1
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Verma NK, Raghav N. Molecular modeling of cellulose tosylate immobilized α-amylases: An in silico case study through MD simulation and refinement. Int J Biol Macromol 2024; 290:138808. [PMID: 39694388 DOI: 10.1016/j.ijbiomac.2024.138808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 11/24/2024] [Accepted: 12/14/2024] [Indexed: 12/20/2024]
Abstract
The use of enzymes as catalysts in industrial processes has been studied, and they offer more ecologically friendly options for chemical reactions. In the current work, we investigated the potential of molecular modeling to solve the ordinarily difficult problem of identifying the amino acids involved in the covalent mode of immobilization by in silico investigations. The immobilized α-Amylase on Cellulose tosylate (henceforth referred to as Celltos) shows extra peaks of OH and NH2, CN, SO, C-O-C, and CS. Celltos exhibits distinct ether, imine, and CS peaks, indicating the potential contribution of α-Amylase's hydroxyl, amino, and thiol groups towards immobilization with cellulose's tosylate group. The native amylase was processed for Molecular Dynamics simulation. The simulated amylase was found to be the root mean squarely deviated to 1.16 Å. Autodock Vina, GOLD, SwissDock, and iGemdock generate output averages of 6.164, 6.549, 9.313 & 137.811 and 5.903, 7.656, 9.752 & 132.218 for an unrefined and refined dataset, respectively. The catalytic site intactness values for unrefined and refined SAT9, SAT13, and LAT21 were 83.3 %, 100 %, 100 %, and 8.33 %, 0 %, and 0 %, respectively. Our findings were additionally confirmed by bond distance similarity computations.
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Affiliation(s)
| | - Neera Raghav
- Chemistry Department, Kurukshetra University, Kurukshetra 136119, Haryana, India.
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2
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Ben Mariem O, Palazzolo L, Torre B, Wei Y, Bianchi D, Guerrini U, Laurenzi T, Saporiti S, De Fabiani E, Pochini L, Indiveri C, Eberini I. Atomistic description of the OCTN1 recognition mechanism via in silico methods. PLoS One 2024; 19:e0304512. [PMID: 38829838 PMCID: PMC11146731 DOI: 10.1371/journal.pone.0304512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
The Organic Cation Transporter Novel 1 (OCTN1), also known as SLC22A4, is widely expressed in various human tissues, and involved in numerous physiological and pathological processes remains. It facilitates the transport of organic cations, zwitterions, with selectivity for positively charged solutes. Ergothioneine, an antioxidant compound, and acetylcholine (Ach) are among its substrates. Given the lack of experimentally solved structures of this protein, this study aimed at generating a reliable 3D model of OCTN1 to shed light on its substrate-binding preferences and the role of sodium in substrate recognition and transport. A chimeric model was built by grafting the large extracellular loop 1 (EL1) from an AlphaFold-generated model onto a homology model. Molecular dynamics simulations revealed domain-specific mobility, with EL1 exhibiting the highest impact on overall stability. Molecular docking simulations identified cytarabine and verapamil as highest affinity ligands, consistent with their known inhibitory effects on OCTN1. Furthermore, MM/GBSA analysis allowed the categorization of substrates into weak, good, and strong binders, with molecular weight strongly correlating with binding affinity to the recognition site. Key recognition residues, including Tyr211, Glu381, and Arg469, were identified through interaction analysis. Ach demonstrated a low interaction energy, supporting the hypothesis of its one-directional transport towards to outside of the membrane. Regarding the role of sodium, our model suggested the involvement of Glu381 in sodium binding. Molecular dynamics simulations of systems at increasing levels of Na+ concentrations revealed increased sodium occupancy around Glu381, supporting experimental data associating Na+ concentration to molecule transport. In conclusion, this study provides valuable insights into the 3D structure of OCTN1, its substrate-binding preferences, and the role of sodium in the recognition. These findings contribute to the understanding of OCTN1 involvement in various physiological and pathological processes and may have implications for drug development and disease management.
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Affiliation(s)
- Omar Ben Mariem
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Beatrice Torre
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Yao Wei
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Davide Bianchi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Uliano Guerrini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Tommaso Laurenzi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Simona Saporiti
- Analytical Excellence and Program Management, Merck Serono S.p.A., Rome, Italy
| | - Emma De Fabiani
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Lorena Pochini
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata CS, Italy
| | - Cesare Indiveri
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata CS, Italy
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
- DSRC, Università degli Studi di Milano, Milan, Italy
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3
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Ben Mariem O, Saporiti S, Guerrini U, Laurenzi T, Palazzolo L, Indiveri C, Barile M, De Fabiani E, Eberini I. In silico investigation on structure-function relationship of members belonging to the human SLC52 transporter family. Proteins 2022; 91:619-633. [PMID: 36511838 DOI: 10.1002/prot.26453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/18/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022]
Abstract
Riboflavin is an essential water-soluble vitamin that needs to be provided through the diet because of the conversion into flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN), important cofactors in hundreds of flavoenzymes. The adsorption and distribution of riboflavin is mediated by transmembrane transporters of the SLC52 family, namely RFVT1-3, whose mutations are mainly associated with two diseases, MADD and the Brown-Vialetto-Van Laere syndrome. Interest in RFVTs as pharmacological targets has increased in the last few years due to their overexpression in several cancer cells, which can be exploited both by blocking the uptake of riboflavin into the cancerous cells, and by performing cancer targeted delivery of drugs with a high affinity for RFVTs. In this work, we propose three-dimensional structural models for all three human riboflavin transporters obtained by state-of-the-art artificial intelligence-based methods, which were then further refined with molecular dynamics simulations. Furthermore, two of the most notable mutations concerning RFVT2 and RFVT3 (W31S and N21S, respectively) were investigated studying the interactions between the wild-type and mutated transporters with riboflavin.
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Affiliation(s)
- Omar Ben Mariem
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Giuseppe Balzaretti 9, Milan, Italy
| | - Simona Saporiti
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Giuseppe Balzaretti 9, Milan, Italy
| | - Uliano Guerrini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Giuseppe Balzaretti 9, Milan, Italy
| | - Tommaso Laurenzi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Giuseppe Balzaretti 9, Milan, Italy
| | - Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Giuseppe Balzaretti 9, Milan, Italy
| | - Cesare Indiveri
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy.,Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via P. Bucci cubo 4C, Arcavacata di Rende, Italy
| | - Maria Barile
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari A.Moro, Bari, Italy
| | - Emma De Fabiani
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Giuseppe Balzaretti 9, Milan, Italy
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Giuseppe Balzaretti 9, Milan, Italy.,DSRC, Università degli Studi di Milano, Milan, Italy
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4
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Megariotis G, Mikaelian G, Avramopoulos A, Romanos N, Theodorou DN. Molecular simulations of fluoxetine in hydrated lipid bilayers, as well as in aqueous solutions containing β-cyclodextrin. J Mol Graph Model 2022; 117:108305. [PMID: 35987186 DOI: 10.1016/j.jmgm.2022.108305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/25/2022] [Accepted: 08/06/2022] [Indexed: 01/14/2023]
Abstract
Fluoxetine, which is a well-known antidepressant drug, is studied in hydrated cholesterol-free and cholesterol-containing lipid bilayers through unbiased and biased atomistic molecular dynamics simulations. The latter are conducted for the calculation of the potential of mean force (PMF) of fluoxetine along an axis perpendicular to the two leaflets of the bilayer. The PMF indicates that the drug prefers to reside inside the lipid phase and allows us to calculate important thermodynamic properties, such as the Gibbs energy difference of partitioning from the water to the lipid phase and the Gibbs energy barrier for hopping events between the two leaflets of the bilayer. The results from the biased simulations are in accord with the mass density profiles calculated from the unbiased simulations. Moreover, we estimate the effect of fluoxetine mole fraction on the order parameters of the lipid alkyl chains and on the area per lipid. It is also found that fluoxetine forms a hydrogen bond network with lipids and water molecules penetrating into the lipid phase. In addition, fluoxoetine is studied in detail in aqueous solutions containing β-cyclodextrin. It is observed from unbiased molecular dynamics simulations that the two aforementioned molecules form a noncovalent complex spontaneously and the calculated binding free energy is in agreement with the literature.
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Affiliation(s)
- Grigorios Megariotis
- School of Chemical Engineering, National Technical University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, Athens, GR, 15780, Greece.
| | - Georgios Mikaelian
- School of Chemical Engineering, National Technical University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, Athens, GR, 15780, Greece
| | - Aggelos Avramopoulos
- Department of Physics, University of Thessaly, 3rd Km Old National Road Lamia Athens, Lamia, GR, 35100, Greece
| | - Nikolaos Romanos
- School of Chemical Engineering, National Technical University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, Athens, GR, 15780, Greece
| | - Doros N Theodorou
- School of Chemical Engineering, National Technical University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, Athens, GR, 15780, Greece
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5
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Cappoli N, Jenkinson MD, Russo CD, Dickens D. LAT1, a novel pharmacological target for the treatment of glioblastoma. Biochem Pharmacol 2022; 201:115103. [PMID: 35618000 DOI: 10.1016/j.bcp.2022.115103] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 11/02/2022]
Abstract
The L-Type Amino Acid transporter, LAT1 (SLC7A5), has a crucial role in mediating amino acid uptake into the cells, thus modulating cell growth and proliferation as well as other intracellular functions. Different studies have reported a central role of LAT1 in glioblastoma development and progression, suggesting that the modulation of its activity could be a novel therapeutic strategy. LAT1 also has an important role in the peripheral immune system, by regulating the activation status of several immune cells through modulation of the mechanistic target of rapamycin kinase. In glioblastoma (GBM), the blood-brain barrier is disrupted, which allows the recruitment of peripheral immune cells to the tumour site. These cells, together with resident microglia, contribute to cancer growth and progression. Currently, little is known about the function of LAT1 in the reprogramming of the immune component of the tumour microenvironment in the context of GBM. In this article, we review the available data on the role of LAT1 in the regulation of GBM biology, including its potential role in the tumour microenvironment, particularly in infiltrating-peripheral immune cells and resident microglial cells. In addition, we review the available data on the main pharmacological inhibitors of LAT1, aiming to evaluate their possible role as novel therapeutics for GBM.
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Affiliation(s)
- Natalia Cappoli
- Department of Healthcare Surveillance and Bioethics, Section of Pharmacology, Università Cattolica del Sacro Cuore-Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Michael D Jenkinson
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology (ISMIB), University of Liverpool, Liverpool, United Kingdom; Department of Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
| | - Cinzia Dello Russo
- Department of Healthcare Surveillance and Bioethics, Section of Pharmacology, Università Cattolica del Sacro Cuore-Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology (ISMIB), University of Liverpool, Liverpool, United Kingdom.
| | - David Dickens
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology (ISMIB), University of Liverpool, Liverpool, United Kingdom
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6
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Huttunen J, Agami M, Tampio J, Montaser AB, Huttunen KM. Comparison of Experimental Strategies to Study l-Type Amino Acid Transporter 1 (LAT1) Utilization by Ligands. Molecules 2021; 27:molecules27010037. [PMID: 35011270 PMCID: PMC8746705 DOI: 10.3390/molecules27010037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 01/08/2023] Open
Abstract
l-Type amino acid transporter 1 (LAT1), expressed abundantly in the brain and placenta and overexpressed in several cancer cell types, has gained a lot of interest in drug research and development, as it can be utilized for brain-targeted drug delivery, as well as inhibiting the essential amino acid supply to cancer cells. The structure of LAT1 is today very well-known and the interactions of ligands at the binding site of LAT1 can be modeled and explained. However, less is known of LAT1′s life cycle within the cells. Moreover, the functionality of LAT1 can be measured by several different methods, which may vary between the laboratories and make the comparison of the results challenging. In the present study, the usefulness of indirect cis-inhibition methods and direct cellular uptake methods and their variations to interpret the interactions of LAT1-ligands were evaluated. Moreover, this study also highlights the importance of understanding the intracellular kinetics of LAT1-ligands, and how they can affect the regular function of LAT1 in critical tissues, such as the brain. Hence, it is discussed herein how the selected methodology influences the outcome and created knowledge of LAT1-utilizing compounds.
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7
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Walczewska-Szewc K, Nowak W. Photo-Switchable Sulfonylureas Binding to ATP-Sensitive Potassium Channel Reveal the Mechanism of Light-Controlled Insulin Release. J Phys Chem B 2021; 125:13111-13121. [PMID: 34825567 PMCID: PMC8667036 DOI: 10.1021/acs.jpcb.1c07292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/13/2021] [Indexed: 11/29/2022]
Abstract
ATP-sensitive potassium (KATP) channels are present in numerous organs, including the heart, brain, and pancreas. Physiological opening and closing of KATPs present in pancreatic β-cells, in response to changes in the ATP/ADP concentration ratio, are correlated with insulin release into the bloodstream. Sulfonylurea drugs, commonly used in type 2 diabetes mellitus treatment, bind to the octamer KATP channels composed of four pore-forming Kir6.2 and four SUR1 subunits and increase the probability of insulin release. Azobenzene-based derivatives of sulfonylureas, such as JB253 inspired by well-established antidiabetic drug glimepiride, allow for control of this process by light. The mechanism of that phenomenon was not known until now. In this paper, we use molecular docking, molecular dynamics, and metadynamics to reveal structural determinants explaining light-controlled insulin release. We show that both trans- and cis-JB253 bind to the same SUR1 cavity as antidiabetic sulfonylurea glibenclamide (GBM). Simulations indicate that, in contrast to trans-JB253, the cis-JB253 structure generated by blue light absorption promotes open structures of SUR1, in close similarity to the GBM effect. We postulate that in the open SUR1 structures, the N-terminal tail from Kir6.2 protruding into the SUR1 pocket is stabilized by flexible enough sulfonylureas. Therefore, the adjacent Kir6.2 pore is more often closed, which in turn facilitates insulin release. Thus, KATP conductance is regulated by peptide linkers between its Kir6.2 and SUR1 subunits, a phenomenon present in other biological signaling pathways. Our data explain the observed light-modulated activity of photoactive sulfonylureas and widen a way to develop new antidiabetic drugs having reduced adverse effects.
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Affiliation(s)
- Katarzyna Walczewska-Szewc
- Faculty of Physics, Astronomy
and Informatics, Nicolaus Copernicus University
in Torun, ul. Grudziadzka 5, 87-100 Torun, Poland
| | - Wieslaw Nowak
- Faculty of Physics, Astronomy
and Informatics, Nicolaus Copernicus University
in Torun, ul. Grudziadzka 5, 87-100 Torun, Poland
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8
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Megariotis G, Romanos N, Avramopoulos A, Mikaelian G, Theodorou DN. In silico study of levodopa in hydrated lipid bilayers at the atomistic level. J Mol Graph Model 2021; 107:107972. [PMID: 34174554 DOI: 10.1016/j.jmgm.2021.107972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/28/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
This article presents atomistic molecular dynamics and umbrella sampling simulations of levodopa at various concentrations in hydrated cholesterol-free 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and cholesterol-containing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. Levodopa is the standard medication for Parkinson's disease and is marketed under various trade names; in the context of this article, the levodopa molecule is mostly studied in its zwitterionic form but some results concerning the neutral levodopa are presented as well for comparison purposes. The motivation is to study in detail how levodopa behaves in different hydrated lipid membranes, primarily from the thermodynamic point of view, and reveal aspects of mechanism of its permeation through them. Dependencies of properties on the levodopa concentration are also investigated. Special attention is paid to the calculation of mass density profiles, order parameters and self-diffusion coefficients. Levodopa zwitterions, which form a hydrogen bond network with water and phospholipid molecules, are found to be preferentially located at the water/lipid interface, as well as in the aqueous phase surrounding the cholesterol-free and cholesterol-containing bilayers. This is concluded from the potentials of mean force calculated by umbrella sampling simulations as levodopa is transferred from the lipid to the aqueous phase along an axis perpendicular to the two leaflets of the membranes.
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Affiliation(s)
- Grigorios Megariotis
- School of Chemical Engineering, National Technical University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, Athens, GR, 15780, Greece.
| | - Nikolaos Romanos
- School of Chemical Engineering, National Technical University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, Athens, GR, 15780, Greece
| | - Aggelos Avramopoulos
- Department of Physics, University of Thessaly, 3rd Km Old National Road Lamia Athens, Lamia, GR, 35100, Greece
| | - Georgios Mikaelian
- School of Chemical Engineering, National Technical University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, Athens, GR, 15780, Greece
| | - Doros N Theodorou
- School of Chemical Engineering, National Technical University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, Athens, GR, 15780, Greece
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9
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Kärkkäinen J, Laitinen T, Markowicz-Piasecka M, Montaser A, Lehtonen M, Rautio J, Gynther M, Poso A, Huttunen KM. Molecular characteristics supporting l-Type amino acid transporter 1 (LAT1)-mediated translocation. Bioorg Chem 2021; 112:104921. [PMID: 33933805 DOI: 10.1016/j.bioorg.2021.104921] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/21/2021] [Accepted: 02/23/2021] [Indexed: 01/02/2023]
Abstract
l-Type amino acid transporter 1 (LAT1) is an interesting protein due to its peculiar expression profile. It can be utilized not only as a carrier for improved or targeted drug delivery, e.g., into the brain but also as a target protein by which amino acid supply can be restricted, e.g., from the cancer cells. The recognition and binding processes of LAT1-ligands, such as amino acids and clinically used small molecules, including l-dopa, gabapentin, and melphalan, are today well-known. Binding to LAT1 is crucial, particularly when designing the LAT1-inhibitors. However, it will not guarantee effective translocation across the cell membrane via LAT1, which is a definite requirement for LAT1-substrates, such as drugs that elicit their pharmacological effects inside the cells. Therefore, in the present study, the accumulation of known LAT1-utilizing compounds into the selected LAT1-expressing cancer cells (MCF-7) was explored experimentally over a time period. The differences found among the transport efficiency and affinity of the studied compounds for LAT1 were subsequently explained by docking the ligands into the human LAT1 model (based on the recent cryo-electron microscopy structure). Thus, the findings of this study clarify the favorable structural requirements of the size, shape, and polarity of the ligands that support the translocation and effective transport across the cell membrane via LAT1. This knowledge can be applied in future drug design to attain improved or targeted drug delivery and hence, successful LAT1-utilizing drugs with increased therapeutic effects.
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Affiliation(s)
- Jussi Kärkkäinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland; Department of Pharmacy, Kuopio University Hospital, Finland, P.O. Box 100, FI-70029, KYS, Kuopio, Finland
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Magdalena Markowicz-Piasecka
- Laboratory of Bioanalysis, Department of Pharmaceutical Chemistry Drug Analysis and Radiopharmacy, Medical University of Lodz, Lodz, Poland
| | - Ahmed Montaser
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Marko Lehtonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Jarkko Rautio
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Mikko Gynther
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Kristiina M Huttunen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
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10
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Cosco J, Scalise M, Colas C, Galluccio M, Martini R, Rovella F, Mazza T, Ecker GF, Indiveri C. ATP modulates SLC7A5 (LAT1) synergistically with cholesterol. Sci Rep 2020; 10:16738. [PMID: 33028978 PMCID: PMC7541457 DOI: 10.1038/s41598-020-73757-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/17/2020] [Indexed: 01/07/2023] Open
Abstract
The plasma membrane transporter hLAT1 is responsible for providing cells with essential amino acids. hLAT1 is over-expressed in virtually all human cancers making the protein a hot-spot in the fields of cancer and pharmacology research. However, regulatory aspects of hLAT1 biology are still poorly understood. A remarkable stimulation of transport activity was observed in the presence of physiological levels of cholesterol together with a selective increase of the affinity for the substrate on the internal site, suggesting a stabilization of the inward open conformation of hLAT1. A synergistic effect by ATP was also observed only in the presence of cholesterol. The same phenomenon was detected with the native protein. Altogether, the biochemical assays suggested that cholesterol and ATP binding sites are close to each other. The computational analysis identified two neighboring regions, one hydrophobic and one hydrophilic, to which cholesterol and ATP were docked, respectively. The computational data predicted interaction of the ϒ-phosphate of ATP with Lys 204, which was confirmed by site-directed mutagenesis. The hLAT1-K204Q mutant showed an impaired function and response to ATP. Interestingly, this residue is conserved in several members of the SLC7 family.
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Affiliation(s)
- Jessica Cosco
- Department of DiBEST (Biologia, Ecologia, Scienze Della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, via Bucci 4C, 87036, Arcavacata di Rende, Italy
| | - Mariafrancesca Scalise
- Department of DiBEST (Biologia, Ecologia, Scienze Della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, via Bucci 4C, 87036, Arcavacata di Rende, Italy
| | - Claire Colas
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090, Wien, Austria
| | - Michele Galluccio
- Department of DiBEST (Biologia, Ecologia, Scienze Della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, via Bucci 4C, 87036, Arcavacata di Rende, Italy
| | - Riccardo Martini
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090, Wien, Austria
| | - Filomena Rovella
- Department of DiBEST (Biologia, Ecologia, Scienze Della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, via Bucci 4C, 87036, Arcavacata di Rende, Italy
| | - Tiziano Mazza
- Department of DiBEST (Biologia, Ecologia, Scienze Della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, via Bucci 4C, 87036, Arcavacata di Rende, Italy
| | - Gerhard F Ecker
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090, Wien, Austria
| | - Cesare Indiveri
- Department of DiBEST (Biologia, Ecologia, Scienze Della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, via Bucci 4C, 87036, Arcavacata di Rende, Italy. .,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), via Amendola 122/O, 70126, Bari, Italy.
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Singh N, Villoutreix BO. Demystifying the Molecular Basis of Pyrazoloquinolinones Recognition at the Extracellular α1+/β3- Interface of the GABA A Receptor by Molecular Modeling. Front Pharmacol 2020; 11:561834. [PMID: 33041802 PMCID: PMC7518038 DOI: 10.3389/fphar.2020.561834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
GABAA receptors are pentameric ligand-gated ion channels that serve as major inhibitory neurotransmitter receptors in the mammalian brain and the target of numerous clinically relevant drugs interacting with different ligand binding sites. Here, we report an in silico approach to investigate the binding of pyrazoloquinolinones (PQs) that mediate allosteric effects through the extracellular α+/β- interface of GABAA receptors. First, we docked a potent prototype of PQs into the α1+/β3- site of a homology model of the human α1β3γ2 subtype of the GABAA receptor. Next, for each docking pose, we computationally derived protein-ligand complexes for 18 PQ analogs with known experimental potency. Subsequently, binding energy was calculated for all complexes using the molecular mechanics-generalized Born surface area method. Finally, docking poses were quantitatively assessed in the light of experimental data to derive a binding hypothesis. Collectively, the results indicate that PQs at the α1+/β3- site likely exhibit a common binding mode that can be characterized by a hydrogen bond interaction with β3Q64 and hydrophobic interactions involving residues α1F99, β3Y62, β3M115, α1Y159, and α1Y209. Importantly, our results are in good agreement with the recently resolved cryo-Electron Microscopy structures of the human α1β3γ2 and α1β2γ2 subtypes of GABAA receptors.
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Affiliation(s)
- Natesh Singh
- Univ. Lille, INSERM, Institut Pasteur de Lille, U1177–Drugs and Molecules for Living Systems, Lille, France
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Bruno O. Villoutreix
- Univ. Lille, INSERM, Institut Pasteur de Lille, U1177–Drugs and Molecules for Living Systems, Lille, France
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Palazzolo L, Paravicini C, Laurenzi T, Adobati S, Saporiti S, Guerrini U, Gianazza E, Indiveri C, Anderson CMH, Thwaites DT, Eberini I. SLC6A14, a Pivotal Actor on Cancer Stage: When Function Meets Structure. SLAS DISCOVERY 2019; 24:928-938. [DOI: 10.1177/2472555219867317] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
SLC6A14 (ATB0,+) is a sodium- and chloride-dependent neutral and dibasic amino acid transporter that regulates the distribution of amino acids across cell membranes. The transporter is overexpressed in many human cancers characterized by an increased demand for amino acids; as such, it was recently acknowledged as a novel target for cancer therapy. The knowledge on the molecular mechanism of SLC6A14 transport is still limited, but some elegant studies on related transporters report the involvement of the 12 transmembrane α-helices in the transport mechanism, and describe structural rearrangements mediated by electrostatic interactions with some pivotal gating residues.In the present work, we constructed a SLC6A14 model in outward-facing conformation via homology modeling and used molecular dynamics simulations to predict amino acid residues critical for substrate recognition and translocation. We docked the proteinogenic amino acids and other known substrates in the SLC6A14 binding site to study both gating regions and the exposed residues involved in transport. Interestingly, some of these residues correspond to those previously identified in other LeuT-fold transporters; however, we could also identify a novel relevant residue with such function.For the first time, by combined approaches of molecular docking and molecular dynamics simulations, we highlight the potential role of these residues in neutral amino acid transport. This novel information unravels new aspects of the human SLC6A14 structure–function relationship and may have important outcomes for cancer treatment through the design of novel inhibitors of SLC6A14-mediated transport.
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Affiliation(s)
- Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italy
| | - Chiara Paravicini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italy
| | - Tommaso Laurenzi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italy
| | - Sara Adobati
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italy
| | - Simona Saporiti
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italy
| | - Uliano Guerrini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italy
| | - Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italy
| | - Cesare Indiveri
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende, Italy
| | - Catriona M. H. Anderson
- Institute for Cell & Molecular Biosciences, Faculty of Medical Sciences, Framlington Place, Newcastle University, Newcastle upon Tyne, UK
| | - David T. Thwaites
- Institute for Cell & Molecular Biosciences, Faculty of Medical Sciences, Framlington Place, Newcastle University, Newcastle upon Tyne, UK
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari & DSRC, Università degli Studi di Milano, Milano, Italy
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13
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Krammer EM, Prévost M. Function and Regulation of Acid Resistance Antiporters. J Membr Biol 2019; 252:465-481. [DOI: 10.1007/s00232-019-00073-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/08/2019] [Indexed: 01/07/2023]
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