CrysXPP: An explainable property predictor for crystalline materials

We present a deep-learning framework, CrysXPP, to allow rapid and accurate prediction of electronic, magnetic, and elastic properties of a wide range of materials. CrysXPP lowers the need for large property tagged datasets by intelligently designing an autoencoder, CrysAE. The important structural and chemical properties captured by CrysAE from a large amount of available crystal graphs data helped in achieving low prediction errors. Moreover, we design a feature selector that helps to interpret the model’s prediction. Most notably, when given a small amount of experimental data, CrysXPP is consistently able to outperform conventional DFT. A detailed ablation study establishes the importance of different design steps. We release the large pre-trained model CrysAE. We believe by fine-tuning the model with a small amount of property-tagged data, researchers can achieve superior performance on various applications with a restricted data source

CrysMMNet: Multimodal Representation for Crystal Property Prediction

Machine Learning models have emerged as a powerful tool for fast and accurate prediction of different crystalline properties. Exiting state-of-the-art models rely on a single modality of crystal data i.e. crystal graph structure, where they construct multi-graph by establishing edges between nearby atoms in 3D space and apply GNN to learn materials representation. Thereby, they encode local chemical semantics around the atoms successfully but fail to capture important global periodic structural information like space group number, crystal symmetry, rotational information, etc, which influence different crystal properties. In this work, we leverage textual descriptions of materials to model global structural information into graph structure and learn a more robust and enriched representation of crystalline materials. To this effect, we first curate a textual dataset for crystalline material databases containing descriptions of each material. Further, we propose CrysMMNet, a simple multi-modal framework, which fuses both structural and textual representation together to generate a joint multimodal representation of crystalline materials. We conduct extensive experiments on two benchmark datasets across ten different properties to show that CrysMMNet outperforms existing state-of-the-art baseline methods with a good margin. We also observe that fusing the textual representation with crystal graph structure provides consistent improvement for all the SOTA GNN models compared to their own vanilla versions. We have shared the textual dataset, that we have curated for both the benchmark material databases, with the community for future use.Comment: 14 pages, 4 fifure

CrysGNN: Distilling Pre-trained Knowledge to Enhance Property Prediction for Crystalline Materials

In recent years, graph neural network (GNN) based approaches have emerged as a powerful technique to encode complex topological structure of crystal materials in an enriched repre- sentation space. These models are often supervised in nature and using the property-specific training data, learn relation- ship between crystal structure and different properties like formation energy, bandgap, bulk modulus, etc. Most of these methods require a huge amount of property-tagged data to train the system which may not be available for different prop- erties. However, there is an availability of a huge amount of crystal data with its chemical composition and structural bonds. To leverage these untapped data, this paper presents CrysGNN, a new pre-trained GNN framework for crystalline materials, which captures both node and graph level structural information of crystal graphs using a huge amount of unla- belled material data. Further, we extract distilled knowledge from CrysGNN and inject into different state of the art prop- erty predictors to enhance their property prediction accuracy. We conduct extensive experiments to show that with distilled knowledge from the pre-trained model, all the SOTA algo- rithms are able to outperform their own vanilla version with good margins. We also observe that the distillation process provides significant improvement over the conventional ap- proach of finetuning the pre-trained model. We will release the pre-trained model along with the large dataset of 800K crys- tal graph which we carefully curated; so that the pre-trained model can be plugged into any existing and upcoming models to enhance their prediction accuracy

Protocatechuic acid, a phenolic from sansevieria roxburghiana leaves, suppresses diabetic cardiomyopathy via stimulating glucose metabolism, ameliorating oxidative stress, and inhibiting inflammation

Persistent hyperglycemia, impairment of redox status and establishment of inflammatory pathophysiology integrally play important role in the pathogenesis of diabetic cardiomyopathy (DC). Present study examined the therapeutic potential of protocatechuic acid isolated from the Sansevieria roxburghiana rhizomes against DC employing rodent model of type 2 diabetes (T2D). T2D was induced by high fat diet + a low-single dose of streptozotocin (35 mg/kg, i.p.). T2D rats exhibited significantly (p < 0.01) high fasting blood glucose level. Alteration in serum lipid profile (p < 0.01) and increased levels of lactate dehydrogenase (p < 0.01) and creatine kinase (p < 0.01) in the sera of T2D rats revealed the occurrence of hyperlipidemia and diabetic pathophysiology. A significantly (p < 0.01) high levels of serum C-reactive protein and pro-inflammatory mediators revealed the establishment of inflammatory occurrence in T2D rats. Besides, significantly high levels of troponins in the sera revealed the establishment of cardiac dysfunctions in T2D rats. However, protocatechuic acid (50 and 100 mg/kg, p.o.) treatment could significantly reverse the changes in serum biochemical parameters related to cardiac dysfunctions. Molecular mechanism studies demonstrated impairment of signaling cascade, IRS1/PI3K/Akt/AMPK/p 38/GLUT4, in glucose metabolism in the skeletal muscle of T2D rats. Significant (p < 0.01) activation of polyol pathway, enhanced production of AGEs, oxidative stress and up-regulation of inflammatory signaling cascades (PKC/NF-κB/PARP) were observed in the myocardial tissue of T2D rats. However, protocatechuic acid (50 and 100 mg/kg, p.o.) treatment could significantly (p < 0.05-0.01) stimulate glucose metabolism in skeletal muscle, regulated glycemic and lipid status, reduced the secretion of pro-inflammatory cytokines, and restored the myocardial physiology in T2D rats near to normalcy. Histological assessments were also in agreement with the above findings. In silico molecular docking study again supported the interactions of protocatechuic acid with different signaling molecules, PI3K, IRS, Akt, AMPK PKC, NF-κB and PARP, involved in glucose utilization and inflammatory pathophysiology. In silico ADME study predicted that protocatechuic acid would support the drug-likeness character. Combining all, results would suggest a possibility of protocatechuic acid to be a new therapeutic agent for DC in future

Sansevieria roxburghiana Schult. & Schult. F. (Family: Asparagaceae) attenuates type 2 diabetes and its associated cardiomyopathy

Background Sansevieria roxburghiana Schult. & Schult. F. (Family: Asparagaceae) rhizome has been claimed to possess antidiabetic activity in the ethno-medicinal literature in India. Therefore, present experiments were carried out to explore the protective role of edible (aqueous) extract of S. roxburghiana rhizome (SR) against experimentally induced type 2 diabetes mellitus (T2DM) and its associated cardiomyopathy in Wistar rats. Methods SR was chemically characterized by GC-MS analysis. Antidiabetic activity of SR (50 and 100 mg/kg, orally) was measured in high fat diets (ad libitum) + low-single dose of streptozotocin (35 mg/kg, intraperitoneal) induced type 2 diabetic (T2D) rat. Fasting blood glucose level was measured at specific intermissions. Serum biochemical and inflammatory markers were estimated after sacrificing the animals. Besides, myocardial redox status, expressions of signal proteins (NF-kB and PKCs), histological and ultrastructural studies of heart were performed in the controls and SR treated T2D rats. Results Phytochemical screening of the crude extract revealed the presence of phenolic compounds, sugar alcohols, sterols, amino acids, saturated fatty acids within SR. T2D rats exhibited significantly (p < 0.01) higher fasting blood glucose level with respect to control. Alteration in serum lipid profile (p < 0.01) and increased levels of lactate dehydrogenase (p < 0.01) and creatine kinase (p < 0.01) in the sera revealed the occurrence of hyperlipidemia and cell destruction in T2D rats. T2DM caused significant (p < 0.05-0.01) alteration in the biochemical markers in the sera. T2DM altered the redox status (p < 0.05-0.01), decreased (p < 0.01) the intracellular NAD and ATP concentrations in the myocardial tissues of experimental rats. While investigating the molecular mechanism, activation PKC isoforms was observed in the selected tissues. T2D rats also exhibited an up-regulation in nuclear NF-kB (p65) in the cardiac tissues. So, oral administration of SR (50 and 500 mg/kg) could reduce hyperglycemia, hyperlipidemia, membrane disintegration, oxidative stress, vascular inflammation and prevented the activation of oxidative stress induced signaling cascades leading to cell death. Histological and ultra-structural studies of cardiac tissues supported the protective characteristics of SR. Conclusions From the present findings it can be concluded that, SR could offer protection against T2DM and its associated cardio-toxicity via multiple mechanisms viz. hypoglycemic, antioxidant and anti-inflammatory actions

Natural Products as Alternative Choices for P-Glycoprotein (P-gp) Inhibition

Multidrug resistance (MDR) is regarded as one of the bottlenecks of successful clinical treatment for numerous chemotherapeutic agents. Multiple key regulators are alleged to be responsible for MDR and making the treatment regimens ineffective. In this review, we discuss MDR in relation to P-glycoprotein (P-gp) and its down-regulation by natural bioactive molecules. P-gp, a unique ATP-dependent membrane transport protein, is one of those key regulators which are present in the lining of the colon, endothelial cells of the blood brain barrier (BBB), bile duct, adrenal gland, kidney tubules, small intestine, pancreatic ducts and in many other tissues like heart, lungs, spleen, skeletal muscles, etc. Due to its diverse tissue distribution, P-gp is a novel protective barrier to stop the intake of xenobiotics into the human body. Over-expression of P-gp leads to decreased intracellular accretion of many chemotherapeutic agents thus assisting in the development of MDR. Eventually, the effectiveness of these drugs is decreased. P-gp inhibitors act by altering intracellular ATP levels which are the source of energy and/or by affecting membrane contours to increase permeability. However, the use of synthetic inhibitors is known to cause serious toxicities. For this reason, the search for more potent and less toxic P-gp inhibitors of natural origin is underway. The present review aims to recapitulate the research findings on bioactive constituents of natural origin with P-gp inhibition characteristics. Natural bioactive constituents with P-gp modulating effects offer great potential for semi-synthetic modification to produce new scaffolds which could serve as valuable investigative tools to recognize the function of complex ABC transporters apart from evading the systemic toxicities shown by synthetic counterparts. Despite the many published scientific findings encompassing P-gp inhibitors, however, this article stand alones because it provides a vivid picture to the readers pertaining to Pgp inhibitors obtained from natural sources coupled with their mode of action and structures. It provides first-hand information to the scientists working in the field of drug discovery to further synthesise and discover new P-gp inhibitors with less toxicity and more efficacies

Carnosic Acid, a Natural Diterpene, Attenuates Arsenic-Induced Hepatotoxicity via Reducing Oxidative Stress, MAPK Activation, and Apoptotic Cell Death Pathway

The present studies have been executed to explore the protective mechanism of carnosic acid (CA) against NaAsO2-induced hepatic injury. CA exhibited a concentration dependent (1-4 μM) increase in cell viability against NaAsO2 (12 μM) in murine hepatocytes. NaAsO2 treatment significantly enhanced the ROS-mediated oxidative stress in the hepatic cells both in in vitro and in vivo systems. Significant activation of MAPK, NF-κB, p53, and intrinsic and extrinsic apoptotic signaling was observed in NaAsO2-exposed hepatic cells. CA could significantly counteract with redox stress and ROS-mediated signaling and thereby attenuated NaAsO2-mediated hepatotoxicity. NaAsO2 (10 mg/kg) treatment caused significant increment in the As bioaccumulation, cytosolic ATP level, DNA fragmentation, and oxidation in the liver of experimental mice (n = 6). The serum biochemical and haematological parameters were significantly altered in the NaAsO2-exposed mice (n = 6). Simultaneous treatment with CA (10 and 20 mg/kg) could significantly reinstate the NaAsO2-mediated toxicological effects in the liver. Molecular docking and dynamics predicted the possible interaction patterns and the stability of interactions between CA and signal proteins. ADME prediction anticipated the drug-likeness characteristics of CA. Hence, there would be an option to employ CA as a new therapeutic agent against As-mediated toxic manifestations in future

Water Spinach, <i>Ipomoea aquatica</i> (Convolvulaceae), Ameliorates Lead Toxicity by Inhibiting Oxidative Stress and Apoptosis

<div><p>Background</p><p><i>Ipomoea aquatica</i> (Convolvulaceae), an aquatic edible plant, is traditionally used against heavy metal toxicity in India. The current study intended to explore the protective role of edible (aqueous) extract of <i>I</i>. <i>aquatica</i> (AEIA) against experimentally induced Pb-intoxication.</p><p>Methods</p><p>The cytoprotective role of AEIA was measured on mouse hepatocytes by cell viability assay followed by Hoechst staining and flow cytometric assay. The effect on ROS production, lipid peroxidation, protein carbonylation, intracellular redox status were measured after incubating the hepatocytes with Pb-acetate (6.8 μM) along with AEIA (400 μg/ml). The effects on the expressions of apoptotic signal proteins were estimated by western blotting. The protective role of AEIA was measured by <i>in vivo</i> assay in mice. Haematological, serum biochemical, tissue redox status, Pb bioaccumulation and histological parameters were evaluated to estimate the protective role of AEIA (100 mg/kg) against Pb-acetate (5 mg/kg) intoxication.</p><p>Results</p><p>Pb-acetate treated hepatocytes showed a gradual reduction of cell viability dose-dependently with an IC₅₀ value of 6.8 μM. Pb-acetate treated hepatocytes exhibited significantly enhanced levels (p < 0.01) of ROS production, lipid peroxidation, protein carbonylation with concomitant depletion (p < 0.01) of antioxidant enzymes and GSH. However, AEIA treatment could significantly restore the aforementioned parameters in murine hepatocytes near to normalcy. Besides, AEIA significantly reversed (p < 0.05–0.01) the alterations of transcription levels of apoptotic proteins viz. Bcl 2, Bad, Cyt C, Apaf-1, cleaved caspases [caspase 3, caspase 8 and caspase 9], Fas and Bid. In <i>in vivo</i> bioassay, Pb-acetate treatment caused significantly high intracellular Pb burden and oxidative pressure in the kidney, liver, heart, brain and testes in mice. In addition, the haematological and serum biochemical factors were changed significantly in Pb-acetate-treated animals. AEIA treatment restored significantly the evaluated-parameters to the near-normal position.</p><p>Conclusion</p><p>The extract may offer the protective effect via counteracting with Pb mediated oxidative stress and/or promoting the elimination of Pb by chelating. The presence of substantial quantities of flavonoids, phenolics and saponins would be responsible for the overall protective effect.</p></div

Effect of SR on body weight of T2D rats.

<p>Effect of SR on body weight of T2D rats.</p