scholarly journals Membrane Environment Modulates Ligand-Binding Propensity of P2Y12 Receptor

Pharmaceutics ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 524
Author(s):  
Fatemeh Haghighi ◽  
Semen Yesylevskyy ◽  
Siamak Davani ◽  
Christophe Ramseyer

The binding of natural ligands and synthetic drugs to the P2Y12 receptor is of great interest because of its crucial role in platelets activation and the therapy of arterial thrombosis. Up to now, all computational studies of P2Y12 concentrated on the available crystal structures, while the role of intrinsic protein dynamics and the membrane environment in the functioning of P2Y12 was not clear. In this work, we performed all-atom molecular dynamics simulations of the full-length P2Y12 receptor in three different membrane environments and in two possible conformations derived from available crystal structures. The binding of ticagrelor, its two major metabolites, adenosine diphosphate (ADP) and 2-Methylthioadenosine diphosphate (2MeS-ADP) as agonist, and ethyl 6-[4-(benzylsulfonylcarbamoyl)piperidin-1-yl]-5-cyano-2-methylpyridine-3-carboxylate (AZD1283)as antagonist were assessed systematically by means of ensemble docking. It is shown that the binding of all ligands becomes systematically stronger with the increase of the membrane rigidity. Binding of all ligands to the agonist-bound-like conformations is systematically stronger in comparison to antagonist-bound-likes ones. This is dramatically opposite to the results obtained for static crystal structures. Our results show that accounting for internal protein dynamics, strongly modulated by its lipid environment, is crucial for correct assessment of the ligand binding to P2Y12.

2021 ◽  
Vol 14 ◽  
pp. 117864692110529
Author(s):  
Manon Mirgaux ◽  
Laurence Leherte ◽  
Johan Wouters

Protein dynamics governs most of the fundamental processes in the human body. Particularly, the dynamics of loops located near an active site can be involved in the positioning of the substrate and the reaction mechanism. The understanding of the functioning of dynamic loops is therefore a challenge, and often requires the use of a multi-disciplinary approach mixing, for example, crystallographic experiments and molecular dynamics simulations. In the present work, the dynamic behavior of the JK-loop of the human indoleamine 2,3-dioxygenase 1 hemoprotein, a target for immunotherapy, is investigated. To overcome the lack of knowledge on this dynamism, the study reported here is based on 3 crystal structures presenting different conformations of the loop, completed with molecular dynamics trajectories and MM-GBSA analyses, in order to trace the reaction pathway of the enzyme. In addition, the crystal structures identify an exo site in the small unit of the enzyme, that is populated redundantly by the substrate or the product of the reaction. The role of this newer reported exo site still needs to be investigated.


2020 ◽  
Author(s):  
Jiming Chen ◽  
Alexandra White ◽  
David C. Nelson ◽  
Diwakar Shukla

Witchweed, or Striga hermonthica, is a parasitic weed that destroys billions of dollars worth of crops globally every year. Its germination is stimulated by strigolactones exuded by its host plants. Despite high sequence, structure, and ligand binding site conservation across different plant species, one strigolactone receptor in witchweed (Sh HTL7) uniquely exhibits a picomolar EC50 for downstream signaling. Previous biochemical and structural analyses have hypothesized that this unique ligand sensitivity can be attributed to a large binding pocket volume in Sh HTL7 resulting in enhanced ability to bind substrates. Additional structural details of the substrate binding process can help explain its role in modulating the ligand selectivity. Using long-timescale molecular dynamics simulations, we demonstrate that mutations at the entrance of the binding pocket facilitate a more direct ligand binding pathway to Sh HTL7, whereas hydrophobicity at the binding pocket entrance results in a stable “anchored” state. We also demonstrate that several residues on the D-loop of At D14 stabilize catalytically inactive conformations. Finally, we show that strigolactone selectivity is not modulated by binding pocket volume. Our results indicate that while ligand binding is not the sole modulator of strigolactone receptor selectivity, it is a significant contributing factor. These results can be used to inform the design of selective antagonists for strigolactone receptors in witchweed.


2017 ◽  
Author(s):  
Emanuele Monza ◽  
George Blouin ◽  
Thomas G. Spiro ◽  
Victor Guallar

AbstractHemoglobin is the paradigm of cooperative protein-ligand binding. Cooperativity is the consequence of inter-subunit allosteric communication: binding at one site increases the affinity of the others. Despite half a century of studies, the mechanism behind oxygen binding in hemoglobin is not fully understood yet. In particular, it is not clear if cooperativity arises from preferential inter-subunit channels and which residues propagate the allosteric signal from one heme to the others. In this work, the heme-heme dynamical interactions have been mapped through a network-based analysis of residue conformational fluctuations, as described by molecular dynamics simulations. In particular, it was possible to suggest which inter-subunit interactions are mostly responsible of allosteric signalling and, within each pair of subunits, which protein fragments convey such signalling process.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 1655-1655
Author(s):  
Tsuyoshi Kamae ◽  
Masamichi Shiraga ◽  
Hirokazu Kashiwagi ◽  
Hisashi Kato ◽  
Seiji Tadokoro ◽  
...  

Abstract Platelet αIIbβ3 (GPIIb-IIIa), a noncovalently associated heterodimer, is a prototypic integrin that functions as a physiologic receptor for fibrinogen and von Willebrand factor. αIIbβ3 plays a crucial role in platelet aggregation, a key event of hemostatic plug formation and pathologic thrombus formation. During thrombogenesis, the affinity of αIIbβ3 for macromolecular ligands is dynamically regulated. After exposure to subendothelial matrix, several mediators such as ADP and thromboxane A2, or shear stress, platelets becomes activated and inside-out signaling that induces a high-affinity state of αIIbβ3 for soluble ligands (αIIbβ3 activation) are generated. Previous studies revealed that activation of αIIbβ3 is a reversible process. When platelets are stimulated with weak agonists such as adenosine diphosphate (ADP) and epinephrine in the absence of fibrinogen, αIIbβ3 gradually looses its binding capacity. In contrast, thrombin can induce long-lasting αIIbβ3 activation in the absence of fibrinogen. Although much attention has been directed to the nature of inside-out signaling, the mechanisms by which αIIbβ3 keep in the high-affinity state still remains elusive. In this study, we have demonstrated a critical role of endogenous ADP via its P2Y12 receptor in the maintenance of αIIbβ3 activation. Washed platelets adjusted to 50 x 106/ml were stimulated with 0.2 U/ml thrombin or 5 mM U46619 under static conditions. After the 15-min stimulation, 1 mM AR-C69931MX (a P2Y12 antagonist), 1 mM A3P5P (a P2Y1 antagonist) or buffer alone was added to the suspensions for additional 5 min. The platelet suspensions were then incubated with FITC-PAC1 and PE-anti-CD62P for 30 min and analyzed in a flow cytometer. AR-C69931MX and A3P5P attenuated the number of activated αIIbβ3 about 95% and 45%, respectively on the already activated platelets with thrombin- or U46619 without inhibiting CD62P expression. In an another set of experiments, platelets stimulated with thrombin or U46619 for 15min were then diluted to 1:100 with buffer containing the same agonist concentration (0.5 x 106/ml). In these conditions the number of activated αIIbβ3 was also markedly decreased (~85% reduction). Furthermore, the reduction in activated αIIbβ3 by the dilution was reversed by the addition of exogenous ADP in a dose-dependent fashion. HPLC analysis revealed that the amounts of ADP released from thrombin- and U46619-stimulated platelets were 2.6 and 0.75 mmol/1011platelets, respectively, and these values were comparable with ADP doses required for sustained αIIbβ3 activation in the diluted platelet suspension. Thus, released endogenous ADP plays a critical role in the maintenance of αIIbβ3 activation, and certain platelet concentrations are needed for this action. We also examined Rap 1b activation during the maintenance of αIIbβ3 activation. Thrombin induced sustained Rap 1b activation in the absence of ligand. However, AR-C69931MX disrupted the sustained Rap 1b activation. Thus, there was a close relationship between the maintenance αIIbβ3 activation and Rap 1b activation. Our data provide that the continuous interaction between released ADP and P2Y12 receptor is critical for the maintenance of αIIbβ3 activation.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Andrea Schenkmayerova ◽  
Gaspar P. Pinto ◽  
Martin Toul ◽  
Martin Marek ◽  
Lenka Hernychova ◽  
...  

AbstractProtein dynamics are often invoked in explanations of enzyme catalysis, but their design has proven elusive. Here we track the role of dynamics in evolution, starting from the evolvable and thermostable ancestral protein AncHLD-RLuc which catalyses both dehalogenase and luciferase reactions. Insertion-deletion (InDel) backbone mutagenesis of AncHLD-RLuc challenged the scaffold dynamics. Screening for both activities reveals InDel mutations localized in three distinct regions that lead to altered protein dynamics (based on crystallographic B-factors, hydrogen exchange, and molecular dynamics simulations). An anisotropic network model highlights the importance of the conformational flexibility of a loop-helix fragment of Renilla luciferases for ligand binding. Transplantation of this dynamic fragment leads to lower product inhibition and highly stable glow-type bioluminescence. The success of our approach suggests that a strategy comprising (i) constructing a stable and evolvable template, (ii) mapping functional regions by backbone mutagenesis, and (iii) transplantation of dynamic features, can lead to functionally innovative proteins.


2021 ◽  
Author(s):  
Son Tung Ngo ◽  
Trung Hai Nguyen ◽  
Nguyen Thanh Tung ◽  
Binh Khanh Mai

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been causing the COVID-19 pandemic resulting in several million death were reported. Numerous investigations have been carried out to discover a compound that can inhibit the biological activity of SARS-CoV-2 main protease, which is an enzyme related to the viral replication. Among these, PF-07321332 is currently under clinical trial for COVID-19 therapy. Therefore, in this work, atomistic and electronic simulations were performed to unravel the binding and covalent inhibition mechanism of the compound to Mpro. Initially, 5 µs of steered-molecular dynamics simulations were carried out to evaluate the ligand-binding process to SARS-CoV-2 Mpro. Successfully generated bound state between two molecules showed the important role of the PF-07321332 pyrrolidinyl group and the residues Glu166 and Gln189 in the ligand-binding process. Moreover, from the MD-refined structure, quantum mechanics/molecular mechanics (QM/MM) calculations were carried out to unravel the reaction mechanism for the formation of thioimidate product from SARS-CoV-2 Mpro and PF07321332 inhibitor. We found that the catalytic triad Cys145–His41–Asp187 of SARS-CoV-2 Mpro plays important role in the activation of PF-07321332 covalent inhibitor, which renders the deprotonation of Cys145 and, thus, facilitates further reaction. Our results are definitely beneficial for better understanding on the inhibition mechanism and designing new effective inhibitors for SARS-CoV-2 Mpro.


2016 ◽  
Vol 70 (7) ◽  
Author(s):  
Milan Senćanski ◽  
Ljiljana Došen-Mićović

AbstractIn the present study, the role of inter-residue interactions in ligand binding and the ligand-receptor interactions were examined. Computational chemistry methods of ligand docking and molecular dynamics simulations were used to study the binding of


2018 ◽  
Author(s):  
Gaëtan Dias Mirandela ◽  
Giulia Tamburrino ◽  
Paul A. Hoskisson ◽  
Ulrich Zachariae ◽  
Arnaud Javelle

AbstractThe movement of ammonium across biological membranes is a fundamental process in all living organisms and is mediated by the ubiquitous Amt/Mep/Rh family of transporters. Recent structural analysis and coupled mass spectrometry studies have shown that theEscherichia coliammonium transporter, AmtB, specifically binds phosphatidylglycerol (PG). Upon PG binding, several residues of AmtB undergo a small conformational change, which stabilizes the protein against unfolding. However, no studies have so far been conducted to explore if PG binding to AmtB has functional consequences. Here, we used an invitroexperimental assay with purified components together with molecular dynamics simulations to characterise the relation between PG binding and AmtB activity. Firstly, our results indicate that the function of Amt in archaebacteria and eubacteria may differ. Secondly, we show that PG is an essential cofactor for AmtB activity and that in the absence of PG AmtB cannot complete the full translocation cycle. Furthermore, our simulations reveal previously undiscovered PG binding sites on the intracellular side of the lipid bilayer between the AmtB subunits. The possible molecular mechanisms explaining the functional role of PG are discussed.


1980 ◽  
Vol 44 (01) ◽  
pp. 006-008 ◽  
Author(s):  
D Bergqvist ◽  
K-E Arfors

SummaryIn a model using an isolated rabbit mesenteric preparation microvessels were transected and the time until haemostatic plugs formed was registered. Perfusion of platelet rich plasma gave no haemostasis whereas whole blood did. Addition of chlorpromazine or adenosine to the whole blood significantly prolonged the time for haemostasis, and addition of ADP to the platelet rich plasma significantly shortened it. It is concluded that red cells are necessary for a normal haemostasis in this model, probably by a combination of a haemodynamic and ADP releasing effect.The fundamental role of platelets in haemostatic plug formation is unquestionable but there are still problems concerning the stimulus for this process to start. Three platelet aggregating substances have been discussed – thrombin, adenosine diphosphate (ADP) and collagen. Evidence speaking in favour of thrombin is, however, very minimal, and the discussion has to be focused on collagen and ADP. In an in vitro system using polyethylene tubings we have shown that "haemostasis" can be obtained without the presence of collagen but against these results can be argued that it is only another in vitro test for platelet aggregation (1).To be able to induce haemostasis in this model, however, the presence of red blood cells is necessary. To further study this problem we have developed a model where haemostatic plug formation can be studied in the isolated rabbit mesentery and we have briefly reported on this (2).Thus, it is possible to perfuse the vessels with whole blood as well as with platelet rich plasma (PRP) and different pharmacological agents of importance.


1985 ◽  
Vol 54 (03) ◽  
pp. 612-616 ◽  
Author(s):  
A J Carter ◽  
S Heptinstall

SummaryThe platelet aggregation that occurred in whole blood in response to several aggregating agents (collagen, arachidonic acid, adenosine diphosphate, adrenaline and thrombin) was measured using an Ultra-Flo 100 Whole Blood Platelet Counter. The amounts of thromboxane B2 produced were measured by radioimmunoassay. The effects of various inhibitors of thromboxane synthesis and the effects of apyrase, an enzyme that destroys adenosine diphosphate, were determined.Platelet aggregation was always accompanied by the production of thromboxane B2, and the amounts produced depended on the nature and concentration of the aggregating agent used. The various inhibitors of thromboxane synthesis - aspirin and flurbiprofen (cyclo-oxygenase inhibitors), BW755C (a cyclo-oxygenase and lipoxygenase inhibitor) and dazoxiben (a selective thromboxane synthase inhibitor) - did not markedly inhibit aggregation. Results obtained using apyrase showed that adenosine diphosphate contributed to the aggregation process, and that its role must be acknowledged when devising means of inhibiting platelet aggregation in vivo.


Sign in / Sign up

Export Citation Format

Share Document