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Heidtmann CV, Fejer AR, Stærk K, Pedersen M, Asmussen MG, Hertz FB, Prabhala BK, Frimodt-Møller N, Klitgaard JK, Andersen TE, Nielsen CU, Nielsen P. Hit-to-Lead Identification and Validation of a Triaromatic Pleuromutilin Antibiotic Candidate. J Med Chem 2024; 67:3692-3710. [PMID: 38385364 DOI: 10.1021/acs.jmedchem.3c02153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Herein, we report the hit-to-lead identification of a drug-like pleuromutilin conjugate 16, based on a triaromatic hit reported in 2020. The lead arose as the clear candidate from a hit-optimization campaign in which Gram-positive antibacterial activity, solubility, and P-gp affinity were optimized. Conjugate 16 was extensively evaluated for its in vitro ADMET performance which, apart from solubility, was overall on par with lefamulin. This evaluation included Caco-2 cell permeability, plasma protein binding, hERG inhibition, cytotoxicity, metabolism in microsomes and CYP3A4, resistance induction, and time-kill kinetics. Intravenous pharmacokinetics of 16 proved satisfactory in both mice and pigs; however, oral bioavailability was limited likely due to insufficient solubility. The in vivo efficacy was evaluated in mice, systemically infected with Staphylococcus aureus, where 16 showed rapid reduction in blood bacteriaemia. Through our comprehensive studies, lead 16 has emerged as a highly promising and safe antibiotic candidate for the treatment of Gram-positive bacterial infections.
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Affiliation(s)
- Christoffer V Heidtmann
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Andreas R Fejer
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Kristian Stærk
- Department of Clinical Research, Research Unit of Clinical Microbiology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Maria Pedersen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Marco G Asmussen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Frederik B Hertz
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Bala K Prabhala
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Niels Frimodt-Møller
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Janne K Klitgaard
- Department of Clinical Research, Research Unit of Clinical Microbiology, University of Southern Denmark, DK-5230 Odense M, Denmark
- Department of Biochemistry and Molecular Biology, Research Unit of Molecular Microbiology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Thomas E Andersen
- Department of Clinical Research, Research Unit of Clinical Microbiology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Carsten U Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Poul Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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2
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Villadsen AB, Holm-Jacobsen JN, Prabhala BK, Bundgaard-Nielsen C, Huntjens P, Kornum JB, Glavind K, Leutscher PDC, Christensen LP, Jeppesen PB, Sørensen S, Arenholt LTS. Use of Fermented Red Clover Isoflavones in the Treatment of Overactive Bladder in Postmenopausal Women: A Randomized, Double-Blinded, Placebo-Controlled Trial. Nutrients 2023; 15:4165. [PMID: 37836449 PMCID: PMC10574253 DOI: 10.3390/nu15194165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Postmenopausal women are at risk of developing an overactive bladder (OAB). Conventional vaginal estrogen has shown promise for symptom relief. Isoflavones have proven effective as an alternative to estrogen treatment against menopause-related symptoms. However, its effect on OAB symptoms has not been studied. This study investigates if fermented red clover isoflavones reduce OAB symptoms in postmenopausal women. In this randomized, double-blinded, placebo-controlled trial, women were administered red clover extract (RCE) or a placebo twice daily for three months. Women filled out the International Consultation on Incontinence Questionnaire Overactive Bladder (ICIQ-OAB) and Urinary Incontinence Short Form (ICIQ-UI-SF), together with a fluid intake and voiding diary. A total of 33 women (16 in the RCE group and 17 in the placebo group) were included in the analysis. Baseline demographics and OAB characteristics were comparable across groups. Intake of RCE did not lead to significant relief in most urinary bladder symptom measures, although a significant reduction in the bother of urinary urgency (p = 0.033) and a tendency towards a decreased ICIQ-OAB score were observed (p = 0.056). In contrast, the placebo exhibited a significant decrease in the ICIQ-OAB score (p = 0.021) and in some diary outcomes. We found that an intake of isoflavones did not relieve OAB symptoms in postmenopausal women.
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Affiliation(s)
- Annemarie B. Villadsen
- Centre for Clinical Research, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (A.B.V.); (J.N.H.-J.); (C.B.-N.); (P.H.); (P.D.C.L.); (S.S.)
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark
| | - Julie N. Holm-Jacobsen
- Centre for Clinical Research, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (A.B.V.); (J.N.H.-J.); (C.B.-N.); (P.H.); (P.D.C.L.); (S.S.)
| | - Bala K. Prabhala
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark; (B.K.P.); (L.P.C.)
| | - Caspar Bundgaard-Nielsen
- Centre for Clinical Research, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (A.B.V.); (J.N.H.-J.); (C.B.-N.); (P.H.); (P.D.C.L.); (S.S.)
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark
| | - Pam Huntjens
- Centre for Clinical Research, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (A.B.V.); (J.N.H.-J.); (C.B.-N.); (P.H.); (P.D.C.L.); (S.S.)
| | - Jette B. Kornum
- Department of Clinical Microbiology, Aalborg University, 9000 Aalborg, Denmark;
| | - Karin Glavind
- Department of Obstetrics and Gynecology, Aalborg University Hospital, 9000 Aalborg, Denmark;
| | - Peter D. C. Leutscher
- Centre for Clinical Research, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (A.B.V.); (J.N.H.-J.); (C.B.-N.); (P.H.); (P.D.C.L.); (S.S.)
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark
| | - Lars P. Christensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark; (B.K.P.); (L.P.C.)
| | - Per B. Jeppesen
- Department of Clinical Medicine, Aarhus University, Aarhus University Hospital, 8200 Aarhus N, Denmark;
| | - Suzette Sørensen
- Centre for Clinical Research, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (A.B.V.); (J.N.H.-J.); (C.B.-N.); (P.H.); (P.D.C.L.); (S.S.)
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark
- Steno Diabetes Center North Denmark, 9000 Aalborg, Denmark
| | - Louise T. S. Arenholt
- Centre for Clinical Research, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (A.B.V.); (J.N.H.-J.); (C.B.-N.); (P.H.); (P.D.C.L.); (S.S.)
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark
- Department of Obstetrics and Gynecology, North Denmark Regional Hospital, 9800 Hjoerring, Denmark
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3
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Gharabli H, Rafiq M, Iqbal A, Yan R, Aduri NG, Sharma N, Prabhala BK, Mirza O. Functional Characterization of the Putative POT from Clostridium perfringens. Biology (Basel) 2023; 12:biology12050651. [PMID: 37237465 DOI: 10.3390/biology12050651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023]
Abstract
Proton-coupled oligopeptide transporters (POTs) are a fundamental part of the cellular transport machinery that provides plants, bacteria, and mammals with nutrition in the form of short peptides. However, POTs are not restricted to peptide transport; mammalian POTs have especially been in focus due to their ability to transport several peptidomimetics in the small intestine. Herein, we studied a POT from Clostridium perfringens (CPEPOT), which unexpectedly exhibited atypical characteristics. First, very little uptake of a fluorescently labelled peptide β-Ala-Lys-AMCA, an otherwise good substrate of several other bacterial POTs, was observed. Secondly, in the presence of a competitor peptide, enhanced uptake of β-Ala-Lys-AMCA was observed due to trans-stimulation. This effect was also observed even in the absence of a proton electrochemical gradient, suggesting that β-Ala-Lys-AMCA uptake mediated by CPEPOT is likely through the substrate-concentration-driving exchange mechanism, unlike any other functionally characterized bacterial POTs.
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Affiliation(s)
- Hani Gharabli
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Maria Rafiq
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Anna Iqbal
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Ruyu Yan
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Nanda G Aduri
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Neha Sharma
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Bala K Prabhala
- Department of Physics, Chemistry and Pharmacy, Faculty of Science, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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4
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Abstract
PTR2/POT/NPF are a family of primarily proton coupled transporters that belong to the major facilitator super family and are found across most kingdoms of life. They are involved in uptake of nutrients, hormones, ions and several orally administered drug molecules. A wealth of structural and functional data is available for this family; the similarity between the protein structural features have been discussed and investigated in detail on several occasions, however there are no reports on the unification of substrate information. In order to fill this gap, we have collected information about substrates across the entire PTR2/POT/NPF family in order to provide key insights into what makes a molecule a substrate and whether there are common features among confirmed substrates. This review will be of particular interest for researchers in the field trying to probe the mechanisms responsible for the different selectivity of these transporters at a molecular resolution, and to design novel substrates.
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Affiliation(s)
- Bala K Prabhala
- Institute of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Moazur Rahman
- School of Biological Sciences, University of the Punjab, Lahore, Punjab, Pakistan; Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
| | - Hussam H Nour-Eldin
- DynaMo Center, Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Flemming Steen Jørgensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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5
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Mutuku SM, Trim PJ, Prabhala BK, Irani S, Bremert KL, Logan JM, Brooks DA, Stahl J, Centenera MM, Snel MF, Butler LM. Evaluation of Small Molecule Drug Uptake in Patient-Derived Prostate Cancer Explants by Mass Spectrometry. Sci Rep 2019; 9:15008. [PMID: 31628408 PMCID: PMC6802206 DOI: 10.1038/s41598-019-51549-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/01/2019] [Indexed: 02/06/2023] Open
Abstract
Patient-derived explant (PDE) culture of solid tumors is increasingly being applied to preclinical evaluation of novel therapeutics and for biomarker discovery. In this technique, treatments are added to culture medium and penetrate the tissue via a gelatin sponge scaffold. However, the penetration profile and final concentrations of small molecule drugs achieved have not been determined to date. Here, we determined the extent of absorption of the clinical androgen receptor antagonist, enzalutamide, into prostate PDEs, using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and matrix-assisted laser/desorption ionisation (MALDI) mass spectrometry imaging (MSI). In a cohort of 11 PDE tissues from eight individual patients, LC-MS/MS quantification of PDE homogenates confirmed enzalutamide (10 µM) uptake by all PDEs, which reached maximal average tissue concentration of 0.24-0.50 ng/µg protein after 48 h culture. Time dependent uptake of enzalutamide (50 µM) in PDEs was visualized using MALDI MSI over 24-48 h, with complete penetration throughout tissues evident by 6 h of culture. Drug signal intensity was not homogeneous throughout the tissues but had areas of markedly high signal that corresponded to drug target (androgen receptor)-rich epithelial regions of tissue. In conclusion, application of MS-based drug quantification and visualization in PDEs, and potentially other 3-dimensional model systems, can provide a more robust basis for experimental study design and interpretation of pharmacodynamic data.
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Affiliation(s)
- Shadrack M Mutuku
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia.,Prostate Cancer Research Group, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
| | - Paul J Trim
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
| | - Bala K Prabhala
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia.,Department of Drug Design and Pharmacology, University of Copenhagen, København, Denmark
| | - Swati Irani
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia.,Prostate Cancer Research Group, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia.,Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Kayla L Bremert
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia.,Prostate Cancer Research Group, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia.,Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jessica M Logan
- Mechanisms in Cell Biology and Disease Research Group, School of Pharmacy and Medical Sciences, Cancer Research Institute, University of South Australia, Adelaide, SA, 5000, Australia
| | - Douglas A Brooks
- Mechanisms in Cell Biology and Disease Research Group, School of Pharmacy and Medical Sciences, Cancer Research Institute, University of South Australia, Adelaide, SA, 5000, Australia
| | - Jürgen Stahl
- Clinpath Laboratories, Adelaide, SA, 5000, Australia
| | - Margaret M Centenera
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia.,Prostate Cancer Research Group, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia.,Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Marten F Snel
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
| | - Lisa M Butler
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia. .,Prostate Cancer Research Group, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia. .,Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, SA, 5005, Australia.
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6
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Aduri NG, Ernst HA, Prabhala BK, Bhatt S, Boesen T, Gajhede M, Mirza O. Human proton coupled folic acid transporter is a monodisperse oligomer in the lauryl maltose neopentyl glycol solubilized state. Biochem Biophys Res Commun 2017; 495:1738-1743. [PMID: 29208467 DOI: 10.1016/j.bbrc.2017.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/01/2017] [Indexed: 01/23/2023]
Abstract
The human proton coupled folic acid transporter PCFT is the major import route for dietary folates. Mutations in the gene encoding PCFT cause hereditary folic acid malabsorption, which manifests itself by compromised folate absorption from the intestine and also in impaired folate transport into the central nervous system. Since its recent discovery, PCFT has been the subject of numerous biochemical studies aiming at understanding its structure and mechanism. One major focus has been its oligomeric state, with some reports supporting oligomers and others a monomer. Here, we report the overexpression and purification of recombinant PCFT. Following detergent screening, n-Dodecyl β-D-maltoside (DDM) and lauryl maltose neopentyl glycol (LMNG) were chosen for further work as they exhibited the most optimal solubilization. We found that purified detergent solubilized PCFT was able to bind folic acid, thus indicating a functionally active protein. Size exclusion chromatography showed that PCFT in DDM was polydisperse; the LMNG preparation was clearly monodisperse but with shorter retention time than the major DDM peak. To assess the oligomeric state negative stain electron microscopy was performed which showed a particle with the size of a PCFT dimer.
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Affiliation(s)
- Nanda G Aduri
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Heidi A Ernst
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bala K Prabhala
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shweta Bhatt
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Boesen
- Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Michael Gajhede
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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7
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Prabhala BK, Aduri NG, Sharma N, Shaheen A, Sharma A, Iqbal M, Hansen PR, Brasen C, Gajhede M, Rahman M, Mirza O. The prototypical proton-coupled oligopeptide transporter YdgR from Escherichia coli facilitates chloramphenicol uptake into bacterial cells. J Biol Chem 2017; 293:1007-1017. [PMID: 29150447 DOI: 10.1074/jbc.m117.805960] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 11/07/2017] [Indexed: 11/06/2022] Open
Abstract
Chloramphenicol (Cam) is a broad-spectrum antibiotic used to combat bacterial infections in humans and animals. Cam export from bacterial cells is one of the mechanisms by which pathogens resist Cam's antibacterial effects, and several different proteins are known to facilitate this process. However, to date no report exists on any specific transport protein that facilitates Cam uptake. The proton-coupled oligopeptide transporter (POT) YdgR from Escherichia coli is a prototypical member of the POT family, functioning in proton-coupled uptake of di- and tripeptides. By following bacterial growth and conducting LC-MS-based assays we show here that YdgR facilitates Cam uptake. Some YdgR variants displaying reduced peptide uptake also exhibited reduced Cam uptake, indicating that peptides and Cam bind YdgR at similar regions. Homology modeling of YdgR, Cam docking, and mutational studies suggested a binding mode that resembles that of Cam binding to the multidrug resistance transporter MdfA. To our knowledge, this is the first report of Cam uptake into bacterial cells mediated by a specific transporter protein. Our findings suggest a specific bacterial transporter for drug uptake that might be targeted to promote greater antibiotic influx to increase cytoplasmic antibiotic concentration for enhanced cytotoxicity.
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Affiliation(s)
- Bala K Prabhala
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2100, Denmark and
| | - Nanda G Aduri
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2100, Denmark and
| | - Neha Sharma
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2100, Denmark and
| | - Aqsa Shaheen
- the Health Biotechnology Divisions, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Arpan Sharma
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2100, Denmark and
| | - Mazhar Iqbal
- the Health Biotechnology Divisions, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Paul R Hansen
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2100, Denmark and
| | - Christoffer Brasen
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2100, Denmark and
| | - Michael Gajhede
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2100, Denmark and
| | - Moazur Rahman
- the Health Biotechnology Divisions, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Osman Mirza
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2100, Denmark and
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8
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Sharma N, Aduri NG, Iqbal A, Prabhala BK, Mirza O. Peptide Selectivity of the Proton-Coupled Oligopeptide Transporter from Neisseria meningitidis. J Mol Microbiol Biotechnol 2016; 26:312-9. [DOI: 10.1159/000447129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 05/26/2016] [Indexed: 11/19/2022] Open
Abstract
Peptide transport in living organisms is facilitated by either primary transport, hydrolysis of ATP, or secondary transport, cotransport of protons. In this study, we focused on investigating the ligand specificity of the <i>Neisseria meningitidis</i> proton-coupled oligopeptide transporter (NmPOT). It has been shown that the gene encoding this transporter is upregulated during infection. NmPOT conformed to the typical chain length preference as observed in prototypical transporters of this family. In contrast to prototypical transporters, it was unable to accommodate a positively charged peptide residue at the C-terminus position of the substrate peptide. Sequence analysis of the active site of NmPOT displayed a distinctive aromatic patch, which has not been observed in any other transporters from this family. This aromatic patch may be involved in providing NmPOT with its atypical preferences. This study provides important novel information towards understanding how these transporters recognize their substrates.
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9
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Abstract
Mass spectrometry (MS) is well suited for analysis of the identity and purity of synthetic peptides. The sequence of a synthetic peptide is most often known, so the analysis is mainly used to confirm the identity and purity of the peptide. Here, simple procedures are described for MALDI-TOF-MS and LC-MS of synthetic peptides.
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Affiliation(s)
- Bala K Prabhala
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Paul R Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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10
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Aduri NG, Prabhala BK, Ernst HA, Jørgensen FS, Olsen L, Mirza O. Salt Bridge Swapping in the EXXERFXYY Motif of Proton-coupled Oligopeptide Transporters. J Biol Chem 2015; 290:29931-40. [PMID: 26483552 DOI: 10.1074/jbc.m115.675603] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Indexed: 01/12/2023] Open
Abstract
Proton-coupled oligopeptide transporters (POTs) couple the inward transport of di- or tripeptides with an inwardly directed transport of protons. Evidence from several studies of different POTs has pointed toward involvement of a highly conserved sequence motif, E1XXE2RFXYY (from here on referred to as E1XXE2R), located on Helix I, in interactions with the proton. In this study, we investigated the intracellular substrate accumulation by motif variants with all possible combinations of glutamate residues changed to glutamine and arginine changed to a tyrosine, the latter being a natural variant found in the Escherichia coli POT YjdL. We found that YjdL motif variants with E1XXE2R, E1XXE2Y, E1XXQ2Y, or Q1XXE2Y were able to accumulate peptide, whereas those with E1XXQ2R, Q1XXE2R, or Q1XXQ2Y were unable to accumulate peptide, and Q1XXQ2R abolished uptake. These results suggest a mechanism that involves swapping of an intramotif salt bridge, i.e. R-E2 to R-E1, which is consistent with previous structural studies. Molecular dynamics simulations of the motif variants E1XXE2R and E1XXQ2R support this mechanism. The simulations showed that upon changing conformation arginine pushes Helix V, through interactions with the highly conserved FYING motif, further away from the central cavity in what could be a stabilization of an inward facing conformation. As E2 has been suggested to be the primary site for protonation, these novel findings show how protonation may drive conformational changes through interactions of two highly conserved motifs.
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Affiliation(s)
- Nanda G Aduri
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Bala K Prabhala
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Heidi A Ernst
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Flemming S Jørgensen
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Lars Olsen
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Osman Mirza
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
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11
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Jensen JM, Aduri NG, Prabhala BK, Jahnsen R, Franzyk H, Mirza O. Critical role of a conserved transmembrane lysine in substrate recognition by the proton-coupled oligopeptide transporter YjdL. Int J Biochem Cell Biol 2014; 55:311-7. [PMID: 25261786 DOI: 10.1016/j.biocel.2014.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 09/12/2014] [Accepted: 09/15/2014] [Indexed: 11/16/2022]
Abstract
Proton-coupled oligopeptide transporters (POTs) utilize an electrochemical proton gradient to accumulate peptides in the cytoplasm. Changing the highly conserved active-site Lys117 in the Escherichia coli POT YjdL to glutamine resulted in loss of ligand affinity as well as inability to distinguish between a dipeptide ligand and the corresponding dipeptide amide. The radically changed pH(Bulk) profiles of Lys117Gln and Lys117Arg mutants indicate an important role of Lys117 in facilitating protonation of the transporter; a notion that is supported by the close proximity of Lys117 to the conserved ExxERFxYY POT motif previously shown to be involved in proton translocation. These results point toward a novel dual role of Lys117 in direct or indirect interaction with both proton and peptide.
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Affiliation(s)
- Johanne M Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nanda G Aduri
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bala K Prabhala
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Jahnsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Prabhala BK, Aduri NG, Hald H, Mirza O. Investigation of the Substrate Specificity of the Proton Coupled Peptide Transporter PepTSo from Shewanella oneidensis. Int J Pept Res Ther 2014. [DOI: 10.1007/s10989-014-9427-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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