1
|
Naik B, Gupta N, Godara P, Srivastava V, Kumar P, Giri R, Prajapati VK, Pandey KC, Prusty D. Structure-based virtual screening approach reveals natural multi-target compounds for the development of antimalarial drugs to combat drug resistance. J Biomol Struct Dyn 2024; 42:7384-7408. [PMID: 37528665 DOI: 10.1080/07391102.2023.2240415] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023]
Abstract
Compared to the previous year, there has been an increase of nearly 2 million malaria cases in 2021. The emergence of drug-resistant strains of Plasmodium falciparum, the most deadly malaria parasite, has led to a decline in the effectiveness of existing antimalarial drugs. To address this problem, the present study aimed to identify natural compounds with the potential to inhibit multiple validated antimalarial drug targets. The natural compounds from the Natural Product Activity and Species Source (NPASS) database were screened against ten validated drug targets of Plasmodium falciparum using a structure-based molecular docking method. Twenty compounds, with targets ranging from three to five, were determined as the top hits. The molecular dynamics simulations of the top six complexes (NPC246162 in complex with PfAdSS, PfGDH, and PfNMT; NPC271270 in complex with PfCK, PfGDH, and PfdUTPase) confirmed their stable binding affinity in the dynamic environment. The Tanimoto coefficient and distance matrix score analysis show the structural divergence of all the hit compounds from known antimalarials, indicating minimum chances of cross-resistance. Thus, we propose further investigating these compounds in biochemical and parasite inhibition studies to reveal the real therapeutic potential. If found successful, these compounds may be a new avenue for future drug discovery efforts to combat existing antimalarial drug resistance.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Biswajit Naik
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Nidhi Gupta
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Priya Godara
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Varshita Srivastava
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Kailash C Pandey
- Icmr-National Institute of Malaria Research, And Academy of Scientific and Innovative Research (AcSIR-ICMR), India
| | - Dhaneswar Prusty
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| |
Collapse
|
2
|
Mazzone F, Hoeppner A, Reiners J, Gertzen CG, Applegate V, Abdullaziz MA, Gottstein J, Degrandi D, Wesemann M, Kurz T, Smits SH, Pfeffer K. 1-Deoxy-d-xylulose 5-phosphate reductoisomerase as target for anti Toxoplasma gondii agents: crystal structure, biochemical characterization and biological evaluation of inhibitors. Biochem J 2024; 481:1075-1096. [PMID: 39105673 PMCID: PMC11346426 DOI: 10.1042/bcj20240110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 07/27/2024] [Accepted: 08/06/2024] [Indexed: 08/07/2024]
Abstract
Toxoplasma gondii is a widely distributed apicomplexan parasite causing toxoplasmosis, a critical health issue for immunocompromised individuals and for congenitally infected foetuses. Current treatment options are limited in number and associated with severe side effects. Thus, novel anti-toxoplasma agents need to be identified and developed. 1-Deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) is considered the rate-limiting enzyme in the non-mevalonate pathway for the biosynthesis of the isoprenoid precursors isopentenyl pyrophosphate and dimethylallyl pyrophosphate in the parasite, and has been previously investigated for its key role as a novel drug target in some species, encompassing Plasmodia, Mycobacteria and Escherichia coli. In this study, we present the first crystal structure of T. gondii DXR (TgDXR) in a tertiary complex with the inhibitor fosmidomycin and the cofactor NADPH in dimeric conformation at 2.5 Å resolution revealing the inhibitor binding mode. In addition, we biologically characterize reverse α-phenyl-β-thia and β-oxa fosmidomycin analogues and show that some derivatives are strong inhibitors of TgDXR which also, in contrast with fosmidomycin, inhibit the growth of T. gondii in vitro. Here, ((3,4-dichlorophenyl)((2-(hydroxy(methyl)amino)-2-oxoethyl)thio)methyl)phosphonic acid was identified as the most potent anti T. gondii compound. These findings will enable the future design and development of more potent anti-toxoplasma DXR inhibitors.
Collapse
Affiliation(s)
- Flaminia Mazzone
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University, Düsseldorf, Germany
- University Hospital Düsseldorf, Düsseldorf, Germany
| | - Astrid Hoeppner
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
| | - Jens Reiners
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
| | - Christoph G.W. Gertzen
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Violetta Applegate
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
| | - Mona A. Abdullaziz
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
- National Research Centre (NRC), Dokki, Cairo, Egypt
| | - Julia Gottstein
- Institute of Biochemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Daniel Degrandi
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University, Düsseldorf, Germany
- University Hospital Düsseldorf, Düsseldorf, Germany
| | - Martina Wesemann
- Institute of Biochemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Thomas Kurz
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Sander H.J. Smits
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
- Institute of Biochemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University, Düsseldorf, Germany
- University Hospital Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
3
|
Kabeche S, Braukmann T, Doenier J, Meister T, Yeh E. A picomolar inhibitor of the Plasmodium falciparum IPP pathway. Antimicrob Agents Chemother 2024; 68:e0123823. [PMID: 39037239 PMCID: PMC11304725 DOI: 10.1128/aac.01238-23] [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: 09/27/2023] [Accepted: 06/30/2024] [Indexed: 07/23/2024] Open
Abstract
We identified MMV026468 as a picomolar inhibitor of blood-stage Plasmodium falciparum. Phenotyping assays, including isopentenyl diphosphate rescue of parasite growth inhibition, demonstrated that it targets MEP isoprenoid precursor biosynthesis. MMV026468-treated parasites showed an overall decrease in MEP pathway intermediates, which could result from inhibition of the first MEP enzyme DXS or steps prior to DXS such as regulation of the MEP pathway. Selection of MMV026468-resistant parasites lacking DXS mutations suggested that other targets are possible. The identification of MMV026468 could lead to a new class of antimalarial isoprenoid inhibitors.
Collapse
Affiliation(s)
- Stephanie Kabeche
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Thomas Braukmann
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Jon Doenier
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Thomas Meister
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA
| | - Ellen Yeh
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| |
Collapse
|
4
|
Bague D, Wang R, Hodge D, Mikati MO, Roma JS, Boshoff HI, Dailey AL, Girma M, Couch RD, Odom John AR, Dowd CS. Inhibition of DXR in the MEP pathway with lipophilic N-alkoxyaryl FR900098 analogs. RSC Med Chem 2024; 15:2422-2439. [PMID: 39026652 PMCID: PMC11253873 DOI: 10.1039/d3md00642e] [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: 11/16/2023] [Accepted: 05/22/2024] [Indexed: 07/20/2024] Open
Abstract
In Mycobacterium tuberculosis (Mtb) and Plasmodium falciparum (Pf), the methylerythritol phosphate (MEP) pathway is responsible for isoprene synthesis. This pathway and its products are vital to bacterial/parasitic metabolism and survival, and represent an attractive set of drug targets due to their essentiality in these pathogens but absence in humans. The second step in the MEP pathway is the conversion of 1-deoxy-d-xylulose-5-phosphate (DXP) to MEP and is catalyzed by 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR). Natural products fosmidomycin and FR900098 inhibit DXR, but are too polar to reach the desired target inside some cells, such as Mtb. Synthesized FR900098 analogs with lipophilic substitution in the position α to the phosphorous atom showed promise, resulting in increased activity against Mtb and Pf. Here, an α substitution, consisting of a 3,4-dichlorophenyl substituent, in combination with various O-linked alkylaryl substituents on the hydroxamate moiety is utilized in the synthesis of a novel series of FR900098 analogs. The purpose of the O-linked alkylaryl substituents is to further enhance DXR inhibition by extending the structure into the adjacent NADPH binding pocket, blocking the binding of both DXP and NADPH. Of the initial O-linked alkylaryl substituted analogs, compound 6e showed most potent activity against Pf parasites at 3.60 μM. Additional compounds varying the phenyl ring of 6e were synthesized. The most potent phosphonic acids, 6l and 6n, display nM activity against PfDXR and low μM activity against Pf parasites. Prodrugs of these compounds were less effective against Pf parasites but showed modest activity against Mtb cells. Data from this series of compounds suggests that this combination of substituents can be advantageous in designing a new generation of antimicrobials.
Collapse
Affiliation(s)
- Darean Bague
- Department of Chemistry, George Washington University Washington D.C. 20052 USA
| | - Ruiqin Wang
- Department of Chemistry, George Washington University Washington D.C. 20052 USA
| | - Dana Hodge
- Division of Infectious Diseases, Children's Hospital of Philadelphia Philadelphia PA 19104 USA
| | - Marwa O Mikati
- Department of Molecular Microbiology, Washington University School of Medicine St. Louis MO 63110 USA
| | - Jose S Roma
- Tuberculosis Research Section, LCIM, NIAID/NIH Bethesda MD 20892 USA
| | - Helena I Boshoff
- Tuberculosis Research Section, LCIM, NIAID/NIH Bethesda MD 20892 USA
| | - Allyson L Dailey
- Department of Chemistry and Biochemistry, George Mason University Fairfax VA 22030 USA
| | - Misgina Girma
- Department of Chemistry and Biochemistry, George Mason University Fairfax VA 22030 USA
| | - Robin D Couch
- Department of Chemistry and Biochemistry, George Mason University Fairfax VA 22030 USA
| | - Audrey R Odom John
- Division of Infectious Diseases, Children's Hospital of Philadelphia Philadelphia PA 19104 USA
- Department of Molecular Microbiology, Washington University School of Medicine St. Louis MO 63110 USA
| | - Cynthia S Dowd
- Department of Chemistry, George Washington University Washington D.C. 20052 USA
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Hogan AM, Rahman ASMZ, Motnenko A, Natarajan A, Maydaniuk DT, León B, Batun Z, Palacios A, Bosch A, Cardona ST. Profiling cell envelope-antibiotic interactions reveals vulnerabilities to β-lactams in a multidrug-resistant bacterium. Nat Commun 2023; 14:4815. [PMID: 37558695 PMCID: PMC10412643 DOI: 10.1038/s41467-023-40494-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023] Open
Abstract
The cell envelope of Gram-negative bacteria belonging to the Burkholderia cepacia complex (Bcc) presents unique restrictions to antibiotic penetration. As a consequence, Bcc species are notorious for causing recalcitrant multidrug-resistant infections in immunocompromised individuals. Here, we present the results of a genome-wide screen for cell envelope-associated resistance and susceptibility determinants in a Burkholderia cenocepacia clinical isolate. For this purpose, we construct a high-density, randomly-barcoded transposon mutant library and expose it to 19 cell envelope-targeting antibiotics. By quantifying relative mutant fitness with BarSeq, followed by validation with CRISPR-interference, we profile over a hundred functional associations and identify mediators of antibiotic susceptibility in the Bcc cell envelope. We reveal connections between β-lactam susceptibility, peptidoglycan synthesis, and blockages in undecaprenyl phosphate metabolism. The synergy of the β-lactam/β-lactamase inhibitor combination ceftazidime/avibactam is primarily mediated by inhibition of the PenB carbapenemase. In comparison with ceftazidime, avibactam more strongly potentiates the activity of aztreonam and meropenem in a panel of Bcc clinical isolates. Finally, we characterize in Bcc the iron and receptor-dependent activity of the siderophore-cephalosporin antibiotic, cefiderocol. Our work has implications for antibiotic target prioritization, and for using additional combinations of β-lactam/β-lactamase inhibitors that can extend the utility of current antibacterial therapies.
Collapse
Affiliation(s)
- Andrew M Hogan
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Anna Motnenko
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Aakash Natarajan
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Dustin T Maydaniuk
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Beltina León
- CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Zayra Batun
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Armando Palacios
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Alejandra Bosch
- CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Silvia T Cardona
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.
| |
Collapse
|
7
|
The Multifaceted MEP Pathway: Towards New Therapeutic Perspectives. Molecules 2023; 28:molecules28031403. [PMID: 36771066 PMCID: PMC9919496 DOI: 10.3390/molecules28031403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Isoprenoids, a diverse class of natural products, are present in all living organisms. Their two universal building blocks are synthesized via two independent pathways: the mevalonate pathway and the 2-C-methyl-ᴅ-erythritol 4-phosphate (MEP) pathway. The presence of the latter in pathogenic bacteria and its absence in humans make all its enzymes suitable targets for the development of novel antibacterial drugs. (E)-4-Hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP), the last intermediate of this pathway, is a natural ligand for the human Vγ9Vδ2 T cells and the most potent natural phosphoantigen known to date. Moreover, 5-hydroxypentane-2,3-dione, a metabolite produced by Escherichia coli 1-deoxy-ᴅ-xylulose 5-phosphate synthase (DXS), the first enzyme of the MEP pathway, structurally resembles (S)-4,5-dihydroxy-2,3-pentanedione, a signal molecule implied in bacterial cell communication. In this review, we shed light on the diversity of potential uses of the MEP pathway in antibacterial therapies, starting with an overview of the antibacterials developed for each of its enzymes. Then, we provide insight into HMBPP, its synthetic analogs, and their prodrugs. Finally, we discuss the potential contribution of the MEP pathway to quorum sensing mechanisms. The MEP pathway, providing simultaneously antibacterial drug targets and potent immunostimulants, coupled with its potential role in bacterial cell-cell communication, opens new therapeutic perspectives.
Collapse
|
8
|
Essential Paralogous Proteins as Potential Antibiotic Multitargets in Escherichia coli. Microbiol Spectr 2022; 10:e0204322. [PMID: 36445138 PMCID: PMC9769728 DOI: 10.1128/spectrum.02043-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Antimicrobial resistance threatens our current standards of care for the treatment and prevention of infectious disease. Antibiotics that have multiple targets have a lower propensity for the development of antibiotic resistance than those that have single targets and therefore represent an important tool in the fight against antimicrobial resistance. In this work, groups of essential paralogous proteins were identified in the important Gram-negative pathogen Escherichia coli that could represent novel targets for multitargeting antibiotics. These groups include targets from a broad range of essential macromolecular and biosynthetic pathways, including cell wall synthesis, membrane biogenesis, transcription, translation, DNA replication, fatty acid biosynthesis, and riboflavin and isoprenoid biosynthesis. Importantly, three groups of clinically validated antibiotic multitargets were identified using this method: the two subunits of the essential topoisomerases, DNA gyrase and topoisomerase IV, and one pair of penicillin-binding proteins. An additional eighteen protein groups represent potentially novel multitargets that could be explored in drug discovery efforts aimed at developing compounds having multiple targets in E. coli and other bacterial pathogens. IMPORTANCE Many types of bacteria have gained resistance to existing antibiotics used in medicine today. Therefore, new antibiotics with novel mechanisms must continue to be developed. One tool to prevent the development of antibiotic resistance is for a single drug to target multiple processes in a bacterium so that more than one change must arise for resistance to develop. The work described here provides a comprehensive search for proteins in the bacterium Escherichia coli that could be targets for such multitargeting antibiotics. Several groups of proteins that are already targets of clinically used antibiotics were identified, indicating that this approach can uncover clinically relevant antibiotic targets. In addition, eighteen currently unexploited groups of proteins were identified, representing new multitargets that could be explored in antibiotic research and development.
Collapse
|
9
|
Over 40 Years of Fosmidomycin Drug Research: A Comprehensive Review and Future Opportunities. Pharmaceuticals (Basel) 2022; 15:ph15121553. [PMID: 36559004 PMCID: PMC9782300 DOI: 10.3390/ph15121553] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
To address the continued rise of multi-drug-resistant microorganisms, the development of novel drugs with new modes of action is urgently required. While humans biosynthesize the essential isoprenoid precursors isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) via the established mevalonate pathway, pathogenic protozoa and certain pathogenic eubacteria use the less well-known methylerythritol phosphate pathway for this purpose. Important pathogens using the MEP pathway are, for example, Plasmodium falciparum, Mycobacterium tuberculosis, Pseudomonas aeruginosa and Escherichia coli. The enzymes of that pathway are targets for antiinfective drugs that are exempt from target-related toxicity. 2C-Methyl-D-erythritol 4-phosphate (MEP), the second enzyme of the non-mevalonate pathway, has been established as the molecular target of fosmidomycin, an antibiotic that has so far failed to be approved as an anti-infective drug. This review describes the development and anti-infective properties of a wide range of fosmidomycin derivatives synthesized over the last four decades. Here we discuss the DXR inhibitor pharmacophore, which comprises a metal-binding group, a phosphate or phosphonate moiety and a connecting linker. Furthermore, non-fosmidomycin-based DXRi, bisubstrate inhibitors and several prodrug concepts are described. A comprehensive structure-activity relationship (SAR) of nearly all inhibitor types is presented and some novel opportunities for further drug development of DXR inhibitors are discussed.
Collapse
|
10
|
Ju KS, Nair SK. Convergent and divergent biosynthetic strategies towards phosphonic acid natural products. Curr Opin Chem Biol 2022; 71:102214. [PMID: 36202046 PMCID: PMC9722595 DOI: 10.1016/j.cbpa.2022.102214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 01/27/2023]
Abstract
The phosphonate class of natural products have received significant interests in the post-genomic era due to the relative ease with which their biosynthetic genes may be identified and the resultant final products be characterized. Recent large-scale studies of the elucidation and distributions of phosphonate pathways have provided a robust landscape for deciphering the underlying biosynthetic logic. A recurrent theme in phosphonate biosynthetic pathways is the interweaving of enzymatic reactions across different routes, which enables diversification to elaborate chemically novel scaffolds. Here, we provide a few vignettes of how Nature has utilized both convergent and divergent biosynthetic strategies to compile pathways for production of novel phosphonates. These examples illustrate how common intermediates may either be generated or intercepted to diversify chemical scaffolds and provides a starting point for both biotechnological and synthetic biological applications towards new phosphonates by similar combinatorial approaches.
Collapse
Affiliation(s)
- Kou-San Ju
- Department of Microbiology, The Ohio State University, Columbus OH 43210,Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus OH 43210,Infectious Diseases Institute. The Ohio State University, Columbus OH 43210,Corresponding authors: Kou-San Ju () and Satish K. Nair ()
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois, Urbana, IL 61801,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL 61801,Carl Woese Institute for Genomic Biology. University of Illinois, Urbana, IL 61801,Corresponding authors: Kou-San Ju () and Satish K. Nair ()
| |
Collapse
|
11
|
Characterization of Domiphen Bromide as a New Fast-Acting Antiplasmodial Agent Inhibiting the Apicoplastidic Methyl Erythritol Phosphate Pathway. Pharmaceutics 2022; 14:pharmaceutics14071320. [PMID: 35890216 PMCID: PMC9319574 DOI: 10.3390/pharmaceutics14071320] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/17/2022] Open
Abstract
The evolution of resistance by the malaria parasite to artemisinin, the key component of the combination therapy strategies that are at the core of current antimalarial treatments, calls for the urgent identification of new fast-acting antimalarials. The apicoplast organelle is a preferred target of antimalarial drugs because it contains biochemical processes absent from the human host. Fosmidomycin is the only drug in clinical trials targeting the apicoplast, where it inhibits the methyl erythritol phosphate (MEP) pathway. Here, we characterized the antiplasmodial activity of domiphen bromide (DB), another MEP pathway inhibitor with a rapid mode of action that arrests the in vitro growth of Plasmodium falciparum at the early trophozoite stage. Metabolomic analysis of the MEP pathway and Krebs cycle intermediates in 20 µM DB-treated parasites suggested a rapid activation of glycolysis with a concomitant decrease in mitochondrial activity, consistent with a rapid killing of the pathogen. These results present DB as a model compound for the development of new, potentially interesting drugs for future antimalarial combination therapies.
Collapse
|
12
|
Duke SO, Dayan FE. The search for new herbicide mechanisms of action: Is there a 'holy grail'? PEST MANAGEMENT SCIENCE 2022; 78:1303-1313. [PMID: 34796620 DOI: 10.1002/ps.6726] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/18/2021] [Indexed: 05/26/2023]
Abstract
New herbicide modes of action (MOAs) are in great demand because of the burgeoning evolution of resistance of weeds to existing commercial herbicides. This need has been exacerbated by the almost complete lack of introduction of herbicides with new MOAs for almost 40 years. There are many highly phytotoxic compounds with MOAs not represented by commercial herbicides, but neither these compounds nor structural analogues have been developed as herbicides for a variety of reasons. Natural products provide knowledge of many MOAs that are not being utilized by commercial herbicides. Other means of identifying new herbicide targets are discussed, including pharmaceutical target sites and metabolomic and proteomic information, as well as the use of artificial intelligence and machine learning to predict herbicidal compounds with new MOAs. Information about several newly discovered herbicidal compounds with new MOAs is summarized. The currently increased efforts of both established companies and start-up companies are likely to result in herbicides with new MOAs that can be used in herbicide resistance management within the next decade. © 2021 Society of Chemical Industry.
Collapse
Affiliation(s)
- Stephen O Duke
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Oxford, MS, USA
| | - Franck E Dayan
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| |
Collapse
|
13
|
Endo T, Takemae H, Sharma I, Furuya T. Multipurpose Drugs Active Against Both Plasmodium spp. and Microorganisms: Potential Application for New Drug Development. Front Cell Infect Microbiol 2021; 11:797509. [PMID: 35004357 PMCID: PMC8740689 DOI: 10.3389/fcimb.2021.797509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/01/2021] [Indexed: 12/29/2022] Open
Abstract
Malaria, a disease caused by the protozoan parasites Plasmodium spp., is still causing serious problems in endemic regions in the world. Although the WHO recommends artemisinin combination therapies for the treatment of malaria patients, the emergence of artemisinin-resistant parasites has become a serious issue and underscores the need for the development of new antimalarial drugs. On the other hand, new and re-emergences of infectious diseases, such as the influenza pandemic, Ebola virus disease, and COVID-19, are urging the world to develop effective chemotherapeutic agents against the causative viruses, which are not achieved to the desired level yet. In this review article, we describe existing drugs which are active against both Plasmodium spp. and microorganisms including viruses, bacteria, and fungi. We also focus on the current knowledge about the mechanism of actions of these drugs. Our major aims of this article are to describe examples of drugs that kill both Plasmodium parasites and other microbes and to provide valuable information to help find new ideas for developing novel drugs, rather than merely augmenting already existing drug repurposing efforts.
Collapse
Affiliation(s)
- Takuro Endo
- Laboratory of Veterinary Infectious Diseases, Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hitoshi Takemae
- Center for Infectious Disease Epidemiology and Prevention Research, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Indu Sharma
- Department of Biological Sciences, Hampton University, Hampton, VA, United States
| | - Tetsuya Furuya
- Laboratory of Veterinary Infectious Diseases, Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| |
Collapse
|
14
|
Bauman KD, Butler KS, Moore BS, Chekan JR. Genome mining methods to discover bioactive natural products. Nat Prod Rep 2021; 38:2100-2129. [PMID: 34734626 PMCID: PMC8597713 DOI: 10.1039/d1np00032b] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Indexed: 12/22/2022]
Abstract
Covering: 2016 to 2021With genetic information available for hundreds of thousands of organisms in publicly accessible databases, scientists have an unprecedented opportunity to meticulously survey the diversity and inner workings of life. The natural product research community has harnessed this breadth of sequence information to mine microbes, plants, and animals for biosynthetic enzymes capable of producing bioactive compounds. Several orthogonal genome mining strategies have been developed in recent years to target specific chemical features or biological properties of bioactive molecules using biosynthetic, resistance, or transporter proteins. These "biosynthetic hooks" allow researchers to query for biosynthetic gene clusters with a high probability of encoding previously undiscovered, bioactive compounds. This review highlights recent case studies that feature orthogonal approaches that exploit genomic information to specifically discover bioactive natural products and their gene clusters.
Collapse
Affiliation(s)
- Katherine D Bauman
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Keelie S Butler
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, 27402, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, 27402, USA.
| |
Collapse
|
15
|
Ball HS, Girma MB, Zainab M, Soojhawon I, Couch RD, Noble SM. Characterization and Inhibition of 1-Deoxy-d-Xylulose 5-Phosphate Reductoisomerase: A Promising Drug Target in Acinetobacter baumannii and Klebsiella pneumoniae. ACS Infect Dis 2021; 7:2987-2998. [PMID: 34672535 PMCID: PMC8594541 DOI: 10.1021/acsinfecdis.1c00132] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The ESKAPE pathogens
comprise a group of multidrug-resistant bacteria
that are the leading cause of nosocomial infections worldwide. The
prevalence of antibiotic resistant strains and the relative ease by
which bacteria acquire resistance genes highlight the continual need
for the development of novel antibiotics against new drug targets.
The methylerythritol phosphate (MEP) pathway is an attractive target
for the development of new antibiotics. The MEP pathway governs the
synthesis of isoprenoids, which are key lipid precursors for vital
cell components such as ubiquinone and bacterial hopanoids. Additionally,
the MEP pathway is entirely distinct from the corresponding mammalian
pathway, the mevalonic acid (MVA) pathway, making the first committed
enzyme of the MEP pathway, 1-deoxy-d-xylulose 5-phosphate
reductoisomerase (IspC), an attractive target for antibiotic development.
To facilitate drug development against two of the ESKAPE pathogens, Acinetobacter baumannii and Klebsiella
pneumoniae, we cloned, expressed, purified, and characterized
IspC from these two Gram-negative bacteria. Enzyme inhibition assays
using IspC from these two pathogens, and compounds fosmidomycin and
FR900098, indicate IC50 values ranging from 19.5–45.5
nM. Antimicrobial susceptibility tests with these inhibitors reveal
that A. baumannii is susceptible to
FR900098, whereas K. pneumoniae is
susceptible to both compounds. Finally, to facilitate structure-based
drug design of inhibitors targeting A. baumannii IspC, we determined the 2.5 Å crystal structure of IspC from A. baumannii in complex with inhibitor FR900098,
and cofactors NADPH and magnesium.
Collapse
Affiliation(s)
- Haley S. Ball
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20109, United States of America
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Springs, Maryland 20910, United States of America
| | - Misgina B. Girma
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20109, United States of America
| | - Mosufa Zainab
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20109, United States of America
| | - Iswarduth Soojhawon
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Springs, Maryland 20910, United States of America
| | - Robin D. Couch
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20109, United States of America
| | - Schroeder M. Noble
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Springs, Maryland 20910, United States of America
| |
Collapse
|
16
|
Chen X, Chen B, Shang X, Fang S. RNA in situ hybridization and expression of related genes regulating the accumulation of triterpenoids in Cyclocarya paliurus. TREE PHYSIOLOGY 2021; 41:2189-2197. [PMID: 33960380 DOI: 10.1093/treephys/tpab067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Cyclocarya paliurus (Batal.) Iljinskaja, a woody medicinal species in the Juglandaceae, grows extensively in subtropical areas of China. Triterpenoids in the leaves have health-promoting effects, including hypoglycemic and hypolipidemic activities. To understand triterpenoid biosynthesis, transport and accumulation in C. paliurus during the growing season, gene cloning, gene expression and RNA in situ hybridization of related genes were used, and accumulation was examined in various organs. The complete coding sequences (CDSs) of three genes, CpHMGR, CpDXR and CpSQS, were obtained from GenBank and RACE. RNA in situ hybridization signals of the three genes mainly occurred in the epidermis, palisade tissue, phloem and xylem of leaf, shoot and root, with the signals generally consistent with the accumulation of metabolites in tissues, except in the xylem. Both gene expression and triterpenoid accumulations showed seasonal variations in all organs. However, total triterpenoid content in the leaves was significantly higher than that in the shoots, with the maximum in shoots in August and in leaves in October. According to Pearson correlation analysis, triterpenoid accumulation in the leaves was significantly positively related with the relative expression of CpSQS. However, the relation between gene expression and accumulation was dependent on the role of the gene in the pathway as well as on the plant organ. The results suggested that most of the intermediates catalyzed by CpHMGR and CpDXR in young shoots and roots were used in growth and flowering in the spring, whereas subsequent triterpenoid biosynthesis in the downstream catalyzed by CpSQS mainly occurred in the leaves by using transferred and in situ intermediates as substrates. Thus, this study provides a reference to improve triterpenoid accumulation in future C. paliurus plantations.
Collapse
Affiliation(s)
- Xiaoling Chen
- College of Forestry, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
| | - Biqin Chen
- College of Forestry, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
| | - Xulan Shang
- College of Forestry, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
| | - Shengzuo Fang
- College of Forestry, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
| |
Collapse
|
17
|
Structural and biophysical characterization of the Burkholderia pseudomallei IspF inhibitor L-tryptophan hydroxamate. Bioorg Med Chem Lett 2021; 48:128273. [PMID: 34298132 DOI: 10.1016/j.bmcl.2021.128273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/15/2021] [Accepted: 07/15/2021] [Indexed: 11/23/2022]
Abstract
The enzyme 2-methylerythritol 2,4-cyclodiphosphate synthase, IspF, is essential for the biosynthesis of isoprenoids in most bacteria, some eukaryotic parasites, and the plastids of plant cells. The development of inhibitors that target IspF may lead to novel classes of anti-infective agents or herbicides. Enantiomers of tryptophan hydroxamate were synthesized and evaluated for binding to Burkholderia pseudomallei (Bp) IspF. The L-isomer possessed the highest potency, binding BpIspF with a KD of 36 µM and inhibited BpIspF activity 55% at 120 µM. The high-resolution crystal structure of the L-tryptophan hydroxamate (3)/BpIspF complex revealed a non-traditional mode of hydroxamate binding where the ligand interacts with the active site zinc ion through the primary amine. In addition, two hydrogen bonds are formed with active site groups, and the indole group is buried within the hydrophobic pocket composed of side chains from the 60 s/70 s loop. Along with the co-crystal structure, STD NMR studies suggest the methylene group and indole ring are potential positions for optimization to enhance binding potency.
Collapse
|
18
|
Pessanha de Carvalho L, Kreidenweiss A, Held J. Drug Repurposing: A Review of Old and New Antibiotics for the Treatment of Malaria: Identifying Antibiotics with a Fast Onset of Antiplasmodial Action. Molecules 2021; 26:2304. [PMID: 33921170 PMCID: PMC8071546 DOI: 10.3390/molecules26082304] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/24/2022] Open
Abstract
Malaria is one of the most life-threatening infectious diseases and constitutes a major health problem, especially in Africa. Although artemisinin combination therapies remain efficacious to treat malaria, the emergence of resistant parasites emphasizes the urgent need of new alternative chemotherapies. One strategy is the repurposing of existing drugs. Herein, we reviewed the antimalarial effects of marketed antibiotics, and described in detail the fast-acting antibiotics that showed activity in nanomolar concentrations. Antibiotics have been used for prophylaxis and treatment of malaria for many years and are of particular interest because they might exert a different mode of action than current antimalarials, and can be used simultaneously to treat concomitant bacterial infections.
Collapse
Affiliation(s)
- Lais Pessanha de Carvalho
- Institute of Tropical Medicine, University of Tuebingen, 72074 Tuebingen, Germany; (L.P.d.C.); (A.K.)
| | - Andrea Kreidenweiss
- Institute of Tropical Medicine, University of Tuebingen, 72074 Tuebingen, Germany; (L.P.d.C.); (A.K.)
- Centre de Recherches Medicales de Lambaréné (CERMEL), Lambaréné BP 242, Gabon
| | - Jana Held
- Institute of Tropical Medicine, University of Tuebingen, 72074 Tuebingen, Germany; (L.P.d.C.); (A.K.)
- Centre de Recherches Medicales de Lambaréné (CERMEL), Lambaréné BP 242, Gabon
| |
Collapse
|
19
|
Bergman ME, González-Cabanelas D, Wright LP, Walker BJ, Phillips MA. Isotope ratio-based quantification of carbon assimilation highlights the role of plastidial isoprenoid precursor availability in photosynthesis. PLANT METHODS 2021; 17:32. [PMID: 33781281 PMCID: PMC8008545 DOI: 10.1186/s13007-021-00731-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/13/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND We report a method to estimate carbon assimilation based on isotope ratio-mass spectrometry (IRMS) of 13CO2 labeled plant tissue. Photosynthetic carbon assimilation is the principal experimental observable which integrates important aspects of primary plant metabolism. It is traditionally measured through gas exchange. Despite its centrality in plant research, gas exchange performs poorly with rosette growth habits typical of Arabidopsis thaliana, mutant lines with limited biomass, and accounts poorly for leaf shading. RESULTS IRMS-based carbon assimilation values from plants labeled at different light intensities were compared to those obtained by gas exchange, and the two methods yielded similar values. Using this method, we observed a strong correlation between 13C content and labeling time (R2 = 0.999) for 158 wild-type plants labeled for 6 to 42 min. Plants cultivated under different light regimes showed a linear response with respect to carbon assimilation, varying from 7.38 nmol 13C mg-1 leaf tissue min-1 at 80 PAR to 19.27 nmol 13C mg-1 leaf tissue min-1 at 500 PAR. We applied this method to examine the link between inhibition of the 2C-methyl-D-erythritol-4-phosphate (MEP) pathway and suppression of photosynthesis. A significant decrease in carbon assimilation was observed when metabolic activity in the MEP pathway was compromised by mutation or herbicides targeting the MEP pathway. Mutants affected in MEP pathway genes 1-DEOXY-D-XYLULOSE 5-PHOSPHATE SYNTHASE (DXS) or 1-HYDROXY-2-METHYL-2-(E)-BUTENYL 4-DIPHOSPHATE SYNTHASE (HDS) showed assimilation rates 36% and 61% lower than wild type. Similarly, wild type plants treated with the MEP pathway inhibitors clomazone or fosmidomycin showed reductions of 52% and 43%, respectively, while inhibition of the analogous mevalonic acid pathway, which supplies the same isoprenoid intermediates in the cytosol, did not, suggesting inhibition of photosynthesis was specific to disruption of the MEP pathway. CONCLUSIONS This method provides an alternative to gas exchange that offers several advantages: resilience to differences in leaf overlap, measurements based on tissue mass rather than leaf surface area, and compatibility with mutant Arabidopsis lines which are not amenable to gas exchange measurements due to low biomass and limited leaf surface area. It is suitable for screening large numbers of replicates simultaneously as well as post-hoc analysis of previously labeled plant tissue and is complementary to downstream detection of isotopic label in targeted metabolite pools.
Collapse
Affiliation(s)
- Matthew E Bergman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | | | - Louwrance P Wright
- Zeiselhof Research Farm, Menlo Park, P.O. Box 35984, Pretoria, 0102, South Africa
| | - Berkley J Walker
- Department of Energy, Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Michael A Phillips
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada.
- Department of Biology, University of Toronto-Mississauga, Mississauga, ON, L5L 1C6, Canada.
| |
Collapse
|
20
|
Stable isotope and chemical inhibition analyses suggested the existence of a non-mevalonate-like pathway in the yeast Yarrowia lipolytica. Sci Rep 2021; 11:5598. [PMID: 33692450 PMCID: PMC7970925 DOI: 10.1038/s41598-021-85170-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/11/2021] [Indexed: 01/31/2023] Open
Abstract
Methyl erythritol phosphate (MEP) is the metabolite found in the MEP pathway for isoprenoid biosynthesis, which is known to be utilized by plants, algae, and bacteria. In this study, an unprecedented observation was found in the oleaginous yeast Yarrowia lipolytica, in which one of the chromatographic peaks was annotated as MEP when cultivated in the nitrogen limiting condition. This finding raised an interesting hypothesis of whether Y. lipolytica utilizes the MEP pathway for isoprenoid biosynthesis or not, because there is no report of yeast harboring the MEP pathway. Three independent approaches were used to investigate the existence of the MEP pathway in Y. lipolytica; the spiking of the authentic standard, the MEP pathway inhibitor, and the 13C labeling incorporation analysis. The study suggested that the mevalonate and MEP pathways co-exist in Y. lipolytica and the nitrogen limiting condition triggers the utilization of the MEP pathway in Y. lipolytica.
Collapse
|
21
|
Mitra S, Estrada-Tejedor R, Volke DC, Phillips MA, Gershenzon J, Wright LP. Negative regulation of plastidial isoprenoid pathway by herbivore-induced β-cyclocitral in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2021; 118:e2008747118. [PMID: 33674379 PMCID: PMC7958287 DOI: 10.1073/pnas.2008747118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Insect damage to plants is known to up-regulate defense and down-regulate growth processes. While there are frequent reports about up-regulation of defense signaling and production of defense metabolites in response to herbivory, much less is understood about the mechanisms by which growth and carbon assimilation are down-regulated. Here we demonstrate that insect herbivory down-regulates the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway in Arabidopsis (Arabidopsis thaliana), a pathway making primarily metabolites for use in photosynthesis. Simulated feeding by the generalist herbivore Spodoptera littoralis suppressed flux through the MEP pathway and decreased steady-state levels of the intermediate 1-deoxy-D-xylulose 5-phosphate (DXP). Simulated herbivory also increased reactive oxygen species content which caused the conversion of β-carotene to β-cyclocitral (βCC). This volatile oxidation product affected the MEP pathway by directly inhibiting DXP synthase (DXS), the rate-controlling enzyme of the MEP pathway in Arabidopsis and inducing plant resistance against S. littoralis βCC inhibited both DXS transcript accumulation and DXS activity. Molecular models suggested that βCC binds to DXS at the binding site for the thymine pyrophosphate cofactor and blocks catalysis, which was confirmed by direct assays of βCC with the purified DXS protein in vitro. Another intermediate of the MEP pathway, 2-C-methyl-D-erythritol-2, 4-cyclodiphosphate, which is known to stimulate salicylate defense signaling, showed greater accumulation and enhanced export out of the plastid in response to simulated herbivory. Together, our work implicates βCC as a signal of herbivore damage in Arabidopsis that increases defense and decreases flux through the MEP pathway, a pathway involved in growth and carbon assimilation.
Collapse
Affiliation(s)
- Sirsha Mitra
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany;
- Department of Botany, Savitribai Phule Pune University, Pune-411007, India
| | - Roger Estrada-Tejedor
- Pharmaceutical Chemistry Group, IQS School of Engineering, Universitat Ramon Llull, 08017 Barcelona, Spain
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Michael A Phillips
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Louwrance P Wright
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany;
| |
Collapse
|
22
|
Piselli C, Benz R. Fosmidomycin transport through the phosphate-specific porins OprO and OprP of Pseudomonas aeruginosa. Mol Microbiol 2021; 116:97-108. [PMID: 33561903 DOI: 10.1111/mmi.14693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/29/2021] [Accepted: 02/03/2021] [Indexed: 01/08/2023]
Abstract
The Gram-negative bacterium Pseudomonas aeruginosa is an opportunistic pathogen, responsible for many hospital-acquired infections. The bacterium is quite resistant toward many antibiotics, in particular because of the fine-tuned permeability of its outer membrane (OM). General diffusion outer membrane pores are quite rare in this organism. Instead, its OM contains many substrate-specific porins. Their expression is varying according to growth conditions and virulence. Phosphate limitations, as well as pathogenicity factors, result in the induction of the two mono- and polyphosphate-specific porins, OprP and OprO, respectively, together with an inner membrane uptake mechanism and a periplasmic binding protein. These outer membrane channels could serve as outer membrane pathways for the uptake of phosphonates. Among them are not only herbicides, but also potent antibiotics, such as fosfomycin and fosmidomycin. In this study, we investigated the interaction between OprP and OprO and fosmidomycin in detail. We could demonstrate that fosmidomycin is able to bind to the phosphate-specific binding site inside the two porins. The inhibition of chloride conductance of OprP and OprO by fosmidomycin is considerably less than that of phosphate or diphosphate, but it can be measured in titration experiments of chloride conductance and also in single-channel experiments. The results suggest that fosmidomycin transport across the OM of P. aeruginosa occurs through OprP and OprO. Our data with the ones already known in the literature show that phosphonic acid-containing antibiotics are in general good candidates to treat the infections of P. aeruginosa at the very beginning through a favorable OM transport system.
Collapse
Affiliation(s)
- Claudio Piselli
- Department of Life Sciences and Chemistry, Focus Health, Jacobs University Bremen, Bremen, Germany
| | - Roland Benz
- Rudolf-Virchow-Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| |
Collapse
|
23
|
Shiomi K. Antiparasitic antibiotics from Japan. Parasitol Int 2021; 82:102298. [PMID: 33548522 DOI: 10.1016/j.parint.2021.102298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/19/2020] [Accepted: 01/27/2021] [Indexed: 11/29/2022]
Abstract
Antibiotics are microbial secondary metabolites and they are important for the treatment of infectious diseases. Japanese researchers have made a large contribution to studies of antibiotics, and they have also been important in the discovery of antiparasitic antibiotics. Satoshi Ōmura received the Nobel Prize in 2015 for the "discoveries concerning a novel therapy against infections caused by roundworm parasites", which means discovery of a new nematocidal antibiotic, avermectin. Here, I review the many antiparasitic antibiotics and their lead compounds that have been discovered for use in human and veterinary medicine.
Collapse
Affiliation(s)
- Kazuro Shiomi
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan.
| |
Collapse
|
24
|
A Phosphonate Natural Product Made by Pantoea ananatis is Necessary and Sufficient for the Hallmark Lesions of Onion Center Rot. mBio 2021; 12:mBio.03402-20. [PMID: 33531390 PMCID: PMC7858074 DOI: 10.1128/mbio.03402-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Pantoea ananatis is the primary cause of onion center rot. Genetic data suggest that a phosphonic acid natural product is required for pathogenesis; however, the nature of the molecule is unknown. Here, we show that P. ananatis produces at least three phosphonates, two of which were purified and structurally characterized. The first, designated pantaphos, was shown to be 2-(hydroxy[phosphono]methyl)maleate; the second, a probable biosynthetic precursor, was shown to be 2-(phosphonomethyl)maleate. Purified pantaphos is both necessary and sufficient for the hallmark lesions of onion center rot. Moreover, when tested against mustard seedlings, the phytotoxic activity of pantaphos was comparable to the widely used herbicides glyphosate and phosphinothricin. Pantaphos was also active against a variety of human cell lines but was significantly more toxic to glioblastoma cells. Pantaphos showed little activity when tested against a variety of bacteria and fungi.IMPORTANCE Pantoea ananatis is a significant plant pathogen that targets a number of important crops, a problem that is compounded by the absence of effective treatments to prevent its spread. Our identification of pantaphos as the key virulence factor in onion center rot suggests a variety of approaches that could be employed to address this significant plant disease. Moreover, the general phytotoxicity of the molecule suggests that it could be developed into an effective herbicide to counter the alarming rise in herbicide-resistant weeds.
Collapse
|
25
|
Shiraishi T, Kuzuyama T. Biosynthetic pathways and enzymes involved in the production of phosphonic acid natural products. Biosci Biotechnol Biochem 2021; 85:42-52. [PMID: 33577658 DOI: 10.1093/bbb/zbaa052] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/04/2020] [Indexed: 02/07/2023]
Abstract
Phosphonates are organophosphorus compounds possessing a characteristic C-P bond in which phosphorus is directly bonded to carbon. As phosphonates mimic the phosphates and carboxylates of biological molecules to potentially inhibit metabolic enzymes, they could be lead compounds for the development of a variety of drugs. Fosfomycin (FM) is a representative phosphonate natural product that is widely used as an antibacterial drug. Here, we review the biosynthesis of FM, which includes a recent breakthrough to find a missing link in the biosynthetic pathway that had been a mystery for a quarter-century. In addition, we describe the genome mining of phosphonate natural products using the biosynthetic gene encoding an enzyme that catalyzes C-P bond formation. We also introduce the chemoenzymatic synthesis of phosphonate derivatives. These studies expand the repertoires of phosphonates and the related biosynthetic machinery. This review mainly covers the years 2012-2020.
Collapse
Affiliation(s)
- Taro Shiraishi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| |
Collapse
|
26
|
Sato S. Plasmodium-a brief introduction to the parasites causing human malaria and their basic biology. J Physiol Anthropol 2021; 40:1. [PMID: 33413683 PMCID: PMC7792015 DOI: 10.1186/s40101-020-00251-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023] Open
Abstract
Malaria is one of the most devastating infectious diseases of humans. It is problematic clinically and economically as it prevails in poorer countries and regions, strongly hindering socioeconomic development. The causative agents of malaria are unicellular protozoan parasites belonging to the genus Plasmodium. These parasites infect not only humans but also other vertebrates, from reptiles and birds to mammals. To date, over 200 species of Plasmodium have been formally described, and each species infects a certain range of hosts. Plasmodium species that naturally infect humans and cause malaria in large areas of the world are limited to five-P. falciparum, P. vivax, P. malariae, P. ovale and P. knowlesi. The first four are specific for humans, while P. knowlesi is naturally maintained in macaque monkeys and causes zoonotic malaria widely in South East Asia. Transmission of Plasmodium species between vertebrate hosts depends on an insect vector, which is usually the mosquito. The vector is not just a carrier but the definitive host, where sexual reproduction of Plasmodium species occurs, and the parasite's development in the insect is essential for transmission to the next vertebrate host. The range of insect species that can support the critical development of Plasmodium depends on the individual parasite species, but all five Plasmodium species causing malaria in humans are transmitted exclusively by anopheline mosquitoes. Plasmodium species have remarkable genetic flexibility which lets them adapt to alterations in the environment, giving them the potential to quickly develop resistance to therapeutics such as antimalarials and to change host specificity. In this article, selected topics involving the Plasmodium species that cause malaria in humans are reviewed.
Collapse
Affiliation(s)
- Shigeharu Sato
- Borneo Medical and Health Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia.
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.
| |
Collapse
|
27
|
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.
Collapse
|
28
|
Pines G, Fankhauser RG, Eckert CA. Predicting Drug Resistance Using Deep Mutational Scanning. Molecules 2020; 25:E2265. [PMID: 32403408 PMCID: PMC7248951 DOI: 10.3390/molecules25092265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/05/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
Drug resistance is a major healthcare challenge, resulting in a continuous need to develop new inhibitors. The development of these inhibitors requires an understanding of the mechanisms of resistance for a critical mass of occurrences. Recent genome editing technologies based on high-throughput DNA synthesis and sequencing may help to predict mutations resulting in resistance by testing large mutagenesis libraries. Here we describe the rationale of this approach, with examples and relevance to drug development and resistance in malaria.
Collapse
Affiliation(s)
- Gur Pines
- Department of Entomology, Agricultural Research Organization, Volcani Center, P.O.B 15159, Rishon LeZion 7505101, Israel
| | - Reilly G. Fankhauser
- Department of Dermatology, Oregon Health & Science University, Baird Hall 3225 SW Pavilion Loop, Portland, OR 97239, USA;
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, 027 UCB, Boulder, CO 80309, USA
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| |
Collapse
|
29
|
Shi L, Wu Z, Zhang Y, Zhang Z, Fang W, Wang Y, Wan Z, Wang K, Ke S. Herbicidal Secondary Metabolites from Actinomycetes: Structure Diversity, Modes of Action, and Their Roles in the Development of Herbicides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:17-32. [PMID: 31809036 DOI: 10.1021/acs.jafc.9b06126] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Weeds had caused significant loss for crop production in the process of agriculture. Herbicides have played an important role in securing crop production. However, the high reliance on herbicides has led to environmental issues as well as the evolution of herbicide resistance. Thus, there is an urgent need for new herbicides with safer toxicological profiles and novel modes of action. Actinomycetes produce very diverse bioactive compounds, of which some show potent biopesticidal activity. The herbicidal secondary metabolites from actinomycetes can be classified into several groups, such as amino acids, peptides, nucleosides, macrolides, lactones, amide, amines, etc., some of which have been successfully developed as commercial herbicides. The structure diversity and evolved biological activity of secondary metabolites from actinomycetes can offer opportunities for the development of both directly used bioherbicides and synthetic herbicides with new target sites, and thus, this review focuses on the structure, herbicidal activity, and modes of action of secondary metabolites from actinomycetes.
Collapse
Affiliation(s)
- Liqiao Shi
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Zhaoyuan Wu
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Yani Zhang
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Zhigang Zhang
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Wei Fang
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Yueying Wang
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Zhongyi Wan
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Kaimei Wang
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Shaoyong Ke
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| |
Collapse
|
30
|
A computational study of the molecular basis of antibiotic resistance in a DXR mutant. J Comput Aided Mol Des 2019; 33:927-940. [DOI: 10.1007/s10822-019-00229-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/28/2019] [Indexed: 10/25/2022]
|
31
|
Parkinson EI, Erb A, Eliot AC, Ju KS, Metcalf WW. Fosmidomycin biosynthesis diverges from related phosphonate natural products. Nat Chem Biol 2019; 15:1049-1056. [PMID: 31451762 PMCID: PMC7098449 DOI: 10.1038/s41589-019-0343-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/09/2019] [Indexed: 12/04/2022]
Abstract
Fosmidomycin and related molecules comprise a family of phosphonate natural products with potent antibacterial, antimalarial and herbicidal activities. To understand the biosynthesis of these compounds, we characterized the fosmidomycin producer, Streptomyces lavendulae, using biochemical and genetic approaches. Surprisingly, we were unable to elicit production of fosmidomycin, instead observing the unsaturated derivative dehydrofosmidomycin, which we showed potently inhibits 1-deoxy-D-xylulose 5-phosphate reductoisomerase and has bioactivity against a number of bacteria. The genes required for dehydrofosmidomycin biosynthesis were established by heterologous expression experiments. Bioinformatics analyses, characterization of intermediates, and in vitro biochemistry show that the biosynthetic pathway involves conversion of a two-carbon phosphonate precursor into the unsaturated three-carbon product via a highly unusual rearrangement reaction, catalyzed by the 2-oxoglutarate dependent dioxygenase DfmD. The required genes and biosynthetic pathway for dehydrofosmidomycin differ substantially from that of the related natural product FR-900098, suggesting that the ability to produce these bioactive molecules arose via convergent evolution.
Collapse
Affiliation(s)
- Elizabeth I Parkinson
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Annette Erb
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andrew C Eliot
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kou-San Ju
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Microbiology and the Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, OH, USA
| | - William W Metcalf
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
32
|
Munier M, Tritsch D, Lièvremont D, Rohmer M, Grosdemange-Billiard C. Synthesis and biological evaluation of aryl phosphoramidate prodrugs of fosfoxacin and its derivatives. Bioorg Chem 2019; 89:103012. [PMID: 31174039 DOI: 10.1016/j.bioorg.2019.103012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 12/26/2022]
Abstract
Aryl phosphoramidate prodrugs of fosfoxacin derivatives 15a-b and 8a-b were synthesized and investigated for their ability to target bacteria. No growth inhibition was observed neither for Mycobacterium smegmatis nor for Escherichia coli on solid medium, demonstrating the absence of release of the active compounds in the bacterial cells. Investigation of the stability of the prodrugs and their multienzymatic cleavage in abiotic and biotic conditions showed that the use of aryl phosphoramidate prodrug approach to deliver non-nucleotides compounds is not obvious and might not be appropriate for an antimicrobial drug.
Collapse
Affiliation(s)
- Mathilde Munier
- Laboratoire Chimie et Biochimie de Molécules Bioactives - Université de Strasbourg/CNRS, UMR 7177, Institut Le Bel, 4 rue Blaise Pascal, 67081 Strasbourg, France
| | - Denis Tritsch
- Laboratoire Chimie et Biochimie de Molécules Bioactives - Université de Strasbourg/CNRS, UMR 7177, Institut Le Bel, 4 rue Blaise Pascal, 67081 Strasbourg, France
| | - Didier Lièvremont
- Laboratoire Chimie et Biochimie de Molécules Bioactives - Université de Strasbourg/CNRS, UMR 7177, Institut Le Bel, 4 rue Blaise Pascal, 67081 Strasbourg, France
| | - Michel Rohmer
- Laboratoire Chimie et Biochimie de Molécules Bioactives - Université de Strasbourg/CNRS, UMR 7177, Institut Le Bel, 4 rue Blaise Pascal, 67081 Strasbourg, France
| | - Catherine Grosdemange-Billiard
- Laboratoire Chimie et Biochimie de Molécules Bioactives - Université de Strasbourg/CNRS, UMR 7177, Institut Le Bel, 4 rue Blaise Pascal, 67081 Strasbourg, France.
| |
Collapse
|
33
|
Phosphonodiamidate prodrugs of N-alkoxy analogs of a fosmidomycin surrogate as antimalarial and antitubercular agents. Bioorg Med Chem Lett 2019; 29:1051-1053. [PMID: 30857749 DOI: 10.1016/j.bmcl.2019.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 11/23/2022]
Abstract
A series of N-alkoxy analogs of a l-leucine ethyl ester phosphonodiamidate prodrug of a fosmidomycin surrogate were synthesized and investigated for their ability to inhibit in vitro growth of P. falciparum and M. tuberculosis. These compounds originate by merging a previously reported successful phosphonate derivatisation with favorable modifications of the hydroxamate moiety. None of the synthesized compounds showed enhanced activity against either P. falciparum or M. tuberculosis in comparison with the parent free hydroxamate analog.
Collapse
|
34
|
Honold A, Lettl C, Schindele F, Illarionov B, Haas R, Witschel M, Bacher A, Fischer M. Inhibitors of the Bifunctional 2‐ C‐Methyl‐ d‐erythritol 4‐Phosphate Cytidylyl Transferase/2‐ C‐Methyl‐ d‐erythritol‐2,4‐cyclopyrophosphate Synthase (IspDF) of Helicobacter pylori. Helv Chim Acta 2019. [DOI: 10.1002/hlca.201800228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Annika Honold
- Hamburg School of Food Science – Institute of Food ChemistryUniversity of Hamburg Grindelallee 117 DE-20146 Hamburg Germany
| | - Clara Lettl
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of MedicineLMU Munich Germany
| | - Franziska Schindele
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of MedicineLMU Munich Germany
| | - Boris Illarionov
- Hamburg School of Food Science – Institute of Food ChemistryUniversity of Hamburg Grindelallee 117 DE-20146 Hamburg Germany
| | - Rainer Haas
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of MedicineLMU Munich Germany
- German Center for Infection Research (DZIF)Munich Site DE-80336 Munich Germany
| | | | - Adelbert Bacher
- Department of ChemistryTechnical University of Munich DE-85747 Garching Germany
| | - Markus Fischer
- Hamburg School of Food Science – Institute of Food ChemistryUniversity of Hamburg Grindelallee 117 DE-20146 Hamburg Germany
| |
Collapse
|
35
|
Amino acid based prodrugs of a fosmidomycin surrogate as antimalarial and antitubercular agents. Bioorg Med Chem 2019; 27:729-747. [DOI: 10.1016/j.bmc.2019.01.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/03/2019] [Accepted: 01/13/2019] [Indexed: 12/29/2022]
|
36
|
Lund S, Hall R, Williams GJ. An Artificial Pathway for Isoprenoid Biosynthesis Decoupled from Native Hemiterpene Metabolism. ACS Synth Biol 2019; 8:232-238. [PMID: 30648856 PMCID: PMC6556385 DOI: 10.1021/acssynbio.8b00383] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isoprenoids are constructed in nature using hemiterpene building blocks that are biosynthesized from lengthy enzymatic pathways with little opportunity to deploy precursor-directed biosynthesis. Here, an artificial alcohol-dependent hemiterpene biosynthetic pathway was designed and coupled to several isoprenoid biosynthetic systems, affording lycopene and a prenylated tryptophan in robust yields. This approach affords a potential route to diverse non-natural hemiterpenes and by extension isoprenoids modified with non-natural chemical functionality. Accordingly, the prototype chemo-enzymatic pathway is a critical first step toward the construction of engineered microbial strains for bioconversion of simple scalable building blocks into complex isoprenoid scaffolds.
Collapse
Affiliation(s)
- Sean Lund
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
- Present address: Amyris, 5885 Hollis St Ste. 100, Emeryville, California 94608, United States
| | - Rachael Hall
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
| | - Gavin J Williams
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
- Comparative Medicine Institute, NC State University, Raleigh, North Carolina 27695, United States
| |
Collapse
|
37
|
Sharma D, Dada R, Tejavath KK, Rai P, Soni R, Yaragorla S, Bhatt TK. A paradigm towards the antimalarial quest: in silico identification and biological evaluation of novel inhibitors targeting 1-deoxy-D-xylulose-5-phosphate reductoisomerase. J Biomol Struct Dyn 2019; 38:295-301. [PMID: 30688162 DOI: 10.1080/07391102.2019.1570342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Drista Sharma
- Department of Biotechnology, Central University of Rajasthan, Ajmer, India
| | | | | | - Praveen Rai
- Department of Biotechnology, Central University of Rajasthan, Ajmer, India
| | - Rani Soni
- Department of Biotechnology, Central University of Rajasthan, Ajmer, India
| | | | - Tarun Kumar Bhatt
- Department of Biotechnology, Central University of Rajasthan, Ajmer, India
| |
Collapse
|
38
|
Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
Collapse
Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| |
Collapse
|
39
|
Guggisberg AM, Frasse PM, Jezewski AJ, Kafai NM, Gandhi AY, Erlinger SJ, Odom John AR. Suppression of Drug Resistance Reveals a Genetic Mechanism of Metabolic Plasticity in Malaria Parasites. mBio 2018; 9:e01193-18. [PMID: 30425143 PMCID: PMC6234871 DOI: 10.1128/mbio.01193-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/10/2018] [Indexed: 11/20/2022] Open
Abstract
In the malaria parasite Plasmodium falciparum, synthesis of isoprenoids from glycolytic intermediates is essential for survival. The antimalarial fosmidomycin (FSM) inhibits isoprenoid synthesis. In P. falciparum, we identified a loss-of-function mutation in HAD2 (P. falciparum 3D7_1226300 [PF3D7_1226300]) as necessary for FSM resistance. Enzymatic characterization revealed that HAD2, a member of the haloacid dehalogenase-like hydrolase (HAD) superfamily, is a phosphatase. Harnessing a growth defect in resistant parasites, we selected for suppression of HAD2-mediated FSM resistance and uncovered hypomorphic suppressor mutations in the locus encoding the glycolytic enzyme phosphofructokinase 9 (PFK9). Metabolic profiling demonstrated that FSM resistance is achieved via increased steady-state levels of methylerythritol phosphate (MEP) pathway and glycolytic intermediates and confirmed reduced PFK9 function in the suppressed strains. We identified HAD2 as a novel regulator of malaria parasite metabolism and drug sensitivity and uncovered PFK9 as a novel site of genetic metabolic plasticity in the parasite. Our report informs the biological functions of an evolutionarily conserved family of metabolic regulators and reveals a previously undescribed strategy by which malaria parasites adapt to cellular metabolic dysregulation.IMPORTANCE Unique and essential aspects of parasite metabolism are excellent targets for development of new antimalarials. An improved understanding of parasite metabolism and drug resistance mechanisms is urgently needed. The antibiotic fosmidomycin targets the synthesis of essential isoprenoid compounds from glucose and is a candidate for antimalarial development. Our report identifies a novel mechanism of drug resistance and further describes a family of metabolic regulators in the parasite. Using a novel forward genetic approach, we also uncovered mutations that suppress drug resistance in the glycolytic enzyme PFK9. Thus, we identify an unexpected genetic mechanism of adaptation to metabolic insult that influences parasite fitness and tolerance of antimalarials.
Collapse
Affiliation(s)
- Ann M Guggisberg
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Philip M Frasse
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrew J Jezewski
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Natasha M Kafai
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Aakash Y Gandhi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Samuel J Erlinger
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Audrey R Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
40
|
Takino J, Kozaki T, Sato Y, Liu C, Ozaki T, Minami A, Oikawa H. Unveiling Biosynthesis of the Phytohormone Abscisic Acid in Fungi: Unprecedented Mechanism of Core Scaffold Formation Catalyzed by an Unusual Sesquiterpene Synthase. J Am Chem Soc 2018; 140:12392-12395. [PMID: 30226766 DOI: 10.1021/jacs.8b08925] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Abscisic acid (ABA) is a well-known phytohormone that regulates abiotic stresses. ABA produced by fungi is also proposed to be a virulence factor of fungal pathogens. Although its biosynthetic pathway in fungi was proposed by a series of feeding experiments, the enzyme catalyzing the reaction from farnesyl diphosphate to α-ionylideneethane remains to be identified. In this work, we identified the novel type of sesquiterpene synthase BcABA3 and its unprecedented three-step reaction mechanism involving two neutral intermediates, β-farnesene and allofarnesene. Database searches showed that BcABA3 has no homology with typical sesquiterpene synthases and that the homologous enzyme genes are found in more than 100 bacteria, suggesting that these enzymes form a new family of sesquiterpene synthases.
Collapse
Affiliation(s)
- Junya Takino
- Department of Chemistry, Faculty of Science , Hokkaido University , Kita-ku Kita 10 Jo Nishi 8 Chome , Sapporo 060-0810 , Japan
| | - Takuto Kozaki
- Department of Chemistry, Faculty of Science , Hokkaido University , Kita-ku Kita 10 Jo Nishi 8 Chome , Sapporo 060-0810 , Japan
| | - Yoshiro Sato
- Department of Chemistry, Faculty of Science , Hokkaido University , Kita-ku Kita 10 Jo Nishi 8 Chome , Sapporo 060-0810 , Japan
| | - Chengwei Liu
- Department of Chemistry, Faculty of Science , Hokkaido University , Kita-ku Kita 10 Jo Nishi 8 Chome , Sapporo 060-0810 , Japan
| | - Taro Ozaki
- Department of Chemistry, Faculty of Science , Hokkaido University , Kita-ku Kita 10 Jo Nishi 8 Chome , Sapporo 060-0810 , Japan
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science , Hokkaido University , Kita-ku Kita 10 Jo Nishi 8 Chome , Sapporo 060-0810 , Japan
| | - Hideaki Oikawa
- Department of Chemistry, Faculty of Science , Hokkaido University , Kita-ku Kita 10 Jo Nishi 8 Chome , Sapporo 060-0810 , Japan
| |
Collapse
|
41
|
He L, He P, Luo X, Li M, Yu L, Guo J, Zhan X, Zhu G, Zhao J. The MEP pathway in Babesia orientalis apicoplast, a potential target for anti-babesiosis drug development. Parasit Vectors 2018; 11:452. [PMID: 30081952 PMCID: PMC6090808 DOI: 10.1186/s13071-018-3038-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/24/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The apicomplexan parasite Babesia orientalis, the causative agent of water buffalo babesiosis in China, is widespread in central and south China, resulting in a huge economic loss annually. Currently, there is no effective vaccine or drug against this disease. Babesia bovis and Plasmodium falciparum were reported to possess an apicoplast which contains the methylerythritol phosphate (MEP) pathway inhibitable by fosmidomycin, suggesting that the pathway could serve as a drug target for screening new drugs. However, it remains unknown in B. orientalis. METHODS Primers were designed according to the seven MEP pathway genes of Babesia microti and Babesia bovis. The genes were cloned, sequenced and analyzed. The open reading frames (ORFs) of the first two enzyme genes, 1-deoxy-D-xylulose 5-phosphate synthase (BoDXS) and 1-Deoxy-D-xylulose 5-phosphate reductoisomerase (BoDXR), were cloned into the pET-32a expression vector and expressed as a Trx-tag fusion protein. Rabbit anti-rBoDXS and rabbit anti-rBoDXR antibodies were generated. Western blot was performed to identify the native proteins of BoDXS and BoDXR in B. orientalis. Fosmidomycin and geranylgeraniol were used for inhibition assay and rescue assay, respectively, in the in vitro cultivation of B. orientalis. RESULTS The seven enzyme genes of the B. orientalis MEP pathway (DXS, DXR, IspD, IspE, IspF, IspG and IspH) were cloned and sequenced, with a full length of 2094, 1554, 1344, 1521, 654, 1932 and 1056 bp, respectively. BoDXS and BoDXR were expressed as Trx-tag fusion proteins, with a size of 95 and 67 kDa, respectively. Western blot identified a 77 kDa band for the native BoDXS and a 49 kDa band for the native BoDXR. The drug assay results showed that fosmidomycin could inhibit the growth of B. orientalis, and geranylgeraniol could reverse the effect of fosmidomycin. CONCLUSIONS Babesia orientalis has the isoprenoid biosynthesis pathway, which could be a potential drug target for controlling and curing babesiosis. Considering the high price and instability of fosmidomycin, further studies should focus on the screening of stable and cheap drugs.
Collapse
Affiliation(s)
- Lan He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 Hubei China
| | - Pei He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
| | - Xiaoying Luo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
| | - Muxiao Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
| | - Long Yu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
| | - Jiaying Guo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
| | - Xueyan Zhan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
| | - Guan Zhu
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas USA
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070 Hubei People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 Hubei China
| |
Collapse
|
42
|
Sanders S, Bartee D, Harrison MJ, Phillips PD, Koppisch AT, Freel Meyers CL. Growth medium-dependent antimicrobial activity of early stage MEP pathway inhibitors. PLoS One 2018; 13:e0197638. [PMID: 29771999 PMCID: PMC5957436 DOI: 10.1371/journal.pone.0197638] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 05/04/2018] [Indexed: 01/01/2023] Open
Abstract
The in vivo microenvironment of bacterial pathogens is often characterized by nutrient limitation. Consequently, conventional rich in vitro culture conditions used widely to evaluate antibacterial agents are often poorly predictive of in vivo activity, especially for agents targeting metabolic pathways. In one such pathway, the methylerythritol phosphate (MEP) pathway, which is essential for production of isoprenoids in bacterial pathogens, relatively little is known about the influence of growth environment on antibacterial properties of inhibitors targeting enzymes in this pathway. The early steps of the MEP pathway are catalyzed by 1-deoxy-d-xylulose 5-phosphate (DXP) synthase and reductoisomerase (IspC). The in vitro antibacterial efficacy of the DXP synthase inhibitor butylacetylphosphonate (BAP) was recently reported to be strongly dependent upon growth medium, with high potency observed under nutrient limitation and exceedingly weak activity in nutrient-rich conditions. In contrast, the well-known IspC inhibitor fosmidomycin has potent antibacterial activity in nutrient-rich conditions, but to date, its efficacy had not been explored under more relevant nutrient-limited conditions. The goal of this work was to thoroughly characterize the effects of BAP and fosmidomycin on bacterial cells under varied growth conditions. In this work, we show that activities of both inhibitors, alone and in combination, are strongly dependent upon growth medium, with differences in cellular uptake contributing to variance in potency of both agents. Fosmidomycin is dissimilar to BAP in that it displays relatively weaker activity in nutrient-limited compared to nutrient-rich conditions. Interestingly, while it has been generally accepted that fosmidomycin activity depends upon expression of the GlpT transporter, our results indicate for the first time that fosmidomycin can enter cells by an alternative mechanism under nutrient limitation. Finally, we show that the potency and relationship of the BAP-fosmidomycin combination also depends upon the growth medium, revealing a striking loss of BAP-fosmidomycin synergy under nutrient limitation. This change in BAP-fosmidomycin relationship suggests a shift in the metabolic and/or regulatory networks surrounding DXP accompanying the change in growth medium, the understanding of which could significantly impact targeting strategies against this pathway. More generally, our findings emphasize the importance of considering physiologically relevant growth conditions for predicting the antibacterial potential MEP pathway inhibitors and for studies of their intracellular targets.
Collapse
Affiliation(s)
- Sara Sanders
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - David Bartee
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Mackenzie J. Harrison
- Department of Chemistry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Paul D. Phillips
- Department of Chemistry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Andrew T. Koppisch
- Department of Chemistry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- * E-mail:
| |
Collapse
|
43
|
Targeting the Nonmevalonate Pathway in Burkholderia cenocepacia Increases Susceptibility to Certain β-Lactam Antibiotics. Antimicrob Agents Chemother 2018; 62:AAC.02607-17. [PMID: 29439968 DOI: 10.1128/aac.02607-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/07/2018] [Indexed: 11/20/2022] Open
Abstract
The nonmevalonate pathway is the sole pathway for isoprenoid biosynthesis in Burkholderia cenocepacia and is possibly a novel target for the development of antibacterial chemotherapy. The goals of the present study were to evaluate the essentiality of dxr, the second gene of the nonmevalonate pathway, in B. cenocepacia and to determine whether interfering with the nonmevalonate pathway increases susceptibility toward antibiotics. To this end, a rhamnose-inducible conditional dxr knockdown mutant of B. cenocepacia strain K56-2 (B. cenocepacia K56-2dxr) was constructed, using a plasmid which enables the delivery of a rhamnose-inducible promoter in the chromosome. Expression of dxr is essential for bacterial growth; the growth defect observed in the dxr mutant could be complemented by expressing dxr in trans under the control of a constitutive promoter, but not by providing 2-C-methyl-d-erythritol-4-phosphate, the reaction product of DXR (1-deoxy-d-xylulose 5-phosphate reductoisomerase). B. cenocepacia K56-2dxr showed markedly increased susceptibility to the β-lactam antibiotics aztreonam, ceftazidime, and cefotaxime, while susceptibility to other antibiotics was not (or was much less) affected; this increased susceptibility could also be complemented by in trans expression of dxr A similarly increased susceptibility was observed when antibiotics were combined with FR900098, a known DXR inhibitor. Our data confirm that the nonmevalonate pathway is essential in B. cenocepacia and suggest that combining potent DXR inhibitors with selected β-lactam antibiotics is a useful strategy to combat B. cenocepacia infections.
Collapse
|
44
|
Kadian K, Vijay S, Gupta Y, Rawal R, Singh J, Anvikar A, Pande V, Sharma A. Structural modeling identifies Plasmodium vivax 4-diphosphocytidyl-2C-methyl-d-erythritol kinase (IspE) as a plausible new antimalarial drug target. Parasitol Int 2018; 67:375-385. [PMID: 29550587 DOI: 10.1016/j.parint.2018.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/12/2018] [Accepted: 03/12/2018] [Indexed: 12/23/2022]
Abstract
Malaria parasites utilize Methylerythritol phosphate (MEP) pathway for synthesis of isoprenoid precursors which are essential for maturation and survival of parasites during erythrocytic and gametocytic stages. The absence of MEP pathway in the human host establishes MEP pathway enzymes as a repertoire of essential drug targets. The fourth enzyme, 4-diphosphocytidyl-2C-methyl-d-erythritol kinase (IspE) has been proved essential in pathogenic bacteria, however; it has not yet been studied in any Plasmodium species. This study was undertaken to investigate genetic polymorphism and concomitant structural implications of the Plasmodium vivax IspE (PvIspE) by employing sequencing, modeling and bioinformatics approach. We report that PvIspE gene displayed six non-synonymous mutations which were restricted to non-conserved regions within the gene from seven topographically distinct malaria-endemic regions of India. Phylogenetic studies reflected that PvIspE occupies unique status within Plasmodia genus and reflects that Plasmodium vivax IspE gene has a distant and non-conserved relation with human ortholog Mevalonate Kinase (MAVK). Structural modeling analysis revealed that all PvIspE Indian isolates have critically conserved canonical galacto-homoserine-mevalonate-phosphomevalonate kinase (GHMP) domain within the active site lying in a deep cleft sandwiched between ATP and CDPME-binding domains. The active core region was highly conserved among all clinical isolates, may be due to >60% β-pleated rigid architecture. The mapped structural analysis revealed the critically conserved active site of PvIspE, both sequence, and spacially among all Indian isolates; showing no significant changes in the active site. Our study strengthens the candidature of Plasmodium vivax IspE enzyme as a future target for novel antimalarials.
Collapse
Affiliation(s)
- Kavita Kadian
- Protein Biochemistry and Structural Biology Laboratory, National Institute of Malaria Research (ICMR), Sector-8, Dwarka, New Delhi, India
| | - Sonam Vijay
- Protein Biochemistry and Structural Biology Laboratory, National Institute of Malaria Research (ICMR), Sector-8, Dwarka, New Delhi, India
| | - Yash Gupta
- Protein Biochemistry and Structural Biology Laboratory, National Institute of Malaria Research (ICMR), Sector-8, Dwarka, New Delhi, India
| | - Ritu Rawal
- Protein Biochemistry and Structural Biology Laboratory, National Institute of Malaria Research (ICMR), Sector-8, Dwarka, New Delhi, India
| | - Jagbir Singh
- Protein Biochemistry and Structural Biology Laboratory, National Institute of Malaria Research (ICMR), Sector-8, Dwarka, New Delhi, India
| | - Anup Anvikar
- Epidemiology and Clinical Research, National Institute of Malaria Research (ICMR), Sector-8, Dwarka, New Delhi, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Arun Sharma
- Protein Biochemistry and Structural Biology Laboratory, National Institute of Malaria Research (ICMR), Sector-8, Dwarka, New Delhi, India.
| |
Collapse
|
45
|
Wang X, Dowd CS. The Methylerythritol Phosphate Pathway: Promising Drug Targets in the Fight against Tuberculosis. ACS Infect Dis 2018; 4:278-290. [PMID: 29390176 DOI: 10.1021/acsinfecdis.7b00176] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a severe infectious disease in need of new chemotherapies especially for drug-resistant cases. To meet the urgent requirement of new TB drugs with novel modes of action, the TB research community has been validating numerous targets from several biosynthetic pathways. The methylerythritol phosphate (MEP) pathway is utilized by Mtb for the biosynthesis of isopentenyl pyrophosphate (IPP) and its isomer dimethylallyl pyrophosphate (DMAPP), the universal five-carbon building blocks of isoprenoids. While being a common biosynthetic pathway in pathogens, the MEP pathway is completely absent in humans. Due to its unique presence in pathogens as well as the essentiality of the MEP pathway in Mtb, the enzymes in this pathway are promising targets for the development of new drugs against tuberculosis. In this Review, we discuss three enzymes in the MEP pathway: 1-deoxy-d-xylulose-5-phosphate synthase (DXS), 1-deoxy-d-xylulose-5-phosphate reductoisomerase (IspC/DXR), and 2 C-methyl-d-erythritol 2,4-cyclodiphosphate synthase (IspF), which appear to be the most promising antitubercular drug targets. Structural and mechanistic features of these enzymes are reviewed, as well as selected inhibitors that show promise as antitubercular agents.
Collapse
Affiliation(s)
- Xu Wang
- Department of Chemistry, George Washington University, 800 22nd Street NW, Washington, D.C. 20052, United States
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, 800 22nd Street NW, Washington, D.C. 20052, United States
| |
Collapse
|
46
|
Chen LX, Méndez-García C, Dombrowski N, Servín-Garcidueñas LE, Eloe-Fadrosh EA, Fang BZ, Luo ZH, Tan S, Zhi XY, Hua ZS, Martinez-Romero E, Woyke T, Huang LN, Sánchez J, Peláez AI, Ferrer M, Baker BJ, Shu WS. Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota. THE ISME JOURNAL 2018; 12:756-775. [PMID: 29222443 PMCID: PMC5864196 DOI: 10.1038/s41396-017-0002-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 08/26/2017] [Accepted: 10/09/2017] [Indexed: 11/17/2022]
Abstract
Small acidophilic archaea belonging to Micrarchaeota and Parvarchaeota phyla are known to physically interact with some Thermoplasmatales members in nature. However, due to a lack of cultivation and limited genomes on hand, their biodiversity, metabolisms, and physiologies remain largely unresolved. Here, we obtained 39 genomes from acid mine drainage (AMD) and hot spring environments around the world. 16S rRNA gene based analyses revealed that Parvarchaeota were only detected in AMD and hot spring habitats, while Micrarchaeota were also detected in others including soil, peat, hypersaline mat, and freshwater, suggesting a considerable higher diversity and broader than expected habitat distribution for this phylum. Despite their small genomes (0.64-1.08 Mb), these archaea may contribute to carbon and nitrogen cycling by degrading multiple saccharides and proteins, and produce ATP via aerobic respiration and fermentation. Additionally, we identified several syntenic genes with homology to those involved in iron oxidation in six Parvarchaeota genomes, suggesting their potential role in iron cycling. However, both phyla lack biosynthetic pathways for amino acids and nucleotides, suggesting that they likely scavenge these biomolecules from the environment and/or other community members. Moreover, low-oxygen enrichments in laboratory confirmed our speculation that both phyla are microaerobic/anaerobic, based on several specific genes identified in them. Furthermore, phylogenetic analyses provide insights into the close evolutionary history of energy related functionalities between both phyla with Thermoplasmatales. These results expand our understanding of these elusive archaea by revealing their involvement in carbon, nitrogen, and iron cycling, and suggest their potential interactions with Thermoplasmatales on genomic scale.
Collapse
Affiliation(s)
- Lin-Xing Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Celia Méndez-García
- Departamento de Biología Funcional-IUBA, Universidad de Oviedo, Oviedo, Spain
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Nina Dombrowski
- Department of Marine Science, University of Texas Austin, Marine Science Institute, Port Aransas, TX, 78373, USA
| | - Luis E Servín-Garcidueñas
- Laboratory of Microbiomics, National School of Higher Studies Morelia, National University of Mexico, Morelia, Michoacan, 58190, Mexico
| | | | - Bao-Zhu Fang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zhen-Hao Luo
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Sha Tan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Zheng-Shuang Hua
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Esperanza Martinez-Romero
- Department of Ecological Genomics, Center for Genomic Sciences, National University of Mexico, Cuernavaca, Morelos, 62210, Mexico
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jesús Sánchez
- Departamento de Biología Funcional-IUBA, Universidad de Oviedo, Oviedo, Spain
| | - Ana Isabel Peláez
- Departamento de Biología Funcional-IUBA, Universidad de Oviedo, Oviedo, Spain
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Brett J Baker
- Department of Marine Science, University of Texas Austin, Marine Science Institute, Port Aransas, TX, 78373, USA.
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China.
| |
Collapse
|
47
|
Validation of Putative Apicoplast-Targeting Drugs Using a Chemical Supplementation Assay in Cultured Human Malaria Parasites. Antimicrob Agents Chemother 2017; 62:AAC.01161-17. [PMID: 29109165 DOI: 10.1128/aac.01161-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/18/2017] [Indexed: 11/20/2022] Open
Abstract
Malaria parasites contain a relict plastid, the apicoplast, which is considered an excellent drug target due to its bacterial-like ancestry. Numerous parasiticidals have been proposed to target the apicoplast, but few have had their actual targets substantiated. Isopentenyl pyrophosphate (IPP) production is the sole required function of the apicoplast in the blood stage of the parasite life cycle, and IPP supplementation rescues parasites from apicoplast-perturbing drugs. Hence, any drug that kills parasites when IPP is supplied in culture must have a nonapicoplast target. Here, we use IPP supplementation to discriminate whether 23 purported apicoplast-targeting drugs are on- or off-target. We demonstrate that a prokaryotic DNA replication inhibitor (ciprofloxacin), several prokaryotic translation inhibitors (chloramphenicol, doxycycline, tetracycline, clindamycin, azithromycin, erythromycin, and clarithromycin), a tRNA synthase inhibitor (mupirocin), and two IPP synthesis pathway inhibitors (fosmidomycin and FR900098) have apicoplast targets. Intriguingly, fosmidomycin and FR900098 leave the apicoplast intact, whereas the others eventually result in apicoplast loss. Actinonin, an inhibitor of bacterial posttranslational modification, does not produce a typical delayed-death response but is rescued with IPP, thereby confirming its apicoplast target. Parasites treated with putative apicoplast fatty acid pathway inhibitors could not be rescued, demonstrating that these drugs have their primary targets outside the apicoplast, which agrees with the dispensability of the apicoplast fatty acid synthesis pathways in the blood stage of malaria parasites. IPP supplementation provides a simple test of whether a compound has a target in the apicoplast and can be used to screen novel compounds for mode of action.
Collapse
|
48
|
Sharkey TD, Monson RK. Isoprene research - 60 years later, the biology is still enigmatic. PLANT, CELL & ENVIRONMENT 2017; 40:1671-1678. [PMID: 28160522 DOI: 10.1111/pce.12930] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 05/26/2023]
Abstract
Isoprene emission is a major component of biosphere-atmosphere interactions. It is the single largest source of non-methane hydrocarbon in the atmosphere. The first report of isoprene emission from plants was published in 1957 by Professor Guivi Sanadze. While humans have smelled the monoterpene hydrocarbons made by coniferous trees since their earliest migrations, only in 1957 did the world became aware that other trees make a type of hydrocarbon in even greater amounts but one to which the human nose is much less sensitive. For this 60th anniversary of the first report of isoprene emission from leaves, we trace the discovery and development of the research field, highlighting some of the most seminal observations and theoretical interpretations. This is not an exhaustive review, and many important papers are not cited, but we hope it will be of general interest to read how research in this field developed, how new observations forced us to reevaluate our theories about the significance of isoprene biosynthesis to plant physiology and adaptation and how scientific serendipity can sometimes drive a topic forward.
Collapse
Affiliation(s)
- Thomas D Sharkey
- Department of Biochemistry and Molecular Biology and Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - Russell K Monson
- School of Natural Resources and the Environment and Laboratory of Tree Ring Research, University of Arizona, Tucson, AZ, 85721, USA
| |
Collapse
|
49
|
Edwards RL, Brothers RC, Wang X, Maron MI, Ziniel PD, Tsang PS, Kraft TE, Hruz PW, Williamson KC, Dowd CS, John ARO. MEPicides: potent antimalarial prodrugs targeting isoprenoid biosynthesis. Sci Rep 2017; 7:8400. [PMID: 28827774 PMCID: PMC5567135 DOI: 10.1038/s41598-017-07159-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 06/21/2017] [Indexed: 01/29/2023] Open
Abstract
The emergence of Plasmodium falciparum resistant to frontline therapeutics has prompted efforts to identify and validate agents with novel mechanisms of action. MEPicides represent a new class of antimalarials that inhibit enzymes of the methylerythritol phosphate (MEP) pathway of isoprenoid biosynthesis, including the clinically validated target, deoxyxylulose phosphate reductoisomerase (Dxr). Here we describe RCB-185, a lipophilic prodrug with nanomolar activity against asexual parasites. Growth of P. falciparum treated with RCB-185 was rescued by isoprenoid precursor supplementation, and treatment substantially reduced metabolite levels downstream of the Dxr enzyme. In addition, parasites that produced higher levels of the Dxr substrate were resistant to RCB-185. Notably, environmental isolates resistant to current therapies remained sensitive to RCB-185, the compound effectively treated sexually-committed parasites, and was both safe and efficacious in malaria-infected mice. Collectively, our data demonstrate that RCB-185 potently and selectively inhibits Dxr in P. falciparum, and represents a promising lead compound for further drug development.
Collapse
Affiliation(s)
- Rachel L Edwards
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert C Brothers
- Department of Chemistry, George Washington University, Washington, DC, USA
| | - Xu Wang
- Department of Chemistry, George Washington University, Washington, DC, USA
| | - Maxim I Maron
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
- Albert Einstein College of Medicine, Bronx, New York, USA
| | - Peter D Ziniel
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Patricia S Tsang
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Thomas E Kraft
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Roche Pharma Research and Early Development, Roche Innovation Center, Munich, Nonnenwald, Penzberg, Germany
| | - Paul W Hruz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kim C Williamson
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Cynthia S Dowd
- Department of Chemistry, George Washington University, Washington, DC, USA
| | - Audrey R Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
50
|
Paramasivan K, Mutturi S. Progress in terpene synthesis strategies through engineering of Saccharomyces cerevisiae. Crit Rev Biotechnol 2017; 37:974-989. [DOI: 10.1080/07388551.2017.1299679] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Sarma Mutturi
- CSIR-Central Food Technological Research Institute, Mysore, India
| |
Collapse
|