HimGNN: a novel hierarchical molecular graph representation learning framework for property prediction.

Accurate prediction of molecular properties is an important topic in drug discovery. Recent works have developed various representation schemes for molecular structures to capture different chemical information in molecules. The atom and motif can be viewed as hierarchical molecular structures that are widely used for learning molecular representations to predict chemical properties. Previous works have attempted to exploit both atom and motif to address the problem of information loss in single representation learning for various tasks. To further fuse such hierarchical information, the correspondence between learned chemical features from different molecular structures should be considered. Herein, we propose a novel framework for molecular property prediction, called hierarchical molecular graph neural networks (HimGNN). HimGNN learns hierarchical topology representations by applying graph neural networks on atom- and motif-based graphs. In order to boost the representational power of the motif feature, we design a Transformer-based local augmentation module to enrich motif features by introducing heterogeneous atom information in motif representation learning. Besides, we focus on the molecular hierarchical relationship and propose a simple yet effective rescaling module, called contextual self-rescaling, that adaptively recalibrates molecular representations by explicitly modelling interdependencies between atom and motif features. Extensive computational experiments demonstrate that HimGNN can achieve promising performances over state-of-the-art baselines on both classification and regression tasks in molecular property prediction.

Multitarget nociceptor sensitization by a promiscuous peptide from the venom of the King Baboon spider.

The King Baboon spider, Pelinobius muticus, is a burrowing African tarantula. Its impressive size and appealing coloration are tempered by reports describing severe localized pain, swelling, itchiness, and muscle cramping after accidental envenomation. Hyperalgesia is the most prominent symptom after bites from P. muticus, but the molecular basis by which the venom induces pain is unknown. Proteotranscriptomic analysis of P. muticus venom uncovered a cysteine-rich peptide, δ/κ-theraphotoxin-Pm1a (δ/κ-TRTX-Pm1a), that elicited nocifensive behavior when injected into mice. In small dorsal root ganglion neurons, synthetic δ/κ-TRTX-Pm1a (sPm1a) induced hyperexcitability by enhancing tetrodotoxin-resistant sodium currents, impairing repolarization and lowering the threshold of action potential firing, consistent with the severe pain associated with envenomation. The molecular mechanism of nociceptor sensitization by sPm1a involves multimodal actions over several ion channel targets, including NaV1.8, KV2.1, and tetrodotoxin-sensitive NaV channels. The promiscuous targeting of peptides like δ/κ-TRTX-Pm1a may be an evolutionary adaptation in pain-inducing defensive venoms.

Rational Design of Potent α-Conotoxin PeIA Analogues with Non-Natural Amino Acids for the Inhibition of Human α9α10 Nicotinic Acetylcholine Receptors.

α-Conotoxins (α-CTxs) are structurally related peptides that antagonize nicotinic acetylcholine receptors (nAChRs), which may serve as new alternatives to opioid-based treatment for pain-related conditions. The non-natural amino acid analogues of α-CTxs have been demonstrated with improved potency compared to the native peptide. In this study, we chemically synthesized Dab/Dap-substituted analogues of α-CTx PeIA and evaluated their activity at heterologously expressed human α9α10 nAChRs. PeIA[S4Dap, S9Dap] had the most potent half-maximal inhibitory concentration (IC50) of 0.93 nM. Molecular dynamic simulations suggested that the side chain amino group of Dap4 formed additional hydrogen bonds with S168 and D169 of the receptor and Dap9 formed an extra hydrogen bond interaction with Q34, which is distinctive to PeIA. Overall, our findings provide new insights into further development of more potent analogues of α-CTxs, and PeIA[S4Dap, S9Dap] has potential as a drug candidate for the treatment of chronic neuropathic pain.

Selective Scatterings of Phonons and Electrons in Defective Half-Heusler Nb1- δ CoSb for the Figure of Merit zT > 1.

The recently developed defective 19-electron half-Heusler (HH) compounds, represented by Nb1- δ CoSb, possess massive intrinsic vacancies at the cation site and thus intrinsically low lattice thermal conductivity that is desirable for thermoelectric (TE) applications. Yet the TE performance of defective HHs with a maximum figure of merit (zT) <1.0 is still inferior to that of the conventional 18-electron ones. Here, a peak zT exceeding unity is obtained at 1123 K for both Nb0.7 Ta0.13 CoSb and Nb0.6 Ta0.23 CoSb, a benchmark value for defective 19-electron HHs. The improved zT results from the achievement of selective scatterings of phonons and electrons in defective Nb0.83 CoSb, using lanthanide contraction as a design factor to select alloying elements that can strongly impede the phonon propagation but weakly disturb the periodic potential. Despite the massive vacancies induced strong point defect scattering of phonons in Nb0.83 CoSb, Ta alloying is still found effective in suppressing lattice thermal conductivity while maintaining the carrier mobility almost unchanged. In comparison, V alloying significantly deteriorates the carrier transport and thus the TE performance. These results enlarge the category of high-performance HH TE materials beyond the conventional 18-electron ones and highlight the effectiveness of selective scatterings of phonons and electrons in developing TE materials even with massive vacancies.

Nicotinic acetylcholine receptor subtype expression, function, and pharmacology: Therapeutic potential of α-conotoxins.

The pentameric nicotinic acetylcholine receptors (nAChRs) are typically classed as muscle- or neuronal-type, however, the latter has also been reported in non-neuronal cells. Given their broad distribution, nAChRs mediate numerous physiological and pathological processes including synaptic transmission, presynaptic modulation of transmitter release, neuropathic pain, inflammation, and cancer. There are 17 different nAChR subunits and combinations of these subunits produce subtypes with diverse pharmacological properties. The expression and role of some nAChR subtypes have been extensively deciphered with the aid of knock-out models. Many nAChR subtypes expressed in heterologous systems are selectively targeted by the disulfide-rich α-conotoxins. α-Conotoxins are small peptides isolated from the venom of cone snails, and a number of them have potential pharmaceutical value.

The Antinociceptive Activity of (E)-3-(thiophen-2-yl)- N -(p-tolyl)acrylamide in Mice Is Reduced by (E)-3-(furan-2-yl)- N -methyl- N -(p-tolyl)acrylamide Through Opposing Modulatory Mechanisms at the α7 Nicotinic Acetylcholine Receptor.

BACKGROUND: The primary objective of this study was to characterize the pharmacological and behavioral activity of 2 novel compounds, DM497 [(E)-3-(thiophen-2-yl)- N -(p-tolyl)acrylamide] and DM490 [(E)-3-(furan-2-yl)- N -methyl- N -(p-tolyl)acrylamide], structural derivatives of PAM-2, a positive allosteric modulator of the α7 nicotinic acetylcholine receptor (nAChR). METHODS: A mouse model of oxaliplatin-induced neuropathic pain (2.4 mg/kg, 10 injections) was used to test the pain-relieving properties of DM497 and DM490. To assess possible mechanisms of action, the activity of these compounds was determined at heterologously expressed α7 and α9α10 nAChRs, and voltage-gated N-type calcium channel (Ca V 2.2) using electrophysiological techniques. RESULTS: Cold plate tests indicated that 10 mg/kg DM497 was able to decrease neuropathic pain in mice induced by the chemotherapeutic agent oxaliplatin. In contrast, DM490 induced neither pro- nor antinociceptive activity but inhibited DM497's effect at equivalent dose (30 mg/kg). These effects are not a product of changes in motor coordination or locomotor activity. At α7 nAChRs, DM497 potentiated whereas DM490 inhibited its activity. In addition, DM490 antagonized the α9α10 nAChR with >8-fold higher potency than that for DM497. In contrast, DM497 and DM490 had minimal inhibitory activity at the Ca V 2.2 channel. Considering that DM497 did not increase the mouse exploratory activity, an indirect anxiolytic mechanism was not responsible for the observed antineuropathic effect. CONCLUSIONS: The antinociceptive activity of DM497 and the concomitant inhibitory effect of DM490 are mediated by opposing modulatory mechanisms on the α7 nAChR, whereas the involvement of other possible nociception targets such as the α9α10 nAChR and Ca V 2.2 channel can be ruled out.

Characterisation of Elevenin-Vc1 from the Venom of Conus victoriae: A Structural Analogue of α-Conotoxins.

Elevenins are peptides found in a range of organisms, including arthropods, annelids, nematodes, and molluscs. They consist of 17 to 19 amino acid residues with a single conserved disulfide bond. The subject of this study, elevenin-Vc1, was first identified in the venom of the cone snail Conus victoriae (Gen. Comp. Endocrinol. 2017, 244, 11-18). Although numerous elevenin sequences have been reported, their physiological function is unclear, and no structural information is available. Upon intracranial injection in mice, elevenin-Vc1 induced hyperactivity at doses of 5 or 10 nmol. The structure of elevenin-Vc1, determined using nuclear magnetic resonance spectroscopy, consists of a short helix and a bend region stabilised by the single disulfide bond. The elevenin-Vc1 structural fold is similar to that of α-conotoxins such as α-RgIA and α-ImI, which are also found in the venoms of cone snails and are antagonists at specific subtypes of nicotinic acetylcholine receptors (nAChRs). In an attempt to mimic the functional motif, Asp-Pro-Arg, of α-RgIA and α-ImI, we synthesised an analogue, designated elevenin-Vc1-DPR. However, neither elevenin-Vc1 nor the analogue was active at six different human nAChR subtypes (α1ß1εδ, α3ß2, α3ß4, α4ß2, α7, and α9α10) at 1 µM concentrations.

In Situ Assembly of Platinum(II)-Metallopeptide Nanostructures Disrupts Energy Homeostasis and Cellular Metabolism.

Nanostructure-based functions are omnipresent in nature and essential for the diversity of life. Unlike small molecules, which are often inhibitors of enzymes or biomimetics with established methods of elucidation, we show that functions of nanoscale structures in cells are complex and can implicate system-level effects such as the regulation of energy and redox homeostasis. Herein, we design a platinum(II)-containing tripeptide that assembles into intracellular fibrillar nanostructures upon molecular rearrangement in the presence of endogenous H2O2. The formed nanostructures blocked metabolic functions, including aerobic glycolysis and oxidative phosphorylation, thereby shutting down ATP production. As a consequence, ATP-dependent actin formation and glucose metabolite-dependent histone deacetylase activity are downregulated. We demonstrate that assembly-driven nanomaterials offer a rich avenue to achieve broad-spectrum bioactivities that could provide new opportunities in drug discovery.

Nanocarriers Made of Proteins: Intracellular Visualization of a Smart Biodegradable Drug Delivery System.

This work analyzes the intracellular fate of protein-based nanocarriers along their endolysosomal pathway by means of correlative light and electron microscopy methods. To unambiguously identify the nanocarriers and their degradation remnants in the cellular environment, they are labeled with fluorescent, inorganic nanoplatelets. This allows tracking the nanocarriers on their intracellular pathway by means of electron microscopy imaging. From the present data, it is possible to identify different cell compartments in which the nanocarriers are processed. Finally, three different terminal routes for the intracellular destiny of the nanocarriers are presented. These findings are important to reveal the degradation process of protein nanocapsules and contribute to the understanding of the therapeutic success of an encapsulated drug.

Single-Disulfide Conopeptide Czon1107, an Allosteric Antagonist of the Human α3ß4 Nicotinic Acetylcholine Receptor.

Conopeptides are peptides in the venom of marine cone snails that are used for capturing prey or as a defense against predators. A new cysteine-poor conopeptide, Czon1107, has exhibited non-competitive inhibition with an undefined allosteric mechanism in the human (h) α3ß4 nicotinic acetylcholine receptors (nAChRs). In this study, the binding mode of Czon1107 to hα3ß4 nAChR was investigated using molecular dynamics simulations coupled with mutagenesis studies of the peptide and electrophysiology studies on heterologous hα3ß4 nAChRs. Overall, this study clarifies the structure-activity relationship of Czon1107 and hα3ß4 nAChR and provides an important experimental and theoretical basis for the development of new peptide drugs.

Unusual Tetrahydropyridoindole-Containing Tetrapeptides with Human Nicotinic Acetylcholine Receptors Targeting Activity Discovered from Antarctica-Derived Psychrophilic Pseudogymnoascus sp. HDN17-933.

Chemical investigation of the psychrophilic fungus Pseudogymnoascus sp. HDN17-933 derived from Antarctica led to the discovery of six new tetrapeptides psegymamides A-F (1-6), whose planar structures were elucidated by extensive NMR and MS spectrometric analyses. Structurally, psegymamides D-F (4-6) possess unique backbones bearing a tetrahydropyridoindoles unit, which make them the first examples discovered in naturally occurring peptides. The absolute configurations of structures were unambiguously determined using solid-phase total synthesis assisted by Marfey's method, and all compounds were evaluated for their inhibition of human (h) nicotinic acetylcholine receptor subtypes. Compound 2 showed significant inhibitory activity. A preliminary structure-activity relationship investigation revealed that the tryptophan residue and the C-terminal with methoxy group were important to the inhibitory activity. Further, the high binding affinity of compound 2 to hα4ß2 was explained by molecular docking studies.

α-Conotoxin Bt1.8 from Conus betulinus selectively inhibits α6/α3ß2ß3 and α3ß2 nicotinic acetylcholine receptor subtypes.

α-Conotoxins are small disulfide-rich peptides found in the venom of marine cone snails and are potent antagonists of nicotinic acetylcholine receptors (nAChRs). They are valuable pharmacological tools and have potential therapeutic applications for the treatment of chronic pain or neurological diseases and disorders. In the present study, we synthesized and functionally characterized a novel α-conotoxin Bt1.8, which was cloned from Conus betulinus. Bt1.8 selectively inhibited ACh-evoked currents in Xenopus oocytes expressing rat(r) α6/α3ß2ß3 and rα3ß2 nAChRs with an IC50 of 2.1 nM and 9.4 nM, respectively, and similar potency for human (h) α6/α3ß2ß3 and hα3ß2 nAChRs. Additionally, Bt1.8 had higher binding affinity with a slower dissociation rate for the rα6/α3ß2ß3 subtype compared to rα3ß2. The amino acid sequence of Bt1.8 is significantly different from other reported α-conotoxins targeting the two nAChR subtypes. Further Alanine scanning analyses demonstrated that residues Ile9, Leu10, Asn11, Asn12 and Asn14 are critical for its inhibitory activity at the α6/α3ß2ß3 and α3ß2 subtypes. Moreover, the NMR structure of Bt1.8 indicated the presence of a relatively larger hydrophobic zone than other α4/7-conotoxins which may explain its potent inhibition at α6/α3ß2ß3 nAChRs.

A Total Lp-Norm Optimization for Bearing-Only Source Localization in Impulsive Noise with SαS Distribution.

This paper considers the problem of robust bearing-only source localization in impulsive noise with symmetric α-stable distribution based on the Lp-norm minimization criterion. The existing Iteratively Reweighted Pseudolinear Least-Squares (IRPLS) method can be used to solve the least LP-norm optimization problem. However, the IRPLS algorithm cannot reduce the bias attributed to the correlation between system matrices and noise vectors. To reduce this kind of bias, a Total Lp-norm Optimization (TLPO) method is proposed by minimizing the errors in all elements of system matrix and data vector based on the minimum dispersion criterion. Subsequently, an equivalent form of TLPO is obtained, and two algorithms are developed to solve the TLPO problem by using Iterative Generalized Eigenvalue Decomposition (IGED) and Generalized Lagrange Multiplier (GLM), respectively. Numerical examples demonstrate the performance advantage of the IGED and GLM algorithms over the IRPLS algorithm.

Fingerprint and multi-index content determination of ethyl acetate extract of Sedum emarginatum Migo.

Sedum emarginatum Migo (Aoyejingtian) is a perennial succulent herb of the sedum genus in the family Crassulaceae, which has the fountion of treating furuncle, swelling and haematemesis, hematochezia, menorrhagia and hepatitis. Preliminary studies of our research group had showed that the ethyl acetate extract of Sedum emarginatum Migo could inhibit the proliferation of liver cancer HepG2 cells. The establishment of a reasonable and feasible quality evaluation method for the effective parts of Sedum emarginatum Migo can provide a scientific basis for the further development and utilization of Sedum emarginatum Migo. In this study, a multi-wavelength conversion method was used to establish high-performance liquid chromatography (HPLC) fingerprints of the ethyl acetate extract of Sedum emarginatum Migo, and the method was also used to simultaneously determine the gallic acid, protocatechuic acid, caffeic acid, and ferulic acid, isoquercitrin and luteolin in the ethyl acetate extract of Sedum emarginatum Migo. The similarity of the fingerprints of the ethyl acetate extract of Sedum emarginatum Migo from different origins and the content of 6 components were compared. The established method was simple, accurate, table and reliable, which could provide a fast, accurate and reliable method for comprehensive evaluation of the quality of Sedum emarginatum Migo.

Controlled Supramolecular Assembly Inside Living Cells by Sequential Multistaged Chemical Reactions.

Synthetic assembly within living cells represents an innovative way to explore purely chemical tools that can direct and control cellular behavior. We use a simple and modular platform that is broadly accessible and yet incorporates highly intricate molecular recognition, immolative, and rearrangement chemistry. Short bimodular peptide sequences undergo a programmed sequence of events that can be tailored within the living intracellular environment. Each sequential stage of the pathways beginning with the cellular uptake, intracellular transport, and localization imposes distinct structural changes that result in the assembly of fibrillar architectures inside cells. The observation of apoptosis, which is characterized by the binding of Annexin V, demonstrates that programmed cell death can be promoted by the peptide assembly. Higher complexity of the assemblies was also achieved by coassembly of two different sequences, resulting in intrinsically fluorescent architectures. As such, we demonstrate that the in situ construction of architectures within cells will broaden the community's perspective toward how structure formation can impact a living system.

Nkx2-5 Regulates the Proliferation and Migration of H9c2 Cells.

BACKGROUND The protein NKX2-5 affects mammalian heart development. In mice, the disruption of Nkx2-5 has been associated with arrhythmias, abnormal myocardial contraction, abnormal cardiac morphogenesis, and death. However, the details of the mechanisms are unclear. This study was designed to investigate them. MATERIAL AND METHODS Rat cardiomyocytes from the H9c2 cell line were used in our study. First, we knocked down Nkx2-5 in the H9c2 cells and then validated consequent changes in cell proliferation and migration. We then used RNA sequencing to determine the changes in transcripts. Finally, we validated these results by quantitative reverse transcription-polymerase chain reaction. RESULTS We confirmed that Nkx2-5 regulates the proliferation and migration of H9c2 cells. In our experiments, Nkx2-5 regulated the expression of genes related to proliferation, migration, heart development, and disease. Based on bioinformatics analysis, knockdown of Nkx2-5 caused differential expression of genes involved in cardiac development, calcium ion-related biological activity, the transforming growth factor (TGF)-ß signaling pathway, pathways related to heart diseases, the MAPK signaling pathway, and other biological processes and signaling pathways. CONCLUSIONS Nkx2-5 may regulate proliferation and migration of the H9c2 cells through the genes Tgfb-2, Bmp10, Id2, Wt1, Hey1, and Cacna1g; rno-miR-1-3p; the TGF­ß signaling pathway; the MAPK signaling pathway; as well as other genes and pathways.

High-Contrast Imaging of Nanodiamonds in Cells by Energy Filtered and Correlative Light-Electron Microscopy: Toward a Quantitative Nanoparticle-Cell Analysis.

Fluorescent nanodiamonds (fNDs) represent an emerging class of nanomaterials offering great opportunities for ultrahigh resolution imaging, sensing and drug delivery applications. Their biocompatibility, exceptional chemical and consistent photostability renders them particularly attractive for correlative light-electron microscopy studies providing unique insights into nanoparticle-cell interactions. Herein, we demonstrate a stringent procedure to image and quantify fNDs with a high contrast down to the single particle level in cells. Individual fNDs were directly visualized by energy-filtered transmission electron microscopy, that is, inside newly forming, early endosomal vesicles during their cellular uptake processes as well as inside cellular organelles such as a mitochondrion. Furthermore, we demonstrate the unequivocal identification, localization, and quantification of individual fNDs in larger fND clusters inside intracellular vesicles. Our studies are of great relevance to obtain quantitative information on nanoparticle trafficking and their various interactions with cells, membranes, and organelles, which will be crucial to design-improved sensors, imaging probes, and nanotherapeutics based on quantitative data.

Analysis of NKX2-5 in 439 Chinese Patients with Sporadic Atrial Septal Defect.

BACKGROUND The NKX2 gene family is made up of core transcription factors that are involved in the morphogenesis of the vertebrate heart. NKx2-5 plays a pivotal role in mouse cardiogenesis, and mutations in NKx2-5 result in an abnormal structure and function of the heart, including atrial septal defect and cardiac electrophysiological abnormalities. MATERIAL AND METHODS To investigate the genetic variation of NKX2-5 in Chinese patients with sporadic atrial septal defect, we sequenced the full length of the NKX2-5 gene in the participants of the study. Four hundred thirty-nine patients and 567 healthy unrelated individuals were recruited. Genomic DNA was extracted from the peripheral blood leukocytes of the participants. DNA samples from the participants were amplified by multiplex PCR and sequenced on an Illumina HiSeq platform. Variations were detected by comparison with a standard reference genome and annotation with a variant effect predictor. RESULTS Thirty variations were detected in Chinese patients with sporadic atrial septal defect, and 6 single nucleotide polymorphisms (SNPs) had a frequency greater than 1%. Among the 30 variations, the SNPs rs2277923 and rs3729753 were extremely prominent, with a high frequency and odds ratio in patients. CONCLUSIONS Single nucleotide variations are the prominent genetic variations of NKX2-5 in Chinese patients with sporadic atrial septal defect. The SNPs rs2277923 and rs3729753 are prominent single nucleotide variations (SNVs) in Chinese patients with sporadic atrial septal defect.

Backbone cyclization of analgesic conotoxin GeXIVA facilitates direct folding of the ribbon isomer.

Conotoxin GeXIVA inhibits the α9α10 nicotinic acetylcholine receptor (nAChR) and is analgesic in animal models of pain. α-Conotoxins have four cysteines that can have three possible disulfide connectivities: globular (CysI-CysIII and CysII-CysIV), ribbon (CysI-CysIV and CysII-CysIII), or bead (CysI-CysII and CysIII-CysIV). Native α-conotoxins preferably adopt the globular connectivity, and previous studies of α-conotoxins have focused on the globular isomers as the ribbon and bead isomers typically have lower potency at nAChRs than the globular form. A recent report showed that the bead and ribbon isomers of GeXIVA are more potent than the globular isomer, with low nanomolar half-maximal inhibitory concentrations (IC50). Despite this high potency, the therapeutic potential of GeXIVA is limited, because like most peptides, it is susceptible to proteolytic degradation and is challenging to synthesize in high yield. Here we used backbone cyclization as a strategy to improve the folding yield as well as increase the serum stability of ribbon GeXIVA while preserving activity at the α9α10 nAChR. Specifically, cyclization of ribbon GeXIVA with a two-residue linker maintained the biological activity at the human α9α10 nAChR and improved stability in human serum. Short linkers led to selective formation of the ribbon disulfide isomer without requiring orthogonal protection. Overall, this study highlights the value of backbone cyclization in directing folding, improving yields, and stabilizing conotoxins with therapeutic potential.

Novel Genetic Variants of Sporadic Atrial Septal Defect (ASD) in a Chinese Population Identified by Whole-Exome Sequencing (WES).

BACKGROUND Recently, mutations in several genes have been described to be associated with sporadic ASD, but some genetic variants remain to be identified. The aim of this study was to use whole-exome sequencing (WES) combined with bioinformatics analysis to identify novel genetic variants in cases of sporadic congenital ASD, followed by validation by Sanger sequencing. MATERIAL AND METHODS Five Han patients with secundum ASD were recruited, and their tissue samples were analyzed by WES, followed by verification by Sanger sequencing of tissue and blood samples. Further evaluation using blood samples included 452 additional patients with sporadic secundum ASD (212 male and 240 female patients) and 519 healthy subjects (252 male and 267 female subjects) for further verification by a multiplexed MassARRAY system. Bioinformatic analyses were performed to identify novel genetic variants associated with sporadic ASD. RESULTS From five patients with sporadic ASD, a total of 181,762 genomic variants in 33 exon loci, validated by Sanger sequencing, were selected and underwent MassARRAY analysis in 452 patients with ASD and 519 healthy subjects. Three loci with high mutation frequencies, the 138665410 FOXL2 gene variant, the 23862952 MYH6 gene variant, and the 71098693 HYDIN gene variant were found to be significantly associated with sporadic ASD (P<0.05); variants in FOXL2 and MYH6 were found in patients with isolated, sporadic ASD (P<5×10^-4). CONCLUSIONS This was the first study that demonstrated variants in FOXL2 and HYDIN associated with sporadic ASD, and supported the use of WES and bioinformatics analysis to identify disease-associated mutations.