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Kesharwani S, Eeba, Tandi M, Agarwal N, Sundriyal S. Design and synthesis of non-hydroxamate lipophilic inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR): in silico, in vitro and antibacterial studies. RSC Adv 2024; 14:27530-27554. [PMID: 39221132 PMCID: PMC11362829 DOI: 10.1039/d4ra05083e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
1-Deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) is a key enzyme of the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway operating in several pathogens, including Mycobacterium and Plasmodium. Since a DXR homologue is not present in humans, it is an important antimicrobial target. Fosmidomycin (FSM) and its analogues inhibit DXR function by chelating the divalent metal (Mn2+ or Mg2+) in its active site via a hydroxamate metal binding group (MBG). The latter, however, enhances the polarity of molecules and is known to display metabolic instability and toxicity issues. While attempts have been made to increase the lipophilicity of FSM by substituting the linker chain and prodrug approach, very few efforts have been made to replace the hydroxamate group with other lipophilic MBGs. We report a systematic in silico and experimental investigation to identify novel MBGs for designing non-hydroxamate lipophilic DXR inhibitors. The SAR studies with selected MBG fragments identified novel inhibitors of E. Coli DXR with IC50 values ranging from 0.29 to 106 μM. The promising inhibitors were also screened against ESKAPE pathogens and M. tuberculosis.
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Affiliation(s)
- Sharyu Kesharwani
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani (BITS) Pilani Campus, Vidya Vihar, Pilani Rajasthan 333 031 India
| | - Eeba
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Mile Stone, Gurugram-Faridabad Expressway Faridabad 121001 Haryana India
| | - Mukesh Tandi
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani (BITS) Pilani Campus, Vidya Vihar, Pilani Rajasthan 333 031 India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Mile Stone, Gurugram-Faridabad Expressway Faridabad 121001 Haryana India
| | - Sandeep Sundriyal
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani (BITS) Pilani Campus, Vidya Vihar, Pilani Rajasthan 333 031 India
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Keroack CD, Elsworth B, Tennessen JA, Paul AS, Hua R, Ramirez-Ramirez L, Ye S, Moreira CK, Meyers MJ, Zarringhalam K, Duraisingh MT. Comparative chemical genomics in Babesia species identifies the alkaline phosphatase PhoD as a determinant of antiparasitic resistance. Proc Natl Acad Sci U S A 2024; 121:e2312987121. [PMID: 38377214 PMCID: PMC10907312 DOI: 10.1073/pnas.2312987121] [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: 08/07/2023] [Accepted: 01/09/2024] [Indexed: 02/22/2024] Open
Abstract
Babesiosis is an emerging zoonosis and widely distributed veterinary infection caused by 100+ species of Babesia parasites. The diversity of Babesia parasites and the lack of specific drugs necessitate the discovery of broadly effective antibabesials. Here, we describe a comparative chemogenomics (CCG) pipeline for the identification of conserved targets. CCG relies on parallel in vitro evolution of resistance in independent populations of Babesia spp. (B. bovis and B. divergens). We identified a potent antibabesial, MMV019266, from the Malaria Box, and selected for resistance in two species of Babesia. After sequencing of multiple independently derived lines in the two species, we identified mutations in a membrane-bound metallodependent phosphatase (phoD). In both species, the mutations were found in the phoD-like phosphatase domain. Using reverse genetics, we validated that mutations in bdphoD confer resistance to MMV019266 in B. divergens. We have also demonstrated that BdPhoD localizes to the endomembrane system and partially with the apicoplast. Finally, conditional knockdown and constitutive overexpression of BdPhoD alter the sensitivity to MMV019266 in the parasite. Overexpression of BdPhoD results in increased sensitivity to the compound, while knockdown increases resistance, suggesting BdPhoD is a pro-susceptibility factor. Together, we have generated a robust pipeline for identification of resistance loci and identified BdPhoD as a resistance mechanism in Babesia species.
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Affiliation(s)
- Caroline D. Keroack
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Brendan Elsworth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Jacob A. Tennessen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Aditya S. Paul
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Renee Hua
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Luz Ramirez-Ramirez
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Sida Ye
- Department of Mathematics, University of Massachusetts, Boston, MA02125
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA02125
| | - Cristina K. Moreira
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Marvin J. Meyers
- Department of Chemistry, Saint Louis University, St. Louis, MO63103
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts, Boston, MA02125
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA02125
| | - Manoj T. Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
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Crispim M, Verdaguer IB, Hernández A, Kronenberger T, Fenollar À, Yamaguchi LF, Alberione MP, Ramirez M, de Oliveira SS, Katzin AM, Izquierdo L. Beyond the MEP Pathway: A novel kinase required for prenol utilization by malaria parasites. PLoS Pathog 2024; 20:e1011557. [PMID: 38277417 PMCID: PMC10849223 DOI: 10.1371/journal.ppat.1011557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 02/07/2024] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
A proposed treatment for malaria is a combination of fosmidomycin and clindamycin. Both compounds inhibit the methylerythritol 4-phosphate (MEP) pathway, the parasitic source of farnesyl and geranylgeranyl pyrophosphate (FPP and GGPP, respectively). Both FPP and GGPP are crucial for the biosynthesis of several essential metabolites such as ubiquinone and dolichol, as well as for protein prenylation. Dietary prenols, such as farnesol (FOH) and geranylgeraniol (GGOH), can rescue parasites from MEP inhibitors, suggesting the existence of a missing pathway for prenol salvage via phosphorylation. In this study, we identified a gene in the genome of P. falciparum, encoding a transmembrane prenol kinase (PolK) involved in the salvage of FOH and GGOH. The enzyme was expressed in Saccharomyces cerevisiae, and its FOH/GGOH kinase activities were experimentally validated. Furthermore, conditional knockout parasites (Δ-PolK) were created to investigate the biological importance of the FOH/GGOH salvage pathway. Δ-PolK parasites were viable but displayed increased susceptibility to fosmidomycin. Their sensitivity to MEP inhibitors could not be rescued by adding prenols. Additionally, Δ-PolK parasites lost their capability to utilize prenols for protein prenylation. Experiments using culture medium supplemented with whole/delipidated human plasma in transgenic parasites revealed that human plasma has components that can diminish the effectiveness of fosmidomycin. Mass spectrometry tests indicated that both bovine supplements used in culture and human plasma contain GGOH. These findings suggest that the FOH/GGOH salvage pathway might offer an alternate source of isoprenoids for malaria parasites when de novo biosynthesis is inhibited. This study also identifies a novel kind of enzyme related to isoprenoid metabolism.
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Affiliation(s)
- Marcell Crispim
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Ignasi Bofill Verdaguer
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
| | - Agustín Hernández
- Center for Biological and Health Sciences, Integrated Unit for Research in Biodiversity (BIOTROP-CCBS), Federal University of São Carlos, São Carlos, Brazil
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany
| | - Àngel Fenollar
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | - María Pía Alberione
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Miriam Ramirez
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | - Alejandro Miguel Katzin
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
| | - Luis Izquierdo
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
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Keroack CD, Elsworth B, Tennessen JA, Paul AS, Hua R, Ramirez-Ramirez L, Ye S, Moreira CM, Meyers MJ, Zarringhalam K, Duraisingh MT. Comparative chemical genomics in Babesia species identifies the alkaline phosphatase phoD as a novel determinant of resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544849. [PMID: 37398106 PMCID: PMC10312741 DOI: 10.1101/2023.06.13.544849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Babesiosis is an emerging zoonosis and widely distributed veterinary infection caused by 100+ species of Babesia parasites. The diversity of Babesia parasites, coupled with the lack of potent inhibitors necessitates the discovery of novel conserved druggable targets for the generation of broadly effective antibabesials. Here, we describe a comparative chemogenomics (CCG) pipeline for the identification of novel and conserved targets. CCG relies on parallel in vitro evolution of resistance in independent populations of evolutionarily-related Babesia spp. ( B. bovis and B. divergens ). We identified a potent antibabesial inhibitor from the Malaria Box, MMV019266. We were able to select for resistance to this compound in two species of Babesia, achieving 10-fold or greater resistance after ten weeks of intermittent selection. After sequencing of multiple independently derived lines in the two species, we identified mutations in a single conserved gene in both species: a membrane-bound metallodependent phosphatase (putatively named PhoD). In both species, the mutations were found in the phoD-like phosphatase domain, proximal to the predicted ligand binding site. Using reverse genetics, we validated that mutations in PhoD confer resistance to MMV019266. We have also demonstrated that PhoD localizes to the endomembrane system and partially with the apicoplast. Finally, conditional knockdown and constitutive overexpression of PhoD alter the sensitivity to MMV019266 in the parasite: overexpression of PhoD results in increased sensitivity to the compound, while knockdown increases resistance, suggesting PhoD is a resistance mechanism. Together, we have generated a robust pipeline for identification of resistance loci, and identified PhoD as a novel determinant of resistance in Babesia species. Highlights Use of two species for in vitro evolution identifies a high confidence locus associated with resistance Resistance mutation in phoD was validated using reverse genetics in B. divergens Perturbation of phoD using function genetics results in changes in the level of resistance to MMV019266Epitope tagging reveals localization to the ER/apicoplast, a conserved localization with a similar protein in diatoms Together, phoD is a novel resistance determinant in multiple Babesia spp .
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Verdaguer IB, Crispim M, Hernández A, Katzin AM. The Biomedical Importance of the Missing Pathway for Farnesol and Geranylgeraniol Salvage. Molecules 2022; 27:molecules27248691. [PMID: 36557825 PMCID: PMC9782597 DOI: 10.3390/molecules27248691] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Isoprenoids are the output of the polymerization of five-carbon, branched isoprenic chains derived from isopentenyl pyrophosphate (IPP) and its isomer, dimethylallyl pyrophosphate (DMAPP). Isoprene units are consecutively condensed to form longer structures such as farnesyl and geranylgeranyl pyrophosphate (FPP and GGPP, respectively), necessary for the biosynthesis of several metabolites. Polyprenyl transferases and synthases use polyprenyl pyrophosphates as their natural substrates; however, it is known that free polyprenols, such as farnesol (FOH), and geranylgeraniol (GGOH) can be incorporated into prenylated proteins, ubiquinone, cholesterol, and dolichols. Furthermore, FOH and GGOH have been shown to block the effects of isoprenoid biosynthesis inhibitors such as fosmidomycin, bisphosphonates, or statins in several organisms. This phenomenon is the consequence of a short pathway, which was observed for the first time more than 25 years ago: the polyprenol salvage pathway, which works via the phosphorylation of FOH and GGOH. Biochemical studies in bacteria, animals, and plants suggest that this pathway can be carried out by two enzymes: a polyprenol kinase and a polyprenyl-phosphate kinase. However, to date, only a few genes have been unequivocally identified to encode these enzymes in photosynthetic organisms. Nevertheless, pieces of evidence for the importance of this pathway abound in studies related to infectious diseases, cancer, dyslipidemias, and nutrition, and to the mitigation of the secondary effects of several drugs. Furthermore, nowadays it is known that both FOH and GGOH can be incorporated via dietary sources that produce various biological effects. This review presents, in a simplified but comprehensive manner, the most important data on the FOH and GGOH salvage pathway, stressing its biomedical importance The main objective of this review is to bring to light the need to discover and characterize the kinases associated with the isoprenoid salvage pathway in animals and pathogens.
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Affiliation(s)
- Ignasi Bofill Verdaguer
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, Av. Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Marcell Crispim
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, Av. Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Agustín Hernández
- Integrated Unit for Research in Biodiversity (BIOTROP-CCBS), Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos 13565-905, Brazil
| | - Alejandro Miguel Katzin
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, Av. Lineu Prestes 1374, São Paulo 05508-000, Brazil
- Correspondence: ; Tel.: +55-11-3091-7330; Fax: +55-11-3091-7417
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Scott JD, Sajid MS, Pascoe EL, Foley JE. Detection of Babesia odocoilei in Humans with Babesiosis Symptoms. Diagnostics (Basel) 2021; 11:diagnostics11060947. [PMID: 34070625 PMCID: PMC8228967 DOI: 10.3390/diagnostics11060947] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/13/2021] [Accepted: 05/24/2021] [Indexed: 12/15/2022] Open
Abstract
Human babesiosis is a life-threatening infectious disease that causes societal and economic impact worldwide. Several species of Babesia cause babesiosis in terrestrial vertebrates, including humans. A one-day clinic was held in Ontario, Canada, to see if a red blood cell parasite, which is present in blacklegged ticks, Ixodes scapularis, is present in humans. Based on PCR testing and DNA sequencing of the 18S rRNA gene, we unveiled B. odocoilei in two of 19 participants. DNA amplicons from these two patients are almost identical matches with the type strains of B. odocoilei in GenBank. In addition, the same two human subjects had the hallmark symptoms of human babesiosis, including night sweats, chills, fevers, and profound fatigue. Based on symptoms and molecular identification, we provide substantive evidence that B. odocoilei is pathogenic to humans. Dataset reveals that B. odocoilei serologically cross-reacts with Babesia duncani. Clinicians must realize that there are more than two Babesia spp. in North America that cause human babesiosis. This discovery signifies the first report of B. odocoilei causing human babesiosis.
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Affiliation(s)
- John D. Scott
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (M.S.S.); (E.L.P.); (J.E.F.)
- Correspondence:
| | - Muhammad S. Sajid
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (M.S.S.); (E.L.P.); (J.E.F.)
- Faculty of Veterinary Medicine, University of Agriculture, Faisalabad 38040, Pakistan
| | - Emily L. Pascoe
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (M.S.S.); (E.L.P.); (J.E.F.)
| | - Janet E. Foley
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (M.S.S.); (E.L.P.); (J.E.F.)
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Non-hydroxamate inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR): A critical review and future perspective. Eur J Med Chem 2020; 213:113055. [PMID: 33303239 DOI: 10.1016/j.ejmech.2020.113055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 12/22/2022]
Abstract
1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) catalyzes the second step of the non-mevalonate (or MEP) pathway that functions in several organisms and plants for the synthesis of isoprenoids. DXR is essential for the survival of multiple pathogenic bacteria/parasites, including those that cause tuberculosis and malaria in humans. DXR function is inhibited by fosmidomycin (1), a natural product, which forms a chelate with the active site divalent metal (Mg2+/Mn2+) through its hydroxamate metal-binding group (MBG). Most of the potent DXR inhibitors are structurally similar to 1 and retain hydroxamate despite the unfavourable pharmacokinetic and toxicity profile of the latter. We provide our perspective on the lack of non-hydroxamate DXR inhibitors. We also highlight the fundamental flaws in the design of MBG in these molecules, primarily responsible for their failure to inhibit DXR. We also suggest that for designing next-generation non-hydroxamate DXR inhibitors, approaches followed for other metalloenzymes targets may be exploited.
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