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Sugar-releasing pathway in GLUT1. Representative snapshots of the glucose movement from the inward binding site along the tunnel into intracellular side in SMD. Putative hydrogen interactions are in dash lines. The N-domain and C-domain are shown in cyan and orange, respectively. The last (D) describes the further glucose path through the tunnel toward the intracellular side.
Source publication
Glucose transporters (GLUTs) provide a pathway for glucose transport across membranes. Human GLUTs are implicated in devastating diseases such as heart disease, hyper- and hypo-glycemia, type 2 diabetes and caner. The human GLUT1 has been recently crystalized in the inward-facing open conformation. However, there is no other structural information...
Contexts in source publication
Context 1
... the SMD simulations, glucose substrate moves downward step-by-step with the help of Trp412, Asn411, and His160 into a new sugar-releasing pocket at the inward gate and subsequently moves down into the intracellular side. First, the hydrogen bonds between glucose and Tyr292, and Glu380 are weakened so that glucose moves downward and forms new hydrogen bonds with Trp412 and Asn411 (Fig 8A and 8B). ...
Context 2
... His160 and Gln161 underneath provide new hydrogen bonds to the glucose to facili- tate its movement further down into a new sugar-releasing pocket formed by His160, Gln161, and Trp388 at the inward gate (Fig 8B and 8C). Then, the glucose moves down through the relatively hydrophobic tunnel and exit into the intracellular side (Fig 8D). ...
Context 3
... His160 and Gln161 underneath provide new hydrogen bonds to the glucose to facili- tate its movement further down into a new sugar-releasing pocket formed by His160, Gln161, and Trp388 at the inward gate (Fig 8B and 8C). Then, the glucose moves down through the relatively hydrophobic tunnel and exit into the intracellular side (Fig 8D). Previous cysteine- scanning mutagenesis studies strongly support this glucose translocation mechanism. ...
Citations
... Characterizing robust free-energy landscapes of conformational cycles of SPs will enable us to better understand the mechanistic basis for sugar transport. Although free-energy landscapes for GLUT transporters have been reported previously (Ke et al., 2017;Park and Huang, 2015;Galochkina et al., 2019;Chen and Phelix, 2019), these were generated from a few structures only, and lacked the most recent structure in the occluded conformation (Drew et al., 2021;Qureshi et al., 2020). Indeed, as coevolution analysis confirms, the occluded state is an intermediate that has a number of important and specific coevolved pairs that are critical for linking the outward and inward-facing conformations. ...
Sugar porters (SPs) represent the largest group of secondary-active transporters. Some members, such as the glucose transporters (GLUTs), are well known for their role in maintaining blood glucose homeostasis in mammals, with their expression upregulated in many types of cancers. Because only a few sugar porter structures have been determined, mechanistic models have been constructed by piecing together structural states of distantly related proteins. Current GLUT transport models are predominantly descriptive and oversimplified. Here, we have combined coevolution analysis and comparative modeling, to predict structures of the entire sugar porter superfamily in each state of the transport cycle. We have analyzed the state-specific contacts inferred from coevolving residue pairs and shown how this information can be used to rapidly generate free-energy landscapes consistent with experimental estimates, as illustrated here for the mammalian fructose transporter GLUT5. By comparing many different sugar porter models and scrutinizing their sequence, we have been able to define the molecular determinants of the transport cycle, which are conserved throughout the sugar porter superfamily. We have also been able to highlight differences leading to the emergence of proton-coupling, validating, and extending the previously proposed latch mechanism. Our computational approach is transferable to any transporter, and to other protein families in general.
... Through a combination of other previously reported methods, we have optimized and scaled-up the synthesis of a verdazyl-based ORCA containing 3-glucosyl and 1,5-N,N-isopropyl groups (4, Fig. 1). While the 3 position glucosyl improves solubility and biocompatibility, the incorporation of the anomeric carbon into the tetrazinanone ring precludes cell uptake through glucose transporters, since the anomeric oxygen is required for substrate interaction with most of the GLUT family 44,45 . We also demonstrate enhanced stability and cytocompatibility of glucoverdazyl relative to a nitroxy radical (TEMPO) and spin trapping agent, 5,5-dimethylpyrroline-N-oxide (DMPO). ...
... Optimized targeted synthesis of glucoverdazyl A combination of previously reported 6-oxoverdazyl syntheses was used to identify an optimized route to glucoverdazyl yielding a high level of molecular purity and scalability that is required for an in vivo contrast agent (Fig. 1). The previously reported hydrazine side chains in the literature were usually limited to short carbon chains or aryl groups 44,[47][48][49][50] . We functionalized the side chains with isopropyl groups, as they were a bulky enough side chain to help protect the delocalized radical while also improving serum retention after injection 51 . ...
... A regional analysis of the data discriminating glucoverdazyl clearance from the cortex versus medulla & renal pelvis was performed ( Supplementary Fig. S18). Here, we are able to clearly discern an impairment in glucoverdazyl clearance caused by a decrease in kidney function, while also mapping where the pathological process is taking place within the kidney, which is valuable towards the evaluation of AKI [44][45][46] . ...
Chronic kidney disease (CKD) and acute kidney injury (AKI) are ongoing global health burdens. Glomerular filtration rate (GFR) is the gold standard measure of kidney function, with clinical estimates providing a global assessment of kidney health without spatial information of kidney- or region-specific dysfunction. The addition of dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) to the anatomical imaging already performed would yield a ‘one-stop-shop’ for renal assessment in cases of suspected AKI and CKD. Towards urography by DCE-MRI, we evaluated a class of nitrogen-centered organic radicals known as verdazyls, which are extremely stable even in highly reducing environments. A glucose-modified verdazyl, glucoverdazyl, provided contrast limited to kidney and bladder, affording functional kidney evaluation in mouse models of unilateral ureteral obstruction (UUO) and folic acid-induced nephropathy (FAN). Imaging outcomes correlated with histology and hematology assessing kidney dysfunction, and glucoverdazyl clearance rates were found to be a reliable surrogate measure of GFR.
... This has been made possible by the obtention of the crystal structure of GLUT1, as well as the three-dimensional models based on the crystallized structures of several bacterial and fungi transporters [24]. The related transporters used have been lactose permease, glycerol-3phosphate permease, fucose transporter, and xylose permease from Escherichia coli [21,25,26]. The 492 residues of GLUT1 have been shown to be arranged in 12 transmembrane helices (TMs) separated into two structurally overlapping domains with the amino and carboxyl termini facing the cytosol [1,24] (Figure 1). ...
... The relationships between the structure and the function of hexose transporters in the GLUT family have been widely explored, especially in the case of GLUT1 [13,[20][21][22][23][24][25][26]]. This has been made possible by the obtention of the crystal structure of GLUT1, as well as the three-dimensional models based on the crystallized structures of several bacterial and fungi transporters [24]. ...
... This has been made possible by the obtention of the crystal structure of GLUT1, as well as the three-dimensional models based on the crystallized structures of several bacterial and fungi transporters [24]. The related transporters used have been lactose permease, glycerol-3-phosphate permease, fucose transporter, and xylose permease from Escherichia coli [21,25,26]. The 492 residues of GLUT1 have been shown to be arranged in 12 transmembrane helices (TMs) separated into two structurally overlapping domains with the amino and carboxyl termini facing the cytosol [1,24] (Figure 1). ...
GLUT1 is a facilitative glucose transporter that can transport oxidized vitamin C (i.e., dehydroascorbic acid) and complements the action of reduced vitamin C transporters. To identify the residues involved in human GLUT1’s transport of dehydroascorbic acid, we performed docking studies in the 5 Å grid of the glucose-binding cavity of GLUT1. The interactions of the bicyclic hemiacetal form of dehydroascorbic acid with GLUT1 through hydrogen bonds with the -OH group of C3 and C5 were less favorable than the interactions with the sugars transported by GLUT1. The eight most relevant residues in such interactions (i.e., F26, Q161, I164, Q282, Y292, and W412) were mutated to alanine to perform functional studies for dehydroascorbic acid and the glucose analog, 2-deoxiglucose, in Xenopus laevis oocytes. All the mutants decreased the uptake of both substrates to less than 50%. The partial effect of the N317A mutant in transporting dehydroascorbic acid was associated with a 30% decrease in the Vmax compared to the wildtype GLUT1. The results show that both substrates share the eight residues studied in GLUT1, albeit with a differential contribution of N317. Our work, combining docking with functional studies, marks the first to identify structural determinants of oxidized vitamin C’s transport via GLUT1.
... Vitexin can improve glucose transporter-2 (GLUT-2), and glucose-stimulated insulin secretion [46][47] C-glycosyl flavone, like schaftoside and vicenin 2, can also inhibit advanced glycation end products (AGE) [31,40]. Our ligands showed binding with residues Thr30, Thr137, Gln282, Gln283, and Asn411 playing critical roles in ligand binding to GLUT [48][49]. ...
... Since glucose is the primary substrate that is transported across the membrane by GLUTs, it has been evident from the literature (Park, 2015), where the steered MD revealed, that the glucose molecule interacts via various bond breaks and formation during the process of its transport where the residues like Gln161, Gln282, Asn288, Trp388 and Asn411 originates the sugar binding from C-terminal of GLUT1 (Figure 8). Compared to the glucose binding site, the glutor molecule binds deeper at the intracellular end, as shown in Figure 8, and hence it may interfere with and possibly inhibit the intracellular sugar transport, which can be identified through the further experimental detailed study. ...
Recent experimental evidence from our and other laboratories has strongly indicated that glutor, a piperazine-2-one derivative, which is a pan-GLUT inhibitor, displays a promising antineoplastic action by hampering glucose uptake owing to its ability to inhibit GLUT1 and GLUT3, which are overexpressed in neoplastic cells. However, the molecular mechanism(s) of the inhibiting action of glutor has remained elusive. Thus, for optimal utilization of the antineoplastic potential of glutor, it is essential to decipher the precise mechanism(s) of its interaction with GLUTs. Therefore, the present investigation was carried out to understand the molecular mechanism(s) of the binding of glutor to GLUT1 and GLUT3 in silico. This study suggests that glutor can effectively bind to GLUTs at the reported binding site. Moreover, the docking of glutor to GLUT was stabilised by several contacts between these two partners as shown by the 200 ns long molecular dynamic simulation carried out using Gromacs, indicating the formation of a stable complex. Moreover, glutor was found to possess all characteristics conducive to its drug-likeness. Hence, these observations suggest that glutor has the potential to be used in antineoplastic therapeutic applications.
Communicated by Ramaswamy H. Sarma
... 32 In addition, molecular dynamics simulation also helped us uncover the dynamic cycle of GLUTs in silico. [38][39][40] ...
Cancer cells shift their glucose catabolism from aerobic respiration to lactic fermentation even in the presence of oxygen, and this is known as the “Warburg effect”. To accommodate the high glucose demands and to avoid lactate accumulation, the expression levels of human glucose transporters (GLUTs) and human monocarboxylate transporters (MCTs) are elevated to maintain metabolic homeostasis. Therefore, inhibition of GLUTs and/or MCTs provides potential therapeutic strategies for cancer treatment. Here, we summarize recent advances in the structural characterization of GLUTs and MCTs, providing a comprehensive understanding of their transport and inhibition mechanisms to facilitate further development of anticancer therapies.
... This transporter shares a structural similarity with the GLUT1−4 proteins (29% sequence identity and 49% similarity), 43 the carbohydrate-binding domain is well preserved, and by virtual mutation of a single amino acid residue, Gln-415 to Asn-415, a structurally similar binding pocket to that in GLUT1 can be constructed. 44,45 The carbohydrate delivery agents exist as a mixture of anomers; however, the individual anomers were initially modeled separately in the docking assay and then the overall mean binding energies were calculated to fit with the experimentally determined anomeric ratios. While the mean binding energies were calculated for both the outside and inside open conformations, the outside open conformation is more important when forming a tie to the experimental affinity data. ...
Glucose- and sodium-dependent glucose transporters (GLUTs and SGLTs) play vital roles in human biology. Of the 14 GLUTs and 12 SGLTs, the GLUT1 transporter has gained the most widespread recognition because GLUT1 is overexpressed in several cancers and is a clinically valid therapeutic target. We have been pursuing a GLUT1-targeting approach in boron neutron capture therapy (BNCT). Here, we report on surprising findings encountered with a set of 6-deoxy-6-thio-carboranyl d-glucoconjugates. In more detail, we show that even subtle structural changes in the carborane cluster, and the linker, may significantly reduce the delivery capacity of GLUT1-based boron carriers. In addition to providing new insights on the substrate specificity of this important transporter, we reach a fresh perspective on the boundaries within which a GLUT1-targeting approach in BNCT can be further refined.
... The transport mechanism of GLUT1 and GLUT3 is well known and they follow a model called a "rocker switch", This mechanism has four distinct states; (1) outwardopen state, in which the ligand binds to the transporter causing the outer gate to close, (2) outward-occluded state, in which a rocker-switch takes place forming (3) inwardoccluded state that is followed by the opening of the inner gate, and finally (4) inward-open state, from which the ligand is released ( Figure 5) [14,15,64]. Today, it is well known which interactions can result in conformational changes in GLUT1 and, thus, induce the translocation of glucose derivatives in the cavity [65][66][67]. Thus, molecular modeling can be a really helpful tool for designing GLUT1 substrates that are truly transported through the protein cavity and not only bind to the protein on the plasma membrane. ...
Membrane transporters have a crucial role in compounds’ brain drug delivery. They allow not only the penetration of a wide variety of different compounds to cross the endothelial cells of the blood–brain barrier (BBB), but also the accumulation of them into the brain parenchymal cells. Solute carriers (SLCs), with nearly 500 family members, are the largest group of membrane transporters. Unfortunately, not all SLCs are fully characterized and used in rational drug design. However, if the structural features for transporter interactions (binding and translocation) are known, a prodrug approach can be utilized to temporarily change the pharmacokinetics and brain delivery properties of almost any compound. In this review, main transporter subtypes that are participating in brain drug disposition or have been used to improve brain drug delivery across the BBB via the prodrug approach, are introduced. Moreover, the ability of selected transporters to be utilized in intrabrain drug delivery is discussed. Thus, this comprehensive review will give insights into the methods, such as computational drug design, that should be utilized more effectively to understand the detailed transport mechanisms. Moreover, factors, such as transporter expression modulation pathways in diseases that should be taken into account in rational (pro)drug development, are considered to achieve successful clinical applications in the future.
... Therefore, computer-based analysis of the structure and function of glycans is important. In particular, molecular dynamics (MD) simulation-based analysis has generated a significant amount of knowledge regarding glycans [5][6][7][8]. However, the performance of the MD method strongly depends on the force field determination accuracy [9][10][11]; hence, accurate force field determination has been important in glycan research. ...
... Table S1: Torsion parameters in Equation (4) of the main text. The columns headed V 1 to V 6 have units of kcal/mol, and the columns headed γ 1 to γ 6 ...
While the construction of a dependable force field for performing classical molecular dynamics (MD) simulation is crucial for elucidating the structure and function of biomolecular systems, the attempts to do this for glycans are relatively sparse compared to those for proteins and nucleic acids. Currently, the use of GLYCAM06 force field is the most popular, but there have been a number of concerns about its accuracy in the systematic description of structural changes. In the present work, we focus on the improvement of the GLYCAM06 force field for β-d-glucose, a simple and the most abundant monosaccharide molecule, with the aid of machine learning techniques implemented with the TensorFlow library. Following the pre-sampling over a wide range of configuration space generated by MD simulation, the atomic charge and dihedral angle parameters in the GLYCAM06 force field were re-optimized to accurately reproduce the relative energies of β-d-glucose obtained by the density functional theory (DFT) calculations according to the structural changes. The validation for the newly proposed force-field parameters was then carried out by verifying that the relative energy errors compared to the DFT value were significantly reduced and that some inconsistencies with experimental (e.g., NMR) results observed in the GLYCAM06 force field were resolved relevantly.
... Among the sugar transporters of the model strain S. cerevisiae, ScHxt1 and 7 have received the most attention (Kasahara et al. 2011;Roy et al. 2015;Roy et al. 2014). Based on previous studies of these two transporters and four structurally resolved sugar transporters (EcXylE, AtStp10, HsGlut1, and HsGlut3), many amino acid residues (especially those involved in glucose coordination) were found to be very conserved (Deng et al. 2015(Deng et al. , 2014Farwick et al. 2014;Kasahara et al. 2011;Park 2015;Paulsen et al. 2019;Sun et al. 2012;Wisedchaisri et al. 2014). Based on this, we initially screened 16 residues (F59, Q189, I192, T193, I196, Q316, Q317, N322, F325, Y326, N351, F421, G426, F430, N453, and W454) that may affect the glucose transport function of CgHxt4 ( Figure S2A). ...
Efficient hexose transporters are essential for the development of industrial yeast strains with high fermentation performance. We previously identified a hexose transporter, CgHxt4, with excellent sugar uptake performance at ultra-high glucose concentrations (200 g/L) in the high sugar fermenting yeast C. glycerinogenes. To understand the working mechanism of this transporter, we constructed 87 mutants and examined their glucose uptake performance. The results revealed that five residues (N321, N322, F325, G426, and P427) are essential for the efficient glucose transport of CgHxt4. Subsequently, we focused our analysis on the roles of N321 and P427. Specifically, N321 and P427 are likely to play a role in glucose coordination and conformational flexibility, respectively. Our results help to expand the application potential of this transporter and provide insights into the working mechanism of yeast hexose transporter.
Key points
• Five residues, transmembrane segments 7 and 10, were found to be essential for CgHxt4.
• N321 and P427 are likely to play a role in glucose coordination and conformational flexibility, respectively.
• Chimeric CgHxt5.4TM7 significantly enhanced the performance of CgHxt5.
