The Molecular Mechanism Underlying Ligand Binding to the Membrane-Embedded Site of a G‑Protein-Coupled Receptor

The crystal structure of P2Y₁ receptor (P2Y₁R), a class A GPCR, revealed a special extra-helical site for its antagonist, BPTU, which locates in-between the membrane and the protein. However, due to the limitation of crystallization experiments, the membrane was mimicked by use of detergents, and the information related to the binding of BPTU to the receptor in the membrane environment is rather limited. In the present work, we conducted a total of ∼7.5 μs all-atom simulations in explicit solvent using conventional molecular dynamics and multiple enhanced sampling methods, with models of BPTU and a POPC bilayer, both in the absence and presence of P2Y₁R. Our simulations revealed that BPTU prefers partitioning into the interface of polar/lipophilic region of the lipid bilayer before associating with the receptor. Then, it interacts with the second extracellular loop of the receptor and reaches the binding site through the lipid–receptor interface. In addition, by use of funnel-metadynamics simulations which efficiently enhance the sampling of bound and unbound states, we provide a statistically accurate description of the underlying binding free energy landscape. The calculated absolute ligand–receptor binding affinity is in excellent agreement with the experimental data (Δ<i>G</i>_{b0_theo} = −11.5 kcal mol^–1, Δ<i>G</i>_{b0_exp}= −11.7 kcal mol^–1). Our study broadens the view of the current experimental/theoretical models and our understanding of the protein–ligand recognition mechanism in the lipid environment. The strategy used in this work is potentially applicable to investigate ligands association/dissociation with other membrane-embedded sites, allowing identification of compounds targeting membrane receptors of pharmacological interest

Label-Free Imaging of Heme Dynamics in Living Organisms by Transient Absorption Microscopy

Heme, a hydrophobic and cytotoxic macrocycle, is an essential cofactor in a large number of proteins and is important for cell signaling. This must mean that heme is mobilized from its place of synthesis or entry into the cell to other parts of the cell where hemoproteins reside. However, the cellular dynamics of heme movement is not well understood, in large part due to the inability to image heme noninvasively in live biological systems. Here, using high-resolution transient absorption microscopy, we showed that heme storage and distribution is dynamic in <i>Caenorhabditis elegans</i>. Intracellular heme exists in concentrated granular puncta which localizes to lysosomal-related organelles. These granules are dynamic, and their breaking down into smaller granules provides a mechanism by which heme stores can be mobilized. Collectively, these direct and noninvasive dynamic imaging techniques provide new insights into heme storage and transport and open a new avenue for label-free investigation of heme function and regulation in living systems

Label-Free Imaging of Heme Dynamics in Living Organisms by Transient Absorption Microscopy

Heme, a hydrophobic and cytotoxic macrocycle, is an essential cofactor in a large number of proteins and is important for cell signaling. This must mean that heme is mobilized from its place of synthesis or entry into the cell to other parts of the cell where hemoproteins reside. However, the cellular dynamics of heme movement is not well understood, in large part due to the inability to image heme noninvasively in live biological systems. Here, using high-resolution transient absorption microscopy, we showed that heme storage and distribution is dynamic in <i>Caenorhabditis elegans</i>. Intracellular heme exists in concentrated granular puncta which localizes to lysosomal-related organelles. These granules are dynamic, and their breaking down into smaller granules provides a mechanism by which heme stores can be mobilized. Collectively, these direct and noninvasive dynamic imaging techniques provide new insights into heme storage and transport and open a new avenue for label-free investigation of heme function and regulation in living systems

Label-Free Imaging of Heme Dynamics in Living Organisms by Transient Absorption Microscopy

Heme, a hydrophobic and cytotoxic macrocycle, is an essential cofactor in a large number of proteins and is important for cell signaling. This must mean that heme is mobilized from its place of synthesis or entry into the cell to other parts of the cell where hemoproteins reside. However, the cellular dynamics of heme movement is not well understood, in large part due to the inability to image heme noninvasively in live biological systems. Here, using high-resolution transient absorption microscopy, we showed that heme storage and distribution is dynamic in <i>Caenorhabditis elegans</i>. Intracellular heme exists in concentrated granular puncta which localizes to lysosomal-related organelles. These granules are dynamic, and their breaking down into smaller granules provides a mechanism by which heme stores can be mobilized. Collectively, these direct and noninvasive dynamic imaging techniques provide new insights into heme storage and transport and open a new avenue for label-free investigation of heme function and regulation in living systems

Structural and Thermodynamic Characterization of Protein–Ligand Interactions Formed between Lipoprotein-Associated Phospholipase A2 and Inhibitors

Lipoprotein-associated phospholipase A2 (Lp-PLA2) represents a promising therapeutic target for atherosclerosis and Alzheimer’s disease. Here we reported the first crystal structures of Lp-PLA2 bound with reversible inhibitors and the thermodynamic characterization of complexes. High rigidity of Lp-PLA2 structure and similar binding modes of inhibitors with completely different scaffolds are revealed. It not only provides the molecular basis for inhibitory activity but also sheds light on the essential features of Lp-PLA2 recognition with reversible inhibitors

Structure-Guided Discovery of Novel, Potent, and Orally Bioavailable Inhibitors of Lipoprotein-Associated Phospholipase A2

Lipoprotein-associated phospholipase A2 (Lp-PLA2) is a promising therapeutic target for atherosclerosis, Alzheimer’s disease, and diabetic macular edema. Here we report the identification of novel sulfonamide scaffold Lp-PLA2 inhibitors derived from a relatively weak fragment. Similarity searching on this fragment followed by molecular docking leads to the discovery of a micromolar inhibitor with a 300-fold potency improvement. Subsequently, by the application of a structure-guided design strategy, a successful hit-to-lead optimization was achieved and a number of Lp-PLA2 inhibitors with single-digit nanomolar potency were obtained. After preliminary evaluation of the properties of drug-likeness in vitro and in vivo, compound <b>37</b> stands out from this congeneric series of inhibitors for good inhibitory activity and favorable oral bioavailability in male Sprague–Dawley rats, providing a quality candidate for further development. The present study thus clearly demonstrates the power and advantage of integrally employing fragment screening, crystal structures determination, virtual screening, and medicinal chemistry in an efficient lead discovery project, providing a good example for structure-based drug design

Additional file 1 of The association of periodontal disease and oral health with hypertension, NHANES 2009–2018

Supplementary Material

Amino acid residues targeted for mutagenesis in <i>L</i>. <i>amazonensis</i> LHR1.

<p><b>A</b>) Alignment of <i>C</i>. <i>elegans</i> CeHRG-4 with <i>L</i>. <i>amazonensis</i> (LmxA) LHR1 and LHR1 homologues from <i>L</i>. <i>major</i> (LmjF) and <i>L</i>. <i>infantum</i> (LinJ) highlighting the residues selected for mutation analysis. Light blue indicates residues found to be involved in heme uptake by <i>C</i>. <i>elegans</i> HRG-4; orange indicates residues selected for mutagenesis in <i>L</i>. <i>amazonensis</i> LHR1; light gray boxes indicate predicted transmembrane domains. <b>B</b>) Predicted structure of LHR1 with amino acids selected for mutation highlighted. Red = tyrosine; purple = histidine; yellow = arginine; light purple = cysteine.</p

Tyr-18, Tyr-80 and Tyr-129 differentially regulate LHR1-mediated uptake of a toxic heme analog.

<p><i>S</i>. <i>cerevisiae</i> W303 expressing vector alone or yeast codon-optimized LHR1-HA WT, Y18A, H36A, Y80A or Y129A were serially diluted and spotted onto agar plates with a range of GaPPIX concentrations, incubated at 30°C for three days and imaged. Images are representative of two experiments using independent transformants.</p

Mutation of Tyr-18, Tyr-80 and Tyr-129 causes varying growth inhibition levels in yeast respiration assays.

<p><b>A</b>) Western blot of <i>S</i>. <i>cerevisiae</i> Δ<i>hem1</i> (6D) expressing vector alone or yeast codon-optimized LHR1-HA WT, Y18A, H36A, Y80A or Y129A. <b>B</b>) Deconvolution fluorescence images of <i>S</i>. <i>cerevisiae</i> Δ<i>hem1</i> (6D) expressing vector alone or yeast codon-optimized WT or mutant LHR1-HA proteins. The arrows point to the yeast cell plasma membrane. Bar = 2 μm. <b>C</b>) <i>S</i>. <i>cerevisiae</i> Δ<i>hem1</i> (6D) expressing vector alone or yeast codon-optimized WT or mutant LHR1-HA proteins were cultivated for 18 h in glycerol/lactate medium, serially diluted and spotted onto agar plates containing glycerol/lactate and supplemented with either 250 μM ALA (positive control) or a range of heme concentrations, incubated at 30°C for four days and imaged. Images are representative of two experiments using independent transformants.</p