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Interaction between (A) GABA, (B-C) sodium and (C) chloride ions with their nearby binding site residues in the fully loaded hGAT1. GABA binding involve direct interaction to the sodium ion at the Na1 site.
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Human γ-Aminobutyric acid transporter 1 (hGAT1) is a Na⁺/Cl⁻ dependent co-transporter that plays a key role in the inhibitory neurotransmission of GABA in the brain. Due to the lack of structural data, the exact co-transport mechanism of GABA reuptake by hGAT1 remains unclear. To examine the roles of the co-transport ions and the nature of their in...
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... and detailed analysis of the protein-ligand interactions, the fully loaded hGAT1 out G, N1+2, C state is the most promising of the four examined GABA bound hGAT1 complexes for GABA trans- port. In addition to its interaction to the Na1 ion, the GABA's carboxylate group also formed a hydrogen bonding interaction with the hydroxyl group of Y140 (Fig. 5A and Fig. 6). The importance of Y140 in hGAT1 has been demonstrated experimentally as a known binding determi- nant of GABA [48,49]. Mutation of Y140 has been shown to abolish its transport ability of GABA in the forward mode [50]. Its importance has also been explored by Skovstrup et al., with constrained MD simulation [18]. Furthermore, as a ...
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... GABA requires a major conformational change in EL4 [53]. The interactions of sodium and chloride ions with the surrounding binding site residues in fully loaded hGAT1 were also examined. Na1 occupied its respective position in the binding pocket by interacting with the side chain atoms of N66, S295 and N327 and carbonyl oxygen of the A61 and S295 (Fig. 5B) along with electrostatic interaction with carboxylate group of GABA (Fig. 6). Yamashita et al., also observed direct interaction between the Na1 and leucine in A a LeuT previously [28] while it was water-mediated between the amino group of dopamine and Na1 in dDAT [25]. On the other hand, the surrounding residues of Na2 showed ...
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... of GABA (Fig. 6). Yamashita et al., also observed direct interaction between the Na1 and leucine in A a LeuT previously [28] while it was water-mediated between the amino group of dopamine and Na1 in dDAT [25]. On the other hand, the surrounding residues of Na2 showed interactions with backbone atoms of G59, I62, L392 and side chain atoms of D395 (Fig. 5C). In addition, the side chain of G63 formed a bridge between Na1 and Na2 in fully loaded hGAT1 (Fig. 5C). The importance of G63 is well studied by Kanner in GABA permeation pathway through mutagenesis study [1]. It has been established that the mutation of G63 to either cysteine or serine abolishes the Na + and Cl − dependent GABA ...
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... LeuT previously [28] while it was water-mediated between the amino group of dopamine and Na1 in dDAT [25]. On the other hand, the surrounding residues of Na2 showed interactions with backbone atoms of G59, I62, L392 and side chain atoms of D395 (Fig. 5C). In addition, the side chain of G63 formed a bridge between Na1 and Na2 in fully loaded hGAT1 (Fig. 5C). The importance of G63 is well studied by Kanner in GABA permeation pathway through mutagenesis study [1]. It has been established that the mutation of G63 to either cysteine or serine abolishes the Na + and Cl − dependent GABA transport both in forward and backward mode ...
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... Cl − ion in fully loaded hGAT1 was found in near proximity of Na1. The residues surrounding the Cl − ion include Y86, S295, N327 and S331 as shown in Fig. 5D. Mari et al., [11], Skovstrup et al., [18] and Zomot et al., [26] demonstrated previously that the side chain of S295 forms a direct bridge between Na1 and Cl − ions, thereby keeping them intact in their respective positions in hGAT1 binding pocket. Although, the side chains of amino acid residues surrounding all of the three ...
Citations
... In 2005, the first crystal structure of LeuT from A. aeolicus was resolved in an outward-facing occluded conformation, in which the substrate binding site S1 was occupied by the substrate (leucine) and shielded by the hydrophobic gate residues (V104, Y108, and F253) from the extracellular environment (Yamashita et al., 2005). The LeuT structures served as the template for the generation of GAT1 homology models, all owing for investigating the binding mode of GABA and analogues (Pallo et al., 2007;Skovstrup et al., 2010;Skovstrup et al., 2012;Zafar and Jabeen, 2018;Zafar et al., 2019;Latka et al., 2020). The endogenous ligand (GABA) was docked in the S1 and showed favorable h-bonding interaction with TM1 (Y60) and TM8 (S396)) (Pallo et al., 2007). ...
... A later docking study using a GAT1 homology model based on the X-ray crystal structure of the open-to-out conformation of the dDAT showed a GABA binding mode that agreed with the earlier studies, in which the carboxyl group completes the coordination of Na + in Na1, while the amino group is mainly stabilized by interactions with Y140 and Zafar and collaborators reported that the presence of the co-transported Na + and Cl − ions increase binding strength, in particular Na + bound to the Na1 site Zafar et al., 2019). ...
γ-aminobutyric acid (GABA) is the primary inhibitory neurotransmitter in the central nervous system (CNS). Its homeostasis is maintained by neuronal and glial GABA transporters (GATs). The four GATs identified in humans are GAT1 (SLC6A1), GAT2 (SLC6A13), GAT3 (SLC6A11), and betaine/GABA transporter-1 BGT-1 (SLC6A12) which are all members of the solute carrier 6 (SLC6) family of sodium-dependent transporters. While GAT1 has been investigated extensively, the other GABA transporters are less studied and their role in CNS is not clearly defined. Altered GABAergic neurotransmission is involved in different diseases, but the importance of the different transporters remained understudied and limits drug targeting. In this review, the well-studied GABA transporter GAT1 is compared with the less-studied BGT-1 with the aim to leverage the knowledge on GAT1 to shed new light on the open questions concerning BGT-1. The most recent knowledge on transporter structure, functions, expression, and localization is discussed along with their specific role as drug targets for neurological and neurodegenerative disorders. We review and discuss data on the binding sites for Na ⁺ , Cl ⁻ , substrates, and inhibitors by building on the recent cryo-EM structure of GAT1 to highlight specific molecular determinants of transporter functions. The role of the two proteins in GABA homeostasis is investigated by looking at the transport coupling mechanism, as well as structural and kinetic transport models. Furthermore, we review information on selective inhibitors together with the pharmacophore hypothesis of transporter substrates.
... The homology for each human transporter related to the others was sequence identified is approximately hDAT/hNET = 67%, hDAT/hSERT = 50%, hNET/hSERT = 53%. The evidence from these studies presents the lower sequence similarity for hNET/hDAT = 58% [34] compared with hGAT1/dDAT = 66% [35] of identity. All these values are quite similar to the sequence of proteins in all the transporters analyzed. ...
... Nevertheless, the analysis of structural similarities calculated as RMS determined by superimposing the structures of two proteins seems to be of key importance in understanding the interaction of various compounds with the analyzed objectives [37]. These results, in contrast to the data routinely presented in the literature based on the amino acid sequence identity technique [29,[32][33][34][35], better highlight the structural differences of the analyzed transporters. These differences are of particular importance within the ligand binding site. ...
... hBGT1 is only found in scarce amounts and hGAT2 is not found in the brain parenchyma at all [82]. hGAT1 is predominantly located on GABAergic nerve terminals [35,59,83], while hGAT3 and hBGT1 are commonly associated with perisynaptic and distal astrocytic sites [28,60]. The location and level of individual transporters in CNS seem to be crucial in the neurogenesis process. ...
Thus far, many hypotheses have been proposed explaining the cause of depression. Among the most popular of these are: monoamine, neurogenesis, neurobiology, inflammation and stress hypotheses. Many studies have proven that neurogenesis in the brains of adult mammals occurs throughout life. The generation of new neurons persists throughout adulthood in the mammalian brain due to the proliferation and differentiation of adult neural stem cells. For this reason, the search for drugs acting in this mechanism seems to be a priority for modern pharmacotherapy. Paroxetine is one of the most commonly used antidepressants. However, the exact mechanism of its action is not fully understood. The fact that the therapeutic effect after the administration of paroxetine occurs after a few weeks, even if the levels of monoamine are rapidly increased (within a few minutes), allows us to assume a neurogenic mechanism of action. Due to the confirmed dependence of depression on serotonin, norepinephrine, dopamine and γ-aminobutyric acid levels, studies have been undertaken into paroxetine interactions with these primary neurotransmitters using in silico and in vitro methods. We confirmed that paroxetine interacts most strongly with monoamine transporters and shows some interaction with γ-aminobutyric acid transporters. However, studies of the potency inhibitors and binding affinity values indicate that the neurogenic mechanism of paroxetine’s action may be determined mainly by its interactions with serotonin transporters.
... An in-house preprocessed hGAT1 model built in open-to-out conformation [35] was used to dock both R-and S-configured tiagabine. Briefly, homology modeling of hGAT1 (UniProt: P30531) in open-to-out conformation was based on the X-ray crystallographic structure of the Drosophila melanogaster dopamine transporter (dDAT) (Protein Data Bank ID: 4XP4) with the bound cocaine substrate and the co-transport di-sodium/chloride (2Na + /1Cl − ) ions within its structurally conserved Moreover, our results could be further strengthened by comparing the interaction pattern of the hGAT1 entry 4 with the Skovstrup's interactions analysis of constraint cis (R) enantiomer of tiagabine that showed hydrogen bond interaction between the protonated -NH group of tiagabine and carbonyl oxygen moiety of F294, however, the constraint trans (S) enantiomer was unable to sustain such interaction [25]. ...
... An in-house preprocessed hGAT1 model built in open-to-out conformation [35] was used to dock both Rand S-configured tiagabine. Briefly, homology modeling of hGAT1 (UniProt: P30531) in open-to-out conformation was based on the X-ray crystallographic structure of the Drosophila melanogaster dopamine transporter (dDAT) (Protein Data Bank ID: 4XP4) with the bound cocaine substrate and the co-transport di-sodium/chloride (2Na + /1Cl − ) ions within its structurally conserved ion/substrate binding sites. ...
... Various reports highlighted the crucial role of Y140 in the GABA-induced translocation through hGAT1 by mediating hydrogen bond interaction with the -COOH group of GABA [35,42]. Therefore, constraint docking on Y140 residue has been performed previously to delineate the molecular basis of ligand-transporter interactions of hGAT1 antagonists [25,27]. ...
The human gamma aminobutyric acid transporter subtype 1 (hGAT1) located in the nerve terminals is known to catalyze the neuronal function by the electrogenic reuptake of γ-aminobutyric acid (GABA) with the co-transport of Na + and Cl − ions. In the past, there has been a major research drive focused on the dysfunction of hGAT1 in several neurological disorders. Thus, hGAT1 of the GABAergic system has been well established as an attractive target for such diseased conditions. Till date, there are various reports about stereo selectivity of-COOH group of tiagabine, a Food and Drug Administration (FDA)-approved hGAT1-selective antiepileptic drug. However, the effect of the stereochemistry of the protonated-NH group of tiagabine has never been scrutinized. Therefore, in this study, tiagabine has been used to explore the binding hypothesis of different enantiomers of tiagabine. In addition, the impact of axial and equatorial configuration of the-COOH group attached at the meta position of the piperidine ring of tiagabine enantiomers was also investigated. Further, the stability of the finally selected four hGAT1-tiagabine enantiomers namely entries 3, 4, 6, and 9 was evaluated through 100 ns molecular dynamics (MD) simulations for the selection of the best probable tiagabine enantiomer. The results indicate that the protonated-NH group in the R-conformation and the-COOH group of Tiagabine in the equatorial configuration of entry 4 provide maximum strength in terms of interaction within the hGAT1 binding pocket to prevent the change in hGAT1 conformational state, i.e., from open-to-out to open-to-in as compared to other selected tiagabine enantiomers 3, 6, and 9.
... In addition, MD analysis of these modeled drug/epitope-protein complexes is a necessary standard for testing the effectiveness of drugs and vaccines. By MD simulation, the binding ability of inhibitors/peptides to proteins and the conformational changes of target proteins will be well reflected [25,26]. ...
Infectious and epidemic diseases caused by bacteria have historically caused great distress to people, and have even resulted in a large number of deaths worldwide. At present, many researchers are working on the discovery of viable drug and vaccine targets for bacteria through multiple methods, including comparative subtractive genome, core genome, replication-related proteins, transcriptomics and riboswitches analyses, which plays a significant part in the treatment of infectious and pandemic diseases. The 3D structures of the desired target proteins, drugs and epitopes can be predicted and modeled through target analysis. Meanwhile, molecular dynamics (MD) analysis of these constructed drug/epitope-protein complexes is an important standard for testing the suitability of these screened drugs and vaccines. Currently, target discovery, target analysis and MD analysis are integrated into a systematic set of drug and vaccine analysis strategy for bacteria. We hope that this comprehensive strategy will help in the design of high-performance vaccines and drugs.
