1
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Wang M, Qing Y, Fan Q, Li S, Yan T, Amakye WK, Xu Y, Liu X, Ren J. Identification of the Wound Healing Activity Peptidome of Edible Bird's Nest Protein Hydrolysate and the In Silico Evaluation of Its Transport and Absorption Potential in Skin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12529-12540. [PMID: 38764367 DOI: 10.1021/acs.jafc.3c08611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
In this study, edible bird's nest (EBN) was proven to be a suitable source of bioactive peptides via enzymatic hydrolysis. The ultrafiltration component of the EBN peptides (EBNPs, Mw < 3 000 Da) could be responsible for moderate moisture retention and filaggrin synthesis. It was found that EBNP had a great capacity to protect HaCaT keratinocytes from DNA damage caused by UVB-irradiation and enhance wound healing by increasing the migratory and proliferative potential of cells. Furthermore, the external application of EBNP could effectively repair high glycolic acid concentration-induced skin burns in mice. A total of 1 188 peptides, predominantly the hydrophobic amino acids (e.g., Leu, Val, Tyr, Phe), were identified in the EBNP by liquid chromatography with tandem mass spectrometry (LC-MS/MS). Molecular docking showed that hydrophobic tripeptides from EBNP had a good binding affinity to proton-dependent oligopeptide transporter PepT1. Our data indicated that the hydrophobic amino acid-rich EBNP plays an important role in skin wound healing.
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Affiliation(s)
- Min Wang
- School of Food Science and Engineering, South China University of Technology, Wushan Road, Tianhe District, Guangzhou 510640, China
| | - Yinglu Qing
- School of Food Science and Engineering, South China University of Technology, Wushan Road, Tianhe District, Guangzhou 510640, China
| | - Qunyan Fan
- Bird's Nest Research Institute of Xiamen Yan Palace Seelong Biotechnology Co., Ltd., Xiamen 361100, China
| | - Shan Li
- School of Food Science and Engineering, South China University of Technology, Wushan Road, Tianhe District, Guangzhou 510640, China
| | - Tao Yan
- School of Food Science and Engineering, South China University of Technology, Wushan Road, Tianhe District, Guangzhou 510640, China
| | - William Kwame Amakye
- School of Food Science and Engineering, South China University of Technology, Wushan Road, Tianhe District, Guangzhou 510640, China
| | - Yongzhao Xu
- School of Food Science and Engineering, South China University of Technology, Wushan Road, Tianhe District, Guangzhou 510640, China
| | - Xuncai Liu
- School of Food Science and Engineering, South China University of Technology, Wushan Road, Tianhe District, Guangzhou 510640, China
- Bird's Nest Research Institute of Xiamen Yan Palace Seelong Biotechnology Co., Ltd., Xiamen 361100, China
| | - Jiaoyan Ren
- School of Food Science and Engineering, South China University of Technology, Wushan Road, Tianhe District, Guangzhou 510640, China
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2
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Newstead S, Parker J, Deme J, Lichtinger S, Kuteyi G, Biggin P, Lea S. Structural basis for antibiotic transport and inhibition in PepT2, the mammalian proton-coupled peptide transporter. RESEARCH SQUARE 2024:rs.3.rs-4435259. [PMID: 38903084 PMCID: PMC11188089 DOI: 10.21203/rs.3.rs-4435259/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The uptake and elimination of beta-lactam antibiotics in the human body are facilitated by the proton-coupled peptide transporters PepT1 (SLC15A1) and PepT2 (SLC15A2). The mechanism by which SLC15 family transporters recognize and discriminate between different drug classes and dietary peptides remains unclear, hampering efforts to improve antibiotic pharmacokinetics through targeted drug design and delivery. Here, we present cryo-EM structures of the mammalian proton-coupled peptide transporter, PepT2, in complex with the widely used beta-lactam antibiotics cefadroxil, amoxicillin and cloxacillin. Our structures, combined with pharmacophore mapping, molecular dynamics simulations and biochemical assays, establish the mechanism of antibiotic recognition and the important role of protonation in drug binding and transport.
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Affiliation(s)
| | | | - Justin Deme
- National Cancer Institute, National Institutes of Health
| | | | | | | | - Susan Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute
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3
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Kotov V, Killer M, Jungnickel KEJ, Lei J, Finocchio G, Steinke J, Bartels K, Strauss J, Dupeux F, Humm AS, Cornaciu I, Márquez JA, Pardon E, Steyaert J, Löw C. Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition. Cell Rep 2023; 42:112831. [PMID: 37467108 DOI: 10.1016/j.celrep.2023.112831] [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: 02/15/2023] [Revised: 06/09/2023] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
Proton-dependent oligopeptide transporters (POTs) are promiscuous transporters of the major facilitator superfamily that constitute the main route of entry for a wide range of dietary peptides and orally administrated peptidomimetic drugs. Given their clinical and pathophysiological relevance, several POT homologs have been studied extensively at the structural and molecular level. However, the molecular basis of recognition and transport of diverse peptide substrates has remained elusive. We present 14 X-ray structures of the bacterial POT DtpB in complex with chemically diverse di- and tripeptides, providing novel insights into the plasticity of the conserved central binding cavity. We analyzed binding affinities for more than 80 peptides and monitored uptake by a fluorescence-based transport assay. To probe whether all 8400 natural di- and tripeptides can bind to DtpB, we employed state-of-the-art molecular docking and machine learning and conclude that peptides with compact hydrophobic residues are the best DtpB binders.
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Affiliation(s)
- Vadim Kotov
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Maxime Killer
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany; Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Hamburg, Germany
| | - Katharina E J Jungnickel
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Jian Lei
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany; State Key Laboratory of Biotherapy and Cancer Center, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan 610041, People's Republic of China
| | - Giada Finocchio
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Josi Steinke
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Kim Bartels
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Jan Strauss
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Florine Dupeux
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - Anne-Sophie Humm
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - Irina Cornaciu
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - José A Márquez
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; VIB-VUB Center for Structural Biology, VIB, 1050 Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; VIB-VUB Center for Structural Biology, VIB, 1050 Brussels, Belgium
| | - Christian Löw
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany.
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4
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Omori A, Sasaki S, Kikukawa T, Shimono K, Miyauchi S. Elucidation of a Thermodynamical Feature Attributed to Substrate Binding to the Prokaryotic H +/Oligopeptide Cotransporter YdgR with Calorimetric Analysis: The Substrate Binding Driven by the Change in Entropy Implies the Release of Bound Water Molecules from the Binding Pocket. Biochemistry 2023. [PMID: 37163674 DOI: 10.1021/acs.biochem.2c00673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Here, we have elucidated the substrate recognition mechanism by a prokaryotic H+/oligopeptide cotransporter, YdgR, using isothermal titration calorimetry. Under acidic conditions (pH 6.0), the binding of a dipeptide, Val-Ala, to YdgR elicited endothermic enthalpy, which compensated for the increase in entropy due to dipeptide binding. A series of dipeptides were used in the binding titration. The dipeptides represent Val-X and X-Val, where X is Ala, Ser, Val, Tyr, or Phe. Most dipeptides revealed endothermic enthalpy, which was completely compensated by the increase in entropy due to dipeptide binding. The change in enthalpy due to binding correlated well with the change in entropy, whereas the Gibbs free energy involved in the binding of the dipeptide to YdgR remained unchanged irrespective of dipeptide sequences, implying that the binding reaction was driven by entropy, that is, the release of bound water molecules in the binding pocket. It is also important to clarify that, based on the prediction of water molecules in the ligand-binding pocket of YdgR, the release of three bound water molecules in the putative substrate binding pocket occurred through binding to YdgR. In the comparison of Val-X and X-Val dipeptides, the N-terminal region of the binding pocket might contain more bound water molecules than the C-terminal region. In light of these findings, we suggest that bound water molecules might play an important role in substrate recognition and binding by YdgR.
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Affiliation(s)
- Akiko Omori
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Shotaro Sasaki
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazumi Shimono
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda Nishi-ku, Kumamoto 860-0082, Japan
| | - Seiji Miyauchi
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
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5
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Gyimesi G, Hediger MA. Transporter-Mediated Drug Delivery. Molecules 2023; 28:molecules28031151. [PMID: 36770817 PMCID: PMC9919865 DOI: 10.3390/molecules28031151] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
Transmembrane transport of small organic and inorganic molecules is one of the cornerstones of cellular metabolism. Among transmembrane transporters, solute carrier (SLC) proteins form the largest, albeit very diverse, superfamily with over 400 members. It was recognized early on that xenobiotics can directly interact with SLCs and that this interaction can fundamentally determine their efficacy, including bioavailability and intertissue distribution. Apart from the well-established prodrug strategy, the chemical ligation of transporter substrates to nanoparticles of various chemical compositions has recently been used as a means to enhance their targeting and absorption. In this review, we summarize efforts in drug design exploiting interactions with specific SLC transporters to optimize their therapeutic effects. Furthermore, we describe current and future challenges as well as new directions for the advanced development of therapeutics that target SLC transporters.
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6
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Zhao Q, Capelli R, Carloni P, Lüscher B, Li J, Rossetti G. Enhanced Sampling Approach to the Induced-Fit Docking Problem in Protein-Ligand Binding: The Case of Mono-ADP-Ribosylation Hydrolase Inhibitors. J Chem Theory Comput 2021; 17:7899-7911. [PMID: 34813698 DOI: 10.1021/acs.jctc.1c00649] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enhanced sampling methods can predict free-energy landscapes associated with protein/ligand binding, characterizing the involved intermolecular interactions in a precise way. However, these in silico approaches can be challenged by induced-fit effects. Here, we present a variant of volume-based metadynamics tailored to tackle this problem in a general and efficient way. The validity of the approach is established by applying it to substrate/enzyme complexes of pharmacological relevance: mono-ADP-ribose (ADPr) in complex with mono-ADP-ribosylation hydrolases (MacroD1 and MacroD2), where induced-fit phenomena are known to be significant. The calculated binding free energies are consistent with experiments, with an absolute error smaller than 0.5 kcal/mol. Our simulations reveal that in all circumstances, the active loops, delimiting the boundaries of the binding site, undergo significant conformation rearrangements upon ligand binding. The calculations further provide, for the first time, the molecular basis of ADPr specificity and the relative changes in its experimental binding affinity on passing from MacroD1 to MacroD2 and all its mutants. Our study paves the way to the quantitative description of induced-fit events in molecular recognition.
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Affiliation(s)
- Qianqian Zhao
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.,College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Riccardo Capelli
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.,Department of Applied Science and Technology, Politecnico di Torino, Torino 10129, Italy
| | - Paolo Carloni
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.,Institute for Neuroscience and Medicine (INM)-11, Forschungszentrum Jülich, 52428 Jülich, Germany.,Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany.,Department of Neurology, RWTH Aachen University, 52062 Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, 52062 Aachen, Germany
| | - Jinyu Li
- College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Giulia Rossetti
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.,Jülich Supercomputing Center (JSC), Forschungszentrum Jülich, 52428 Jülich, Germany.,Department of Neurology, RWTH Aachen University, 52062 Aachen, Germany
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7
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Kell DB. The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes. Molecules 2021; 26:5629. [PMID: 34577099 PMCID: PMC8470029 DOI: 10.3390/molecules26185629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Mellizyme Biotechnology Ltd., IC1, Liverpool Science Park, Mount Pleasant, Liverpool L3 5TF, UK
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8
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Immadisetty K, Moradi M. Mechanistic Picture for Chemomechanical Coupling in a Bacterial Proton-Coupled Oligopeptide Transporter from Streptococcus Thermophilus. J Phys Chem B 2021; 125:9738-9750. [PMID: 34424716 DOI: 10.1021/acs.jpcb.1c03982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proton-coupled oligopeptide transporters (POTs) use the proton electrochemical gradient to transport peptides across the cell membrane. Despite the significant biological and biomedical relevance of these proteins, a detailed mechanistic picture for chemomechanical couplings involved in substrate/proton transport and protein structural changes is missing. Therefore, we performed microsecond-level molecular dynamics simulations of bacterial POT PepTSt, which shares ∼80% sequence identity with the human POT, PepT1, in the substrate-binding region. Three different conformational states of PepTSt were simulated, including (i) occluded, apo, (ii) inward-facing, apo, and (iii) inward-facingoccluded, Leu-Ala bound. We propose that the interaction of R33 with E299 and E300 acts as a conformational switch (i.e., to trigger the conformational change from an inward- to outward-facing state) in the substrate transport. Additionally, we propose that E299 and E400 disengage from interacting with the substrate either through protonation or through coordination with a cation for the substrate to get transported. This study provides clues to understand the chemomechanical couplings in POTs and paves the way to decipher the molecular-level underpinnings of the structure-function relationship in this important family of transporters.
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Affiliation(s)
| | - Mahmoud Moradi
- University of Arkansas, Fayetteville, Arkansas 72701, United States
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9
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Recent advances in understanding prodrug transport through the SLC15 family of proton-coupled transporters. Biochem Soc Trans 2021; 48:337-346. [PMID: 32219385 PMCID: PMC7200629 DOI: 10.1042/bst20180302] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/15/2020] [Accepted: 03/04/2020] [Indexed: 12/28/2022]
Abstract
Solute carrier (SLC) transporters play important roles in regulating the movement of small molecules and ions across cellular membranes. In mammals, they play an important role in regulating the uptake of nutrients and vitamins from the diet, and in controlling the distribution of their metabolic intermediates within the cell. Several SLC families also play an important role in drug transport and strategies are being developed to hijack SLC transporters to control and regulate drug transport within the body. Through the addition of amino acid and peptide moieties several novel antiviral and anticancer agents have been developed that hijack the proton-coupled oligopeptide transporters, PepT1 (SCL15A1) and PepT2 (SLC15A2), for improved intestinal absorption and renal retention in the body. A major goal is to understand the rationale behind these successes and expand the library of prodrug molecules that utilise SLC transporters. Recent co-crystal structures of prokaryotic homologues of the human PepT1 and PepT2 transporters have shed important new insights into the mechanism of prodrug recognition. Here, I will review recent developments in our understanding of ligand recognition and binding promiscuity within the SLC15 family, and discuss current models for prodrug recognition.
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10
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Wan S, Bhati AP, Zasada SJ, Coveney PV. Rapid, accurate, precise and reproducible ligand-protein binding free energy prediction. Interface Focus 2020; 10:20200007. [PMID: 33178418 PMCID: PMC7653346 DOI: 10.1098/rsfs.2020.0007] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2020] [Indexed: 02/06/2023] Open
Abstract
A central quantity of interest in molecular biology and medicine is the free energy of binding of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding affinity had been widely regarded as out of reach of theoretical methods owing to the lack of reproducibility of the available methods, not to mention their complexity, computational cost and time-consuming procedures. The lack of reproducibility stems primarily from the chaotic nature of classical molecular dynamics (MD) and the associated extreme sensitivity of trajectories to their initial conditions. Here, we review computational approaches for both relative and absolute binding free energy calculations, and illustrate their application to a diverse set of ligands bound to a range of proteins with immediate relevance in a number of medical domains. We focus on ensemble-based methods which are essential in order to compute statistically robust results, including two we have recently developed, namely thermodynamic integration with enhanced sampling and enhanced sampling of MD with an approximation of continuum solvent. Together, these form a set of rapid, accurate, precise and reproducible free energy methods. They can be used in real-world problems such as hit-to-lead and lead optimization stages in drug discovery, and in personalized medicine. These applications show that individual binding affinities equipped with uncertainty quantification may be computed in a few hours on a massive scale given access to suitable high-end computing resources and workflow automation. A high level of accuracy can be achieved using these approaches.
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Affiliation(s)
- Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Agastya P. Bhati
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Stefan J. Zasada
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Peter V. Coveney
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, 1098XH Amsterdam, The Netherlands
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11
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Studies of structural determinants of substrate binding in the Creatine Transporter (CreaT, SLC6A8) using molecular models. Sci Rep 2020; 10:6241. [PMID: 32277128 PMCID: PMC7148354 DOI: 10.1038/s41598-020-63189-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/26/2020] [Indexed: 01/17/2023] Open
Abstract
Creatine is a crucial metabolite that plays a fundamental role in ATP homeostasis in tissues with high-energy demands. The creatine transporter (CreaT, SLC6A8) belongs to the solute carrier 6 (SLC6) transporters family, and more particularly to the GABA transporters (GATs) subfamily. Understanding the molecular determinants of specificity within the SLC6 transporters in general, and the GATs in particular is very challenging due to the high similarity of these proteins. In the study presented here, our efforts focused on finding key structural features involved in binding selectivity for CreaT using structure-based computational methods. Due to the lack of three-dimensional structures of SLC6A8, our approach was based on the realization of two reliable homology models of CreaT using the structures of two templates, i.e. the human serotonin transporter (hSERT) and the prokaryotic leucine transporter (LeuT). Our models reveal that an optimal complementarity between the shape of the binding site and the size of the ligands is necessary for transport. These findings provide a framework for a deeper understanding of substrate selectivity of the SLC6 family and other LeuT fold transporters.
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12
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Jiang T, Wen PC, Trebesch N, Zhao Z, Pant S, Kapoor K, Shekhar M, Tajkhorshid E. Computational Dissection of Membrane Transport at a Microscopic Level. Trends Biochem Sci 2020; 45:202-216. [PMID: 31813734 PMCID: PMC7024014 DOI: 10.1016/j.tibs.2019.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/16/2019] [Accepted: 09/03/2019] [Indexed: 01/28/2023]
Abstract
Membrane transporters are key gatekeeper proteins at cellular membranes that closely control the traffic of materials. Their function relies on structural rearrangements of varying degrees that facilitate substrate translocation across the membrane. Characterizing these functionally important molecular events at a microscopic level is key to our understanding of membrane transport, yet challenging to achieve experimentally. Recent advances in simulation technology and computing power have rendered molecular dynamics (MD) simulation a powerful biophysical tool to investigate a wide range of dynamical events spanning multiple spatial and temporal scales. Here, we review recent studies of diverse membrane transporters using computational methods, with an emphasis on highlighting the technical challenges, key lessons learned, and new opportunities to illuminate transporter structure and function.
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Affiliation(s)
- Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Po-Chao Wen
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Noah Trebesch
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhiyu Zhao
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Karan Kapoor
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mrinal Shekhar
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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13
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Batista MRB, Watts A, José Costa-Filho A. Exploring Conformational Transitions and Free-Energy Profiles of Proton-Coupled Oligopeptide Transporters. J Chem Theory Comput 2019; 15:6433-6443. [PMID: 31639304 DOI: 10.1021/acs.jctc.9b00524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteins involved in peptide uptake and transport belong to the proton-coupled oligopeptide transporter (POT) family. Crystal structures of POT family members reveal a common fold consisting of two domains of six transmembrane α helices that come together to form a "V" shaped transporter with a central substrate binding site. Proton-coupled oligopeptide transporters operate through an alternate access mechanism, where the membrane transporter undergoes global conformational changes, alternating between inward-facing (IF), outward-facing (OF), and occluded (OC) states. Conformational transitions are promoted by proton and ligand binding; however, due to the absence of crystallographic models of the outward-open state, the role of H+ and ligands is still not fully understood. To provide a comprehensive picture of the POT conformational equilibrium, conventional and enhanced sampling molecular dynamics simulations of PepTst in the presence or absence of ligand and protonation were performed. Free-energy profiles of the conformational variability of PepTst were obtained from microseconds of adaptive biasing force (ABF) simulations. Our results reveal that both proton and ligand significantly change the conformational free-energy landscape. In the absence of ligand and protonation, only transitions involving IF and OC states are allowed. After protonation of the residue Glu300, the wider free-energy well for Glu300 protonated PepTst indicates a greater conformational variability relative to the apo system, and OF conformations became accessible. For the Glu300 protonated Holo-PepTst, the presence of a second free-energy minimum suggests that OF conformations are not only accessible, but also stable. The differences in the free-energy profiles demonstrate that transitions toward outward-facing conformation occur only after protonation, which is likely the first step in the mechanism of peptide transport. Our extensive ABF simulations provide a fully atomic description of all states of the transport process, offering a model for the alternating access mechanism and how protonation and ligand control the conformational changes.
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Affiliation(s)
- Mariana R B Batista
- Ribeirão Preto School of Philosophy, Sciences and Letters , University of São Paulo , Ribeirao Preto , São Paulo 14040901 , Brazil
| | - Anthony Watts
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 2JD , United Kingdom
| | - Antonio José Costa-Filho
- Ribeirão Preto School of Philosophy, Sciences and Letters , University of São Paulo , Ribeirao Preto , São Paulo 14040901 , Brazil
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14
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Garibsingh RAA, Schlessinger A. Advances and Challenges in Rational Drug Design for SLCs. Trends Pharmacol Sci 2019; 40:790-800. [PMID: 31519459 DOI: 10.1016/j.tips.2019.08.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 01/25/2023]
Abstract
There are over 420 human solute carrier (SLC) transporters from 65 families that are expressed ubiquitously in the body. The SLCs mediate the movement of ions, drugs, and metabolites across membranes and their dysfunction has been associated with a variety of diseases, such as diabetes, cancer, and central nervous system (CNS) disorders. Thus, SLCs are emerging as important targets for therapeutic intervention. Recent technological advances in experimental and computational biology allow better characterization of SLC pharmacology. Here we describe recent approaches to modulate SLC transporter function, with an emphasis on the use of computational approaches and computer-aided drug design (CADD) to study nutrient transporters. Finally, we discuss future perspectives in the rational design of SLC drugs.
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Affiliation(s)
- Rachel-Ann A Garibsingh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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15
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Ural-Blimke Y, Flayhan A, Strauss J, Rantos V, Bartels K, Nielsen R, Pardon E, Steyaert J, Kosinski J, Quistgaard EM, Löw C. Structure of Prototypic Peptide Transporter DtpA from E. coli in Complex with Valganciclovir Provides Insights into Drug Binding of Human PepT1. J Am Chem Soc 2019; 141:2404-2412. [DOI: 10.1021/jacs.8b11343] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yonca Ural-Blimke
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Ali Flayhan
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Jan Strauss
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Vasileios Rantos
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Kim Bartels
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Rolf Nielsen
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels 1050, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels 1050, Belgium
| | - Jan Kosinski
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Esben M. Quistgaard
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177 Stockholm, Sweden
- Department of Molecular Biology and Genetics − DANDRITE, Gustav Wieds Vej 10, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607 Hamburg, Germany
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177 Stockholm, Sweden
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16
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Structural basis for prodrug recognition by the SLC15 family of proton-coupled peptide transporters. Proc Natl Acad Sci U S A 2019; 116:804-809. [PMID: 30602453 PMCID: PMC6338836 DOI: 10.1073/pnas.1813715116] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Poor oral bioavailability is one of the leading causes of compound failure in drug development and a major challenge for the pharmaceutical industry. A successful approach to address this challenge has been the development of prodrugs that target the intestinal peptide transporter, PepT1 (SLC15A1). PepT1 exhibits a remarkably promiscuous binding site and is known to transport many different drug molecules, making it an excellent target for prodrug design and delivery. However, the structural basis for drug recognition remains largely unknown. Here we present the structure of a bacterial homolog of PepT1 bound to both an antiviral prodrug, valacyclovir, and anticancer drug 5-aminolevulinic acid. These structures enable a pharmacophore model to be developed that will aid future prodrug design. A major challenge in drug development is the optimization of intestinal absorption and cellular uptake. A successful strategy has been to develop prodrug molecules, which hijack solute carrier (SLC) transporters for active transport into the body. The proton-coupled oligopeptide transporters, PepT1 and PepT2, have been successfully targeted using this approach. Peptide transporters display a remarkable capacity to recognize a diverse library of di- and tripeptides, making them extremely promiscuous and major contributors to the pharmacokinetic profile of several important drug classes, including beta-lactam antibiotics and antiviral and antineoplastic agents. Of particular interest has been their ability to recognize amino acid and peptide-based prodrug molecules, thereby providing a rational approach to improving drug transport into the body. However, the structural basis for prodrug recognition has remained elusive. Here we present crystal structures of a prokaryotic homolog of the mammalian transporters in complex with the antiviral prodrug valacyclovir and the peptide-based photodynamic therapy agent, 5-aminolevulinic acid. The valacyclovir structure reveals that prodrug recognition is mediated through both the amino acid scaffold and the ester bond, which is commonly used to link drug molecules to the carrier’s physiological ligand, whereas 5-aminolevulinic acid makes far fewer interactions compared with physiological peptides. These structures provide a unique insight into how peptide transporters interact with xenobiotic molecules and provide a template for further prodrug development.
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17
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Schlessinger A, Welch MA, van Vlijmen H, Korzekwa K, Swaan PW, Matsson P. Molecular Modeling of Drug-Transporter Interactions-An International Transporter Consortium Perspective. Clin Pharmacol Ther 2018; 104:818-835. [PMID: 29981151 PMCID: PMC6197929 DOI: 10.1002/cpt.1174] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/30/2018] [Indexed: 12/31/2022]
Abstract
Membrane transporters play diverse roles in the pharmacokinetics and pharmacodynamics of small-molecule drugs. Understanding the mechanisms of drug-transporter interactions at the molecular level is, therefore, essential for the design of drugs with optimal therapeutic effects. This white paper examines recent progress, applications, and challenges of molecular modeling of membrane transporters, including modeling techniques that are centered on the structures of transporter ligands, and those focusing on the structures of the transporters. The goals of this article are to illustrate current best practices and future opportunities in using molecular modeling techniques to understand and predict transporter-mediated effects on drug disposition and efficacy.Membrane transporters from the solute carrier (SLC) and ATP-binding cassette (ABC) superfamilies regulate the cellular uptake, efflux, and homeostasis of many essential nutrients and significantly impact the pharmacokinetics of drugs; further, they may provide targets for novel therapeutics as well as facilitate prodrug approaches. Because of their often broad substrate selectivity they are also implicated in many undesirable and sometimes life-threatening drug-drug interactions (DDIs).5,6.
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Affiliation(s)
- Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Matthew A. Welch
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD
| | - Herman van Vlijmen
- Computational Chemistry, Discovery Sciences, Janssen Research & Development, Beerse, Belgium
| | - Ken Korzekwa
- Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA
| | - Peter W. Swaan
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD
| | - Pär Matsson
- Department of Pharmacy, Uppsala University, Sweden
,Address correspondence to: Pär Matsson, Department of Pharmacy, Uppsala University, Box 580, SE-75123 Uppsala, Sweden, Phone: +46-(0)18-471 46 30, Fax: +46-(0)18-471 42 23,
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18
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Smith PW, Zuccotto F, Bates RH, Martinez-Martinez MS, Read KD, Peet C, Epemolu O. Pharmacokinetics of β-Lactam Antibiotics: Clues from the Past To Help Discover Long-Acting Oral Drugs in the Future. ACS Infect Dis 2018; 4:1439-1447. [PMID: 30141902 PMCID: PMC6189874 DOI: 10.1021/acsinfecdis.8b00160] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
β-Lactams
represent perhaps the most important class of antibiotics
yet discovered. However, despite many years of active research, none
of the currently approved drugs in this class combine oral activity
with long duration of action. Recent developments suggest that new
β-lactam antibiotics with such a profile would have utility
in the treatment of tuberculosis. Consequently, the historical β-lactam
pharmacokinetic data have been compiled and analyzed to identify possible
directions and drug discovery strategies aimed toward new β-lactam
antibiotics with this profile.
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Affiliation(s)
| | - Fabio Zuccotto
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee. DDI 5EH, U.K
| | - Robert H. Bates
- Global Health R&D, GlaxoSmithKline, Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | | | - Kevin D. Read
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee. DDI 5EH, U.K
| | - Caroline Peet
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee. DDI 5EH, U.K
| | - Ola Epemolu
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee. DDI 5EH, U.K
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19
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Fowler PW, Cole K, Gordon NC, Kearns AM, Llewelyn MJ, Peto TEA, Crook DW, Walker AS. Robust Prediction of Resistance to Trimethoprim in Staphylococcus aureus. Cell Chem Biol 2018; 25:339-349.e4. [PMID: 29307840 DOI: 10.1016/j.chembiol.2017.12.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/24/2017] [Accepted: 12/08/2017] [Indexed: 01/28/2023]
Abstract
The rise of antibiotic resistance threatens modern medicine; to combat it new diagnostic methods are required. Sequencing the whole genome of a pathogen offers the potential to accurately determine which antibiotics will be effective to treat a patient. A key limitation of this approach is that it cannot classify rare or previously unseen mutations. Here we demonstrate that alchemical free energy methods, a well-established class of methods from computational chemistry, can successfully predict whether mutations in Staphylococcus aureus dihydrofolate reductase confer resistance to trimethoprim. We also show that the method is quantitatively accurate by calculating how much the most common resistance-conferring mutation, F99Y, reduces the binding free energy of trimethoprim and comparing predicted and experimentally measured minimum inhibitory concentrations for seven different mutations. Finally, by considering up to 32 free energy calculations for each mutation, we estimate its specificity and sensitivity.
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Affiliation(s)
- Philip W Fowler
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK.
| | - Kevin Cole
- Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, Brighton and Sussex Medical School, Brighton BN1 9PS, UK
| | - N Claire Gordon
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK
| | - Angela M Kearns
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, Colindale NW9 5EQ, UK
| | - Martin J Llewelyn
- Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, Brighton and Sussex Medical School, Brighton BN1 9PS, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK
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20
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Samsudin F, Boags A, Piggot TJ, Khalid S. Braun's Lipoprotein Facilitates OmpA Interaction with the Escherichia coli Cell Wall. Biophys J 2017; 113:1496-1504. [PMID: 28978443 DOI: 10.1016/j.bpj.2017.08.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/13/2017] [Accepted: 08/02/2017] [Indexed: 11/29/2022] Open
Abstract
Gram-negative bacteria such as Escherichia coli are protected by a complex cell envelope. The development of novel therapeutics against these bacteria necessitates a molecular level understanding of the structure-dynamics-function relationships of the various components of the cell envelope. We use atomistic MD simulations to reveal the details of covalent and noncovalent protein interactions that link the outer membrane to the aqueous periplasmic region. We show that the Braun's lipoprotein tilts and bends, and thereby lifts the cell wall closer to the outer membrane. Both monomers and dimers of the outer membrane porin OmpA can interact with peptidoglycan in the presence of Braun's lipoprotein, but in the absence of the latter, only dimers of OmpA show a propensity to form contacts with peptidoglycan. Our study provides a glimpse of how the molecular components of the bacterial cell envelope interact with each other to mediate cell wall attachment in E. coli.
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Affiliation(s)
- Firdaus Samsudin
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
| | - Alister Boags
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
| | - Thomas J Piggot
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom; CBR Division, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom.
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21
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Colas C, Masuda M, Sugio K, Miyauchi S, Hu Y, Smith DE, Schlessinger A. Chemical Modulation of the Human Oligopeptide Transporter 1, hPepT1. Mol Pharm 2017; 14:4685-4693. [PMID: 29111754 DOI: 10.1021/acs.molpharmaceut.7b00775] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In humans, peptides derived from dietary proteins and peptide-like drugs are transported via the proton-dependent oligopeptide transporter hPepT1 (SLC15A1). hPepT1 is located across the apical membranes of the small intestine and kidney, where it serves as a high-capacity low-affinity transporter of a broad range of di- and tripeptides. hPepT1 is also overexpressed in the colon of inflammatory bowel disease (IBD) patients, where it mediates the transport of harmful peptides of bacterial origin. Therefore, hPepT1 is a drug target for prodrug substrates interacting with intracellular proteins or inhibitors blocking the transport of toxic bacterial products. In this study, we construct multiple structural models of hPepT1 representing different conformational states that occur during transport and inhibition. We then identify and characterize five ligands of hPepT1 using computational methods, such as virtual screening and QM-polarized ligand docking (QPLD), and experimental testing with uptake kinetic measurements and electrophysiological assays. Our results improve our understanding of the substrate and inhibitor specificity of hPepT1. Furthermore, the newly discovered ligands exhibit unique chemotypes, providing a framework for developing tool compounds with optimal intestinal absorption as well as future IBD therapeutics against this emerging drug target.
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Affiliation(s)
- Claire Colas
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Masayuki Masuda
- Faculty of Pharmaceutical Sciences, Toho University , Funabashi, Chiba 274-8510, Japan
| | - Kazuaki Sugio
- Faculty of Pharmaceutical Sciences, Toho University , Funabashi, Chiba 274-8510, Japan
| | - Seiji Miyauchi
- Faculty of Pharmaceutical Sciences, Toho University , Funabashi, Chiba 274-8510, Japan
| | - Yongjun Hu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - David E Smith
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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22
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23
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Symmetry and Structure in the POT Family of Proton Coupled Peptide Transporters. Symmetry (Basel) 2017. [DOI: 10.3390/sym9060085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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24
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Aldeghi M, Heifetz A, Bodkin MJ, Knapp S, Biggin PC. Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations. J Am Chem Soc 2017; 139:946-957. [PMID: 28009512 PMCID: PMC5253712 DOI: 10.1021/jacs.6b11467] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Binding selectivity is a requirement for the development of a safe drug, and it is a critical property for chemical probes used in preclinical target validation. Engineering selectivity adds considerable complexity to the rational design of new drugs, as it involves the optimization of multiple binding affinities. Computationally, the prediction of binding selectivity is a challenge, and generally applicable methodologies are still not available to the computational and medicinal chemistry communities. Absolute binding free energy calculations based on alchemical pathways provide a rigorous framework for affinity predictions and could thus offer a general approach to the problem. We evaluated the performance of free energy calculations based on molecular dynamics for the prediction of selectivity by estimating the affinity profile of three bromodomain inhibitors across multiple bromodomain families, and by comparing the results to isothermal titration calorimetry data. Two case studies were considered. In the first one, the affinities of two similar ligands for seven bromodomains were calculated and returned excellent agreement with experiment (mean unsigned error of 0.81 kcal/mol and Pearson correlation of 0.75). In this test case, we also show how the preferred binding orientation of a ligand for different proteins can be estimated via free energy calculations. In the second case, the affinities of a broad-spectrum inhibitor for 22 bromodomains were calculated and returned a more modest accuracy (mean unsigned error of 1.76 kcal/mol and Pearson correlation of 0.48); however, the reparametrization of a sulfonamide moiety improved the agreement with experiment.
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Affiliation(s)
- Matteo Aldeghi
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
| | - Alexander Heifetz
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Michael J Bodkin
- Evotec (U.K.) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Stefan Knapp
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7BN, U.K.,Institute for Pharmaceutical Chemistry, Goethe University Frankfurt , 60438 Frankfurt, Germany
| | - Philip C Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
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25
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Newstead S. Recent advances in understanding proton coupled peptide transport via the POT family. Curr Opin Struct Biol 2016; 45:17-24. [PMID: 27865112 DOI: 10.1016/j.sbi.2016.10.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/22/2016] [Accepted: 10/26/2016] [Indexed: 10/20/2022]
Abstract
The POT family of membrane transporters use the inwardly directed proton electrochemical gradient to drive the uptake of essential nutrients into the cell. Originally discovered in bacteria, members of the family have been found in all kingdoms of life except the archaea. A remarkable feature of the family is their diverse substrate promiscuity. Whereas in mammals and bacteria they are predominantly di- and tri-peptide transporters, in plants the family has diverged to recognize nitrate, plant defence compounds and hormones. This promiscuity has led to the development of peptide-based pro-drugs that use PepT1 and PepT2, the mammalian homologues, to improve oral drug delivery. Recent crystal structures from bacterial and plant members of the family have revealed conserved features of the ligand-binding site and provided insights into post-translational regulation. Here I review the current understanding of transport, ligand promiscuity and regulation within the POT family.
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Affiliation(s)
- Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
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26
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Di- and tripeptide transport in vertebrates: the contribution of teleost fish models. J Comp Physiol B 2016; 187:395-462. [PMID: 27803975 DOI: 10.1007/s00360-016-1044-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/12/2016] [Accepted: 10/20/2016] [Indexed: 02/06/2023]
Abstract
Solute Carrier 15 (SLC15) family, alias H+-coupled oligopeptide cotransporter family, is a group of membrane transporters known for their role in the cellular uptake of di- and tripeptides (di/tripeptides) and peptide-like molecules. Of its members, SLC15A1 (PEPT1) chiefly mediates intestinal absorption of luminal di/tripeptides from dietary protein digestion, while SLC15A2 (PEPT2) mainly allows renal tubular reabsorption of di/tripeptides from ultrafiltration, SLC15A3 (PHT2) and SLC15A4 (PHT1) possibly interact with di/tripeptides and histidine in certain immune cells, and SLC15A5 has unknown function. Our understanding of this family in vertebrates has steadily increased, also due to the surge of genomic-to-functional information from 'non-conventional' animal models, livestock, poultry, and aquaculture fish species. Here, we review the literature on the SLC15 transporters in teleost fish with emphasis on SLC15A1 (PEPT1), one of the solute carriers better studied amongst teleost fish because of its relevance in animal nutrition. We report on the operativity of the transporter, the molecular diversity, and multiplicity of structural-functional solutions of the teleost fish orthologs with respect to higher vertebrates, its relevance at the intersection of the alimentary and osmoregulative functions of the gut, its response under various physiological states and dietary solicitations, and its possible involvement in examples of total body plasticity, such as growth and compensatory growth. By a comparative approach, we also review the few studies in teleost fish on SLC15A2 (PEPT2), SLC15A4 (PHT1), and SLC15A3 (PHT2). By representing the contribution of teleost fish to the knowledge of the physiology of di/tripeptide transport and transporters, we aim to fill the gap between higher and lower vertebrates.
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27
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Colas C, Smith DE, Schlessinger A. Computing Substrate Selectivity in a Peptide Transporter. Cell Chem Biol 2016; 23:211-213. [PMID: 26971872 DOI: 10.1016/j.chembiol.2016.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The human proton-coupled peptide transporter 1 (PepT1) is responsible for the absorption of di- and tri-peptides from the diet and peptide-like drugs. In this issue of Cell Chemical Biology, Samsudin et al. (2016) use an integrated computational and experimental approach to provide new insights into understanding substrate selectivity of PepTSt, a prokaryotic homolog of the human PepT1.
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Affiliation(s)
- Claire Colas
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David E Smith
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Avner Schlessinger
- Departments of Pharmacology and Systems Therapeutics, and Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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28
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Colas C, Ung PMU, Schlessinger A. SLC Transporters: Structure, Function, and Drug Discovery. MEDCHEMCOMM 2016; 7:1069-1081. [PMID: 27672436 PMCID: PMC5034948 DOI: 10.1039/c6md00005c] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The human Solute Carrier (SLC) transporters are important targets for drug development. Structure-based drug discovery for SLC transporters requires the description of their structure, dynamics, and mechanism of interaction with small molecule ligands and ions. The recent determination of atomic structures of human SLC transporters and their homologs, combined with improved computational power and prediction methods have led to an increased applicability of structure-based drug design methods for human SLC members. In this review, we provide an overview of the SLC transporters' structures and transport mechanisms. We then describe computational techniques, such as homology modeling and virtual screening that are emerging as key tools to discover chemical probes for human SLC members. We illustrate the utility of these methods by presenting case studies in which rational integration of computation and experiment was used to characterize SLC members that transport key nutrients and metabolites, including the amino acid transporters LAT-1 and ASCT2, the SLC13 family of citric acid cycle intermediate transporters, and the glucose transporter GLUT1. We conclude with a brief discussion about future directions in structure-based drug discovery for the human SLC superfamily, one of the most structurally and functionally diverse protein families in human.
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Affiliation(s)
- Claire Colas
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Peter Man-Un Ung
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Avner Schlessinger
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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