania enzyme, whereas mutational analysis of conserved His453 in the core DNA-binding domain (LdTOPIL) strongly suggested that its role is to stabilize the enzyme-DNA transition state through hydrogen bonding to one of the nonbridging oxygens. Taken together, our findings provide an insight into the details of the unusual structure of bisubunit topoisomerase I of Leishmania donovani.
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Affiliation(s)
- Benu B Das
- Department of Molecular Parasitology, Indian Institute of Chemical Biology, Kolkata, India
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Ganguly A, Das BB, Sen N, Roy A, Dasgupta SB, Majumder HK. 'LeishMan' topoisomerase I: an ideal chimera for unraveling the role of the small subunit of unusual bi-subunit topoisomerase I from Leishmania donovani. Nucleic Acids Res 2006; 34:6286-97. [PMID: 17098934 PMCID: PMC1669778 DOI: 10.1093/nar/gkl829] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The active site tyrosine residue of all monomeric type IB topoisomerases resides in the C-terminal domain of the enzyme. Leishmania donovani, possesses unusual heterodimeric type IB topoisomerase. The small subunit harbors the catalytic tyrosine within the SKXXY motif. To explore the functional relationship between the two subunits, we have replaced the small subunit of L.donovani topoisomerase I with a C-terminal fragment of human topoisomerase I (HTOP14). The purified LdTOP1L (large subunit of L.donovani topoisomerase I) and HTOP14 were able to reconstitute topoisomerase I activity when mixed in vitro. This unusual enzyme, 'LeishMan' topoisomerase I (Leish for Leishmania and Man for human) exhibits less efficiency in DNA binding and strand passage compared with LdTOP1L/S. Fusion of LdTOP1L with HTOP14 yielded a more efficient enzyme with greater affinity for DNA and faster strand passage ability. Both the chimeric enzymes are less sensitive to camptothecin than LdTOP1L/S. Restoration of topoisomerase I activity by LdTOP1L and HTOP14 suggests that the small subunit of L.donovani topoisomerase I is primarily required for supplying the catalytic tyrosine. Moreover, changes in the enzyme properties due to substitution of LdTOP1S with HTOP14 indicate that the small subunit contributes to subunit interaction and catalytic efficiency of the enzyme.
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Affiliation(s)
| | | | | | | | | | - Hemanta K. Majumder
- To whom correspondence should be addressed. Tel: +91 33 2412 3207; Fax: +91 33 2473 5197;
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Das BB, Sengupta T, Ganguly A, Majumder HK. Topoisomerases of kinetoplastid parasites: why so fascinating? Mol Microbiol 2006; 62:917-27. [PMID: 17042788 DOI: 10.1111/j.1365-2958.2006.05428.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA topoisomerases are the key enzymes involved in carrying out high precision DNA transactions inside the cells. However, they are detrimental to the cell when a wide variety of topoisomerase-targeted drugs generate cytotoxic lesions by trapping the enzymes in covalent complexes on the DNA. The discovery of unusual heterodimeric topoisomerase I in kinetoplastid family added a new twist in topoisomerase research related to evolution, functional conservation and their preferential sensitivity to Camptothecin. On the other hand, structural and mechanistic studies on kinetoplastid topoisomerase II delineate some distinguishing features that differentiate the parasitic enzyme from its prokaryotic and eukaryotic counterparts. This review summarizes the recent advances in research in kinetoplastid topoisomerases, their evolutionary significance and the death of the unicellular parasite Leishmania donovani induced by topoisomerase I inhibitor camptothecin.
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Affiliation(s)
- Benu Brata Das
- Department of Molecular Parasitology, Indian Institute of Chemical Biology, Kolkata 700032, India
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Balaña-Fouce R, Redondo CM, Pérez-Pertejo Y, Díaz-González R, Reguera RM. Targeting atypical trypanosomatid DNA topoisomerase I. Drug Discov Today 2006; 11:733-40. [PMID: 16846801 DOI: 10.1016/j.drudis.2006.06.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 04/21/2006] [Accepted: 06/16/2006] [Indexed: 11/26/2022]
Abstract
Tropical diseases produced by kinetoplastid protozoa are among humanity's costliest banes, owing to high mortality and the economic burden resulting from morbidity. Drug resistant strains of parasites, together with insecticide-resistant vectors, are contributing to their increased prevalence in the developing world. Their extension now threatens industrialized countries because of opportunistic infections in immuno-compromised individuals. Current chemotherapy is expensive, has undesirable side effects and, in many patients, is only marginally effective. Based on the clinical success of camptothecin derivatives as anticancer agents, DNA topoisomerases have been identified as targets for drug development. The substantial differences in homology between trypanosome and leishmania DNA topoisomerase IB compared with the human form provides a new lead in the study of the structural determinants that can be targeted.
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Affiliation(s)
- Rafael Balaña-Fouce
- Department of Pharmacology and Toxicology, University of León, Campus de Vegazana s/n 24071 León, Spain.
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Reguera RM, Redondo CM, Gutierrez de Prado R, Pérez-Pertejo Y, Balaña-Fouce R. DNA topoisomerase I from parasitic protozoa: A potential target for chemotherapy. ACTA ACUST UNITED AC 2006; 1759:117-31. [PMID: 16757380 DOI: 10.1016/j.bbaexp.2006.03.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Revised: 03/22/2006] [Accepted: 03/30/2006] [Indexed: 11/28/2022]
Abstract
The growing occurrence of drug resistant strains of unicellular prokaryotic parasites, along with insecticide-resistant vectors, are the factors contributing to the increased prevalence of tropical diseases in underdeveloped and developing countries, where they are endemic. Malaria, cryptosporidiosis, African and American trypanosomiasis and leishmaniasis threaten human beings, both for the high mortality rates involved and the economic loss resulting from morbidity. Due to the fact that effective immunoprophylaxis is not available at present; preventive sanitary measures and pharmacological approaches are the only sources to control the undesirable effects of such diseases. Current anti-parasitic chemotherapy is expensive, has undesirable side effects or, in many patients, is only marginally effective. Under this point of view molecular biology techniques and drug discovery must walk together in order to find new targets for chemotherapy intervention. The identification of DNA topoisomerases as a promising drug target is based on the clinical success of camptothecin derivatives as anticancer agents. The recent detection of substantial differences between trypanosome and leishmania DNA topoisomerase IB with respect to their homologues in mammals has provided a new lead in the study of the structural determinants that can be effectively targeted. The present report is an up to date review of the new findings on type IB DNA topoisomerase in unicellular parasites and the role of these enzymes as targets for therapeutic agents.
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Affiliation(s)
- R M Reguera
- Dpto. Farmacología y Toxicología (INTOXCAL), Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
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Das BB, Sen N, Roy A, Dasgupta SB, Ganguly A, Mohanta BC, Dinda B, Majumder HK. Differential induction of Leishmania donovani bi-subunit topoisomerase I-DNA cleavage complex by selected flavones and camptothecin: activity of flavones against camptothecin-resistant topoisomerase I. Nucleic Acids Res 2006; 34:1121-32. [PMID: 16488884 PMCID: PMC1373691 DOI: 10.1093/nar/gkj502] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Emergence of the bi-subunit topoisomerase I in the kinetoplastid family (Trypanosoma and Leishmania) has brought a new twist in topoisomerase research related to evolution, functional conservation and preferential sensitivities to the specific inhibitors of type IB topoisomerase family. In the present study, we describe that naturally occurring flavones baicalein, luteolin and quercetin are potent inhibitors of the recombinant Leishmania donovani topoisomerase I. These compounds bind to the free enzyme and also intercalate into the DNA at a very high concentration (300 µM) without binding to the minor grove. Here, we show that inhibition of topoisomerase I by these flavones is due to stabilization of topoisomerase I–DNA cleavage complexes, which subsequently inhibit the religation step. Their ability to stabilize the covalent topoisomerase I–DNA complex in vitro and in living cells is similar to that of the known topoisomerase I inhibitor camptothecin (CPT). However, in contrast to CPT, baicalein and luteolin failed to inhibit the religation step when the drugs were added to pre-formed enzyme substrate binary complex. This differential mechanism to induce the stabilization of cleavable complex with topoisomerase I and DNA by these selected flavones and CPT led us to investigate the effect of baicalein and luteolin on CPT-resistant mutant enzyme LdTOP1Δ39LS lacking 1–39 amino acids of the large subunit [B. B. Das, N. Sen, S. B. Dasgupta, A. Ganguly and H. K. Majumder (2005) J. Biol. Chem. 280, 16335–16344]. Baicalein and luteolin stabilize duplex oligonucleotide cleavage with LdTOP1Δ39LS. This observation was further supported by the stabilization of in vivo cleavable complex by baicalein and luteolin with highly CPT-resistant L.donovani strain. Taken together, our data suggest that the interacting amino acid residues of topoisomerase I may be partially overlapping or different for flavones and CPT. This study illuminates new properties of the flavones and provide additional insights into the ligand binding properties of L.donovani topoisomerase I.
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Affiliation(s)
| | | | | | | | | | | | - Biswanath Dinda
- Department of Chemistry, Tripura UniversitySuryamaninagar 799130, Tripura, India
| | - Hemanta K. Majumder
- To whom correspondence should be addressed. Tel: +91 33 2412 3207; Fax: +91 33 2473 5197;
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