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Hamid A, Mäser P, Mahmoud AB. Drug Repurposing in the Chemotherapy of Infectious Diseases. Molecules 2024; 29:635. [PMID: 38338378 PMCID: PMC10856722 DOI: 10.3390/molecules29030635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Repurposing is a universal mechanism for innovation, from the evolution of feathers to the invention of Velcro tape. Repurposing is particularly attractive for drug development, given that it costs more than a billion dollars and takes longer than ten years to make a new drug from scratch. The COVID-19 pandemic has triggered a large number of drug repurposing activities. At the same time, it has highlighted potential pitfalls, in particular when concessions are made to the target product profile. Here, we discuss the pros and cons of drug repurposing for infectious diseases and analyze different ways of repurposing. We distinguish between opportunistic and rational approaches, i.e., just saving time and money by screening compounds that are already approved versus repurposing based on a particular target that is common to different pathogens. The latter can be further distinguished into divergent and convergent: points of attack that are divergent share common ancestry (e.g., prokaryotic targets in the apicoplast of malaria parasites), whereas those that are convergent arise from a shared lifestyle (e.g., the susceptibility of bacteria, parasites, and tumor cells to antifolates due to their high rate of DNA synthesis). We illustrate how such different scenarios can be capitalized on by using examples of drugs that have been repurposed to, from, or within the field of anti-infective chemotherapy.
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Affiliation(s)
- Amal Hamid
- Faculty of Pharmacy, University of Khartoum, Khartoum 11111, Sudan;
| | - Pascal Mäser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, 4123 Basel, Switzerland
- Faculty of Science, University of Basel, 4001 Basel, Switzerland
| | - Abdelhalim Babiker Mahmoud
- Faculty of Pharmacy, University of Khartoum, Khartoum 11111, Sudan;
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbruecken, Germany
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
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2
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Kameda T, Isami S, Togashi Y, Nishimori H, Sakamoto N, Awazu A. The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry. Front Physiol 2017; 8:103. [PMID: 28382002 PMCID: PMC5361685 DOI: 10.3389/fphys.2017.00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 02/07/2017] [Indexed: 11/18/2022] Open
Abstract
Coarse-grained models of DNA have made important contributions to the determination of the physical properties of genomic DNA, working as a molecular machine for gene regulation. In this study, to analyze the global dynamics of long DNA sequences with consideration of sequence-dependent geometry, we propose elastic network models of DNA where each particle represents k nucleotides (1-particle-per-k-nucleotides, 1PkN). The models were adjusted according to profiles of the anisotropic fluctuations obtained from our previous 1-particle-per-1-nucleotide (1P1N) model, which was proven to reproduce such profiles of all-atom models. We confirmed that the 1P3N and 1P4N models are suitable for the analysis of detailed dynamics such as local twisting motion. The models are intended for the analysis of large structures, e.g., 10-nm fibers in the nucleus, and nucleoids of mitochondrial or phage DNA at low computational costs. As an example, we surveyed the physical characteristics of the whole mitochondrial human and Plasmodium falciparum genomes.
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Affiliation(s)
- Takeru Kameda
- Department of Mathematical and Life Sciences, Hiroshima University Hiroshima, Japan
| | - Shuhei Isami
- Department of Mathematical and Life Sciences, Hiroshima University Hiroshima, Japan
| | - Yuichi Togashi
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University Hiroshima, Japan
| | - Hiraku Nishimori
- Department of Mathematical and Life Sciences, Hiroshima UniversityHiroshima, Japan; Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima UniversityHiroshima, Japan
| | - Naoaki Sakamoto
- Department of Mathematical and Life Sciences, Hiroshima UniversityHiroshima, Japan; Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima UniversityHiroshima, Japan
| | - Akinori Awazu
- Department of Mathematical and Life Sciences, Hiroshima UniversityHiroshima, Japan; Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima UniversityHiroshima, Japan
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3
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Castelli S, Vieira S, D'Annessa I, Katkar P, Musso L, Dallavalle S, Desideri A. A derivative of the natural compound kakuol affects DNA relaxation of topoisomerase IB inhibiting the cleavage reaction. Arch Biochem Biophys 2012; 530:7-12. [PMID: 23262316 DOI: 10.1016/j.abb.2012.12.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 12/06/2012] [Accepted: 12/09/2012] [Indexed: 11/28/2022]
Abstract
Topoisomerases IB are anticancer and antimicrobial targets whose inhibition by several natural and synthetic compounds has been documented over the last three decades. Here we show that kakuol, a natural compound isolated from the rhizomes of Asarum sieboldii, and a derivative analogue are able to inhibit the DNA relaxation mediated by the human enzyme. The analogue is the most efficient one and the inhibitory effect is enhanced upon pre-incubation with the enzyme. Analysis of the different steps of the catalytic cycle indicates that the inhibition occurs at the cleavage level and does not prevent DNA binding. Molecular docking shows that the compound preferentially binds near the active site at the bottom of the catalytic residue Tyr723, providing an atomistic explanation for its inhibitory activity.
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Affiliation(s)
- Silvia Castelli
- University of Rome Tor Vergata, Department of Biology, Via Della Ricerca Scientifica, 00133 Rome, Italy
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4
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Effect of topoisomerase inhibitors and DNA-binding drugs on the cell proliferation and ultrastructure of Trypanosoma cruzi. Int J Antimicrob Agents 2011; 37:449-56. [DOI: 10.1016/j.ijantimicag.2010.11.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 10/31/2010] [Accepted: 11/01/2010] [Indexed: 11/22/2022]
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5
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Chollet C, Baliani A, Wong PE, Barrett MP, Gilbert IH. Targeted delivery of compounds to Trypanosoma brucei using the melamine motif. Bioorg Med Chem 2009; 17:2512-23. [PMID: 19250832 DOI: 10.1016/j.bmc.2009.01.058] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 01/21/2009] [Accepted: 01/25/2009] [Indexed: 11/29/2022]
Abstract
There is an urgent need for the development of new drugs for the treatment of human African trypanosomiasis. The causative organism, Trypanosoma brucei, has been shown to have some unusual plasma membrane transporters, in particular the P2 aminopurine transporter and related permeases, which have been used for the selective targeting of trypanocidal compounds to the organism. In this paper, we report the addition of melamine-based P2-targeting motifs to three different classes of compound in order to try and improve activity through increased selective uptake. The classes reported here are fluoroquinolones, difluoromethylornithine and artesunate derivatives.
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Affiliation(s)
- Constance Chollet
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Sir James Black Centre, Dundee DD1 5EH, UK
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6
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Oxygenated chalcones and bischalcones as a new class of inhibitors of DNA topoisomerase II of malarial parasites. Med Chem Res 2007. [DOI: 10.1007/s00044-007-9057-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Sengupta T, Mukherjee M, Das A, Mandal C, Das R, Mukherjee T, Majumder H. Characterization of the ATPase activity of topoisomerase II from Leishmania donovani and identification of residues conferring resistance to etoposide. Biochem J 2006; 390:419-26. [PMID: 15901238 PMCID: PMC1198921 DOI: 10.1042/bj20042128] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We have cloned and expressed the 43 kDa N-terminal domain of Leishmania donovani topoisomerase II. This protein has an intrinsic ATPase activity and obeys Michaelis-Menten kinetics. Cross-linking studies indicate that the N-terminal domain exists as a dimer both in the presence and absence of nucleotides. Etoposide, an effective antitumour drug, traps eukaryotic DNA topoisomerase II in a covalent complex with DNA. In the present study, we report for the first time that etoposide inhibits the ATPase activity of the recombinant N-terminal domain of L. donovani topoisomerase II. We have modelled the structure of this 43 kDa protein and performed molecular docking analysis with the drug. Mutagenesis of critical amino acids in the vicinity of the ligand-binding pocket reveals less efficient inhibition of the ATPase activity of the enzyme by etoposide. Taken together, these results provide an insight for the development of newer therapeutic agents with specific selectivity.
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Affiliation(s)
- Tanushri Sengupta
- *Molecular Parasitology Laboratory, Indian Institute of Chemical Biology, Kolkata-700032, India
| | - Mandira Mukherjee
- *Molecular Parasitology Laboratory, Indian Institute of Chemical Biology, Kolkata-700032, India
| | - Aditi Das
- †Sealy Center for Molecular Sciences, University of Texas Medical Branch at Galveston, Galveston, TX-77555, U.S.A
| | - Chhabinath Mandal
- ‡Department of Drug Design, Development and Molecular Modeling, Indian Institute of Chemical Biology, Kolkata-700032, India
| | - Rakhee Das
- *Molecular Parasitology Laboratory, Indian Institute of Chemical Biology, Kolkata-700032, India
| | - Tanmoy Mukherjee
- §Infectious Disease Group, Indian Institute of Chemical Biology, Kolkata-700032, India
| | - Hemanta K. Majumder
- *Molecular Parasitology Laboratory, Indian Institute of Chemical Biology, Kolkata-700032, India
- To whom correspondence should be addressed (email )
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Didier ES, Bowers L, Stovall ME, Kuebler D, Mittleider D, Brindley PJ, Didier PJ. Antimicrosporidial activity of (fluoro)quinolones in vitro and in vivo. Folia Parasitol (Praha) 2005; 52:173-81. [PMID: 16004377 DOI: 10.14411/fp.2005.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Microsporidia are a cause of emerging and opportunistic infections in humans and animals. Although two drugs are currently being used to treat microsporidiosis, concerns exist that albendazole is only selective for inhibiting some species of microsporidia that infect mammals, and fumagillin appears to have been found to be toxic. During a limited sequence survey of the Vittaforma corneae genome, a partial gene encoding for the ParC topoisomerase IV subunit was identified. The purpose of this set of studies was to determine if fluoroquinolones, which target topoisomerase IV, exert activity against Encephalitozoon intestinalis and V. corneae in vitro, and whether these compounds could prolong survival of V. corneae-infected athymic mice. Fifteen fluoroquinolones were tested. Of these, norfloxacin and ofloxacin inhibited E. intestinalis replication by more than 70% compared with non-treated control cultures, while gatifloxacin, lomefloxacin, moxifloxacin, and nalidixic acid (sodium salt) inhibited both E. intestinalis and V. corneae by at least 60% at concentrations not toxic to the host cells. These drugs were tested in vivo also, where gatifloxacin, lomefloxacin, norfloxacin, and ofloxacin prolonged survival of V. corneae-infected athymic mice (P < 0.05), whereas moxifloxacin and nalidixic acid failed to prolong survival. Therefore, these results support continued studies for evaluating the efficacy of the fluoroquinolones for treating microsporidiosis and for characterizing the target(s) of these fluoroquinolones in the microsporidia.
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Affiliation(s)
- Elizabeth S Didier
- Division of Microbiology and Immunology, Tulane National Primate Research Center, Covington, Louisiana 70433, USA.
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Podestá D, Stoppani A, Villamil SF. Inactivation of Trypanosoma cruzi and Crithidia fasciculata topoisomerase I by Fenton systems. Redox Rep 2004; 8:357-63. [PMID: 14980068 DOI: 10.1179/135100003225003366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Fenton systems (H(2)O(2)/Fe(II) or H(2)O(2)/Cu(II)) inhibited Trypanosoma cruzi and Crithidia fasciculata topoisomerase I activity. About 61-71% inactivation was produced by 25 microM Fe(II) or Cu(II) with 3.0 mM H(2)O(2). Thiol compounds and free radical scavengers prevented Fenton system effects, depending on the topoisomerase assayed. With the T. cruzi enzyme, reduced glutathione (GSH), dithiothreitol (DTT), cysteine and N-acetyl-L-cysteine (NAC) entirely prevented the effect of the H(2)O(2)/Fe(II) system; mannitol protected 37%, whereas histidine and ethanol were ineffective. With C. fasciculata topoisomerase, GSH, DTT and NAC protected 100%, cysteine, histidine and mannitol protected 28%, 34% and 48%, respectively, whereas ethanol was ineffective. With the H(2)O(2)/Cu(II) system and T. cruzi topoisomerase, DTT and histidine protected 100% and 60%, respectively, but the other assayed protectors were less effective. Similar results were obtained with the C. fasciculata enzyme. Topoisomerase inactivation by the H(2)O(2)/Fe(II) or H(2)O(2)/Cu(II) systems proved to be irreversible since it was not reversed by the more effective enzyme protectors. It is suggested that topoisomerases could act either as targets of 'reactive oxygen species' (ROS) generated by Fenton systems or bind the corresponding metal ions, whose redox cycling would generate reactive oxygen species in situ.
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Affiliation(s)
- Dolores Podestá
- Bioenergetics Research Centre (CONICET) and School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
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10
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Bodley AL, Chakraborty AK, Xie S, Burri C, Shapiro TA. An unusual type IB topoisomerase from African trypanosomes. Proc Natl Acad Sci U S A 2003; 100:7539-44. [PMID: 12810956 PMCID: PMC164622 DOI: 10.1073/pnas.1330762100] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
African trypanosomes are ancient eukaryotes that cause lethal disease in humans and cattle. Available drugs are inadequate and the need for new therapeutic targets is great. Trypanosoma brucei and related pathogens differ strikingly from higher eukaryotes in many aspects of nucleic acid structure and metabolism. We find yet another example of this in their unusual DNA topoisomerase IB. Type IB topoisomerases relieve the supercoils that accumulate during DNA and RNA synthesis, and are of considerable importance as the target for antitumor camptothecins. Dozens of type IB topoisomerases sequenced from eukaryotes, bacteria, and pox viruses are all encoded by a single gene that predictably contains a highly conserved DNA binding domain and C-terminal catalytic domain, linked by a nonconserved hydrophilic region. We find that topoisomerase IB in T. brucei is encoded by two genes: one for the DNA-binding domain and a second for the C-terminal catalytic domain. In keeping with this, highly purified fractions of native T. brucei topoisomerase IB catalytic activity contain two proteins, of 90 and 36 kDa. The native enzyme is conventional in its Mg2+-independence, ability to relax positive and negative supercoils, and inhibition by camptothecin. Camptothecin promotes the formation of a covalent complex between 32P-labeled substrate DNA and the small subunit. This unusual structural organization may provide a missing link in the evolution of type IB enzymes, which are thought to have arisen over time from the fusion of two independent domains. It also provides another basis for the design of selectively toxic drug candidates.
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Affiliation(s)
- Annette L Bodley
- Division of Clinical Pharmacology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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11
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Schnaufer A, Domingo GJ, Stuart K. Natural and induced dyskinetoplastic trypanosomatids: how to live without mitochondrial DNA. Int J Parasitol 2002; 32:1071-84. [PMID: 12117490 DOI: 10.1016/s0020-7519(02)00020-6] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Salivarian trypanosomes are the causative agents of several diseases of major social and economic impact. The most infamous parasites of this group are the African subspecies of the Trypanosoma brucei group, which cause sleeping sickness in humans and nagana in cattle. In terms of geographical distribution, however, Trypanosoma equiperdum and Trypanosoma evansi have been far more successful, causing disease in livestock in Africa, Asia, and South America. In these latter forms the mitochondrial DNA network, the kinetoplast, is altered or even completely lost. These natural dyskinetoplastic forms can be mimicked in bloodstream form T. brucei by inducing the loss of kinetoplast DNA (kDNA) with intercalating dyes. Dyskinetoplastic T. brucei are incapable of completing their usual developmental cycle in the insect vector, due to their inability to perform oxidative phosphorylation. Nevertheless, they are usually as virulent for their mammalian hosts as parasites with intact kDNA, thus questioning the therapeutic value of attempts to target mitochondrial gene expression with specific drugs. Recent experiments, however, have challenged this view. This review summarises the data available on dyskinetoplasty in trypanosomes and revisits the roles the mitochondrion and its genome play during the life cycle of T. brucei.
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Affiliation(s)
- Achim Schnaufer
- Seattle Biomedical Research Institute, 4 Nickerson Street, Suite 200, Seattle, WA 98109, USA.
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12
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Wang Z, Englund PT. RNA interference of a trypanosome topoisomerase II causes progressive loss of mitochondrial DNA. EMBO J 2001; 20:4674-83. [PMID: 11532932 PMCID: PMC125608 DOI: 10.1093/emboj/20.17.4674] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We studied the function of a Trypanosoma brucei topoisomerase II using RNA interference (RNAi). Expression of a topoisomerase II double-stranded RNA as a stem-loop caused specific degradation of mRNA followed by loss of protein. After 6 days of RNAi, the parasites' growth rate declined and the cells subsequently died. The most striking phenotype upon induction of RNAi was the loss of kinetoplast DNA (kDNA), the cell's catenated mitochondrial DNA network. The loss of kDNA was preceded by gradual shrinkage of the network and accumulation of gapped free minicircle replication intermediates. These facts, together with the localization of the enzyme in two antipodal sites flanking the kDNA, show that a function of this topoisomerase II is to attach free minicircles to the network periphery following their replication.
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MESH Headings
- Animals
- DNA Replication
- DNA Topoisomerases, Type II/genetics
- DNA Topoisomerases, Type II/metabolism
- DNA, Kinetoplast/genetics
- DNA, Kinetoplast/metabolism
- DNA, Kinetoplast/ultrastructure
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- DNA, Mitochondrial/ultrastructure
- DNA, Protozoan/genetics
- DNA, Protozoan/metabolism
- DNA, Protozoan/ultrastructure
- Kinetics
- Phenotype
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Protozoan/genetics
- Time Factors
- Trypanosoma brucei brucei/enzymology
- Trypanosoma brucei brucei/genetics
- Trypanosoma brucei brucei/growth & development
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Affiliation(s)
| | - Paul T. Englund
- Department of Biological Chemistry, Johns Hopkins Medical School, 725 N. Wolfe Street, Baltimore, MD 21205, USA
Corresponding author e-mail:
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13
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Abstract
Numerous drugs are known to deplete mitochondrial DNA (mtDNA) from mammalian cells. These include DNA polymerase gamma and type II topoisomerase inhibitors, lipophilic cationic compounds, and DNA intercalating and non intercalating agents. The effects of these drugs on mtDNA metabolism will be discussed and potential mechanisms underlying their depletion of mtDNA presented.
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Affiliation(s)
- T C Rowe
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, FL 32610-0267, USA.
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Morris JC, Drew ME, Klingbeil MM, Motyka SA, Saxowsky TT, Wang Z, Englund PT. Replication of kinetoplast DNA: an update for the new millennium. Int J Parasitol 2001; 31:453-8. [PMID: 11334929 DOI: 10.1016/s0020-7519(01)00156-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In this review we will describe the replication of kinetoplast DNA, a subject that our lab has studied for many years. Our knowledge of kinetoplast DNA replication has depended mostly upon the investigation of the biochemical properties and intramitochondrial localisation of replication proteins and enzymes as well as a study of the structure and dynamics of kinetoplast DNA replication intermediates. We will first review the properties of the characterised kinetoplast DNA replication proteins and then describe our current model for kinetoplast DNA replication.
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Affiliation(s)
- J C Morris
- Department of Biological Chemistry, Johns Hopkins Medical School, 21205, Baltimore, MD, USA.
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Abstract
The African trypanosomes remain well recognised for their role as an interesting model eukaryote for basic science, but are loosing ground in their ability to contribute to understanding common cellular mechanisms. At the same time, the diseases they cause remain as prevalent as ever, but appear increasingly irrelevant in their wider medical, social, economic and political context. What can be done to keep trypanosome biology relevant and vigorous in the 21st century?
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Affiliation(s)
- G A Cross
- Laboratory of Molecular Parasitology, The Rockefeller University, Box 185, 1230 York Avenue, 10021-6399, New York, NY, USA.
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