Molecular insights of anti-diabetic compounds and its hyaluronic acid conjugates against aldose reductase enzyme through molecular modeling and simulations study-a novel treatment option for inflammatory diabetes

CONTEXT

Chronic inflammation is a risk factor for diabetes, but it can also be a complication of diabetes, leading to severe diabetes and causing many other clinical manifestations. Inflammation is a major emerging complication in both type I and type II diabetes, which causes increasing interest in targeting inflammation to improve and control diabetes. Diabetes with insulin resistance and impaired glucose utilization in humans and their underlying mechanism is not fully understood. But a growing understanding of the intricacy of the insulin signaling cascade in diabetic inflammatory cells reveals potential target genes and their proteins responsible for severe insulin resistance. With this baseline concept, the current project explores the binding affinities of the hyaluronic acid anti-diabetic compounds conjugates to such target proteins in diabetic inflammatory cells and their molecular geometries. A range of 48 anti-diabetic compounds was screened against aldose reductase binding pocket 3 protein target through in silico molecular docking, and results revealed that three compounds viz, metformin (CID:4091), phenformin (CID:8249), sitagliptin (CID:4,369,359), possess significant binding affinity out of 48 chosen drugs. Further, these three anti-diabetic compounds were conjugated with hyaluronic acid (HA), and their binding affinity and their molecular geometrics towards aldose reductase enzyme were screened compared with the free form of the drug. The molecular geometries of three shortlisted drugs (metformin, phenformin, sitagliptin) and their HA conjugates were also explored through density functional theory studies, and it proves their good molecular geometry towards pocket 3 of aldose reductase target. Further, MD simulation trajectories affirm that HA conjugates possess good binding affinity and simulation trajectories with protein target aldose reductase than a free form of the drug. Our current study unravels the new mechanism of drug targeting for diabetes through HA conjugation for inflammatory diabetes. HA conjugates act as novel drug candidates for treating inflammatory diabetes; however, it needs further human clinical trials.

METHODS

For ligand structure, PubChem, ACD chem sketch, and online structure file generator platform are utilized for ligand preparation. Target protein aldose reductase obtained from protein database (PDB). For molecular docking analysis, AutoDock Vina (Version 4) was utilized. pKCSM online server used to predict ADMET properties of the above three shortlisted drugs from the docking study. Using mol-inspiration software (version 2011.06), three shortlisted compounds' bioactivity scores were predicted. DFT analysis for three shortlisted anti-diabetic drugs and their hyaluronic acid conjugates were calculated using a functional B3LYP set of Gaussian 09 software. Molecular dynamics simulation calculations for six chosen protein-ligand complexes were done through YASARA dynamics software and AMBER14 force field.

Comparative anti-Diabetic potential of phytocompounds from Dr. Duke's phytochemical and ethnobotanical database and standard antidiabetic drugs against diabetes hyperglycemic target proteins: an in silico validation

In the current investigation, the antidiabetic potential of 40 phytocompounds from Dr. Dukes phytochemical and ethanobotanical database and three antidiabetic pharmaceuticals from the market comparatively validated against hyperglycemic target proteins. Silymarin, proanthocyanidins, merremoside, rutin, mangiferin-7-O-beta-glucoside, and gymnemic acid exhibited good binding affinity toward protein targets of diabetes among the 40 phytocompounds from Dr.Dukes database over three chosen antidiabetic pharmaceutical compounds. Further these phytocompounds and sitagliptin are validated for its ADMET and bioactivity score to screen its pharmacological and pharmacokinetics properties. Silymarin, proanthocyanidins, rutin along with sitagliptin screened for DFT analysis found that phytocompounds have great Homo-Lumo orbital energies over commercial pharmaceutical sitagliptin. Finally, four complexes of alpha amylase-silymarin, alpha amylase-sitagliptin, aldose reductase-proanthocyanidins, and aldose reductase-sitagliptin screened for MD simulation and MMGBSA analysis, results shown that the phytocompounds silymarin and proanthocyanidins have strong affinities for binding to the binding pockets of alpha amylase and aldose reductase respectively over antidiabetic pharmaceuticals. Our current study proven proanthocyanidins and silymarin act as novel antidiabetic compounds toward diabetic target protein but it require clinical trial to evaluate its clinical pertinence toward diabetic target proteins.Communicated by Ramaswamy Sarma.

Increased level of plasma Cyclophilin A in early diabetic population suggesting it as a reliable pro inflammatory biomarker of coronary artery disease in diabetic patients

Funding Acknowledgements

Type of funding sources: Other. Main funding source(s): Institute of Cardiovascular disease, Madras Medical Mission

Background

Type 2 Diabetes (DM) is a pro-inflammatory state in the pathogenesis of Atherosclerosis with the presence of many active proteins, of which CyclophilinA (CypA) has been shown to have a positive correlation with the presence and severity of vascular diseases. As Cyp A is proven to be secreted in varying levels from cells, in response to inflammatory stimuli, viz., hypoxia, infection, and oxidative stress, it is found ideal, to study it further as one of a reliable pro-inflammatory biomarker responsible for the progression of Coronary Artery Disease (CAD) in early DM.

Purpose

A prospective cross-sectional study was conducted to quantify CypA in the early phase of DM before the onset of CAD, in comparison to non-diabetic volunteers and to review it as one of the pro-inflammatory biomarkers of CAD, in association with hsCRP and other proven biomarkers (Insulin, Lipid profile, HBA1C, and Glucose).

Methods

The study subject comprised 299 patients with DM and 50 healthy volunteers. History of duration of DM and other co-morbidities was obtained. A comprehensive clinical examination and non-invasive evaluation of atherosclerotic vascular disease were done to rule out CAD. CypA was analyzed by ELISA kit in serum. P-value of <0.05 was considered statistically significant.

Results

The average age group of study population is 51­ with an SD of 9.4(Male 206; Female 143). The observed range of CypA in our study is 50–1974 ng/ml, which is much higher than the values obtained in other studies (2–200 ng/ml). An increased level of CYP A is seen in DM than control group with a significant P Value of <0.001 [DM - Mean 462.5 ; Median of 328 ng/ml; Control group(Non diabetic) - Mean 273 ; Median 190 ng/ml]. CypA value in early diabetics (<5 years) is higher than patients with >5 years of DM (one-way ANOVA).

Review of hsCRP shows statistically different levels between DM and the control group (p=0.012). Scatter plots of CypA and hsCRP concentration showed values within 500 ng/ml of CypA distributed in the mid to average risk category of hsCRP (<1–3 mg/l). The probability of proposing CypA as a pro-inflammatory biomarker compared to hsCRP in DM is reviewed by the ROC curve (AUC 0.684 with a sensitivity of 80% and specificity of 50%). Increased CypA and hsCRP are observed in females than males (CypA: p=0.04 and hsCRP: p<0.001). No significant difference is observed between the two groups in other variables (Insulin (P=0.69), Cholesterol (P= 0.33), TGL (P=0.77), HDL (P=0.17), LDL (P=0.06).

Conclusion

In our study CypA level is increased in the early stage of DM when compared with non-Diabetes. The range obtained is higher than the previous study values. CypA value of <500 ng/ml is observed to be related to CAD when reviewed along with the hsCRP cardiac risk stratification range. The scope of CypA as a reliable pro-inflammatory biomarker of CAD in early DM is more promising and its edge over hsCRP as an early biomarker is to be reviewed further.

Shimon Vega in the eyes of his students and postdocs

Professor Shimon Vega (1943-2021) of the Weizmann Institute of Science passed away on the 16-th of November. Shimon Vega established theoretical frameworks to develop and explain solid-state nuclear magnetic resonance (NMR) and dynamic nuclear polarization (DNP) techniques and methodologies. His departure left a profound mark on his many students, postdocs, and colleagues. Shortly after his passing, we all assembled spontaneously for an international online meeting to share our reflections and memories of our experiences in Shimon's lab and how they affected us deeply during that period of timeand throughout our scientific careers. These thoughts and feelings were put here into writing.

Simplification of the purification of heat stable recombinant low molecular weight proteins and peptides from GST-fusion products

The synthesis and purification of peptides of importance in the fields of research and medicine continue to be a challenging task. Chemical synthesis of oligopeptides, especially those greater than 25 amino acids, is cost prohibitive. On the other hand, several bottlenecks exist in the production of recombinant short peptides in heterologous expression hosts such as Escherichia coli (E. coli). In this study, a rapid, cost-effective, and reliable method for the production and single-step-purification of peptides and small proteins was developed. Five peptides and small proteins were overexpressed in E. coli as GST-fusion products in high yields. The recombinant peptides or proteins were successfully purified after enzymatic cleavage with selective heat-induced precipitation of the GST-affinity tag. Qualitative and quantitative analysis using SDS-PAGE and mass spectrometric methods suggest that the recombinant peptides/ proteins were purified to greater than 95% homogeneity. Results of biophysical experiments, including multi-dimensional NMR spectroscopy, show that the purified proteins/ peptides retain their native conformation. Isothermal titration calorimetry studies indicate no significant change in the binding affinity of the heat-treated purified product to their interacting partner(s) compared to the recombinant peptides purified by conventional chromatographic procedures without subjecting to heat treatment. In our opinion, the results reported render the purification of recombinant proteins/ peptides of biomedical relevance using our proposed method easy and reliable.

Analysis of Microarray Data by Empirical Wavelet Transform for Cancer Classification Using Block by Block Method

In this study, DNA microarray data is analyzed from a signal processing perspective for cancer classification. An adaptive wavelet transform named Empirical Wavelet Transform (EWT) is analyzed using block-by-block procedure to characterize microarray data. The EWT wavelet basis depends on the input data rather predetermined like in conventional wavelets. Thus, EWT gives more sparse representations than wavelets. The characterization of microarray data is made by block-by-block procedure with predefined block sizes in powers of 2 that starts from 128 to 2048. After characterization, a statistical hypothesis test is employed to select the informative EWT coefficients. Only the selected coefficients are used for Microarray Data Classification (MDC) by the Support Vector Machine (SVM). Computational experiments are employed on five microarray datasets; colon, breast, leukemia, CNS and ovarian to test the developed cancer classification system. The obtained results demonstrate that EWT coefficients with SVM emerged as an effective approach with no misclassification for MDC system.

Molecular insights on cytochrome c and nucleotide regulation of apoptosome function and its implication in cancer

Cytochrome c (Cyt c) released from mitochondria interacts with Apaf-1 to form the heptameric apoptosome, which initiates the caspase cascade to execute apoptosis. Although lysine residue at 72 (K72) of Cyt c plays an important role in the Cyt c-Apaf-1 interaction, the underlying mechanism of interaction between Cyt c and Apaf-1 is still not clearly defined. Here we identified multiple lysine residues including K72, which are also known to interact with ATP, to play a key role in Cyt c-Apaf-1 interaction. Mutation of these lysine residues abrogates the apoptosome formation causing inhibition of caspase activation. Using in-silico molecular docking, we have identified Cyt c-binding interface on Apaf-1. Although mutant Cyt c shows higher affinity for Apaf-1, the presence of Cyt c-WT restores the apoptosome activity. ATP addition modulates only mutant Cyt c binding to Apaf-1 but not WT Cyt c binding to Apaf-1. Using TCGA and cBioPortal, we identified multiple mutations in both Apaf-1 and Cyt c that are predicted to interfere with apoptosome assembly. We also demonstrate that transcript levels of various enzymes involved with dATP or ATP synthesis are increased in various cancers. Silencing of nucleotide metabolizing enzymes such as ribonucleotide reductase subunit M1 (RRM1) and ATP-producing glycolytic enzymes PKM2 attenuated ATP production and enhanced caspase activation. These findings suggest important role for lysine residues of Cyt c and nucleotides in the regulation of apoptosome-dependent apoptotic cell death as well as demonstrate how these mutations and nucleotides may have a pivotal role in human diseases such as cancer.

A Study on Hepatitis B Viral Seromarkers and Associated Risk Factors among the Patients Suffering from Acute and Chronic Hepatitis B Infection

Background:

Hepatitis B viral infection is the most common cause of hepatitis, and it leads to serious liver diseases such as cirrhosis and hepatocellular carcinoma.

Aim:

The aim of the study is to differentiate acute hepatitis B and chronic hepatitis B (CHB) among patients seropositive for hepatitis B surface antigen (HBsAg).

Materials and Methods:

This study was carried out in the Department of Microbiology, Chettinad Hospital and Research Institute, Kelambakkam, Tamil Nadu, India, for a period of 6 months (January 2018–June 2018). Blood samples were collected from 87 patients for the detection of hepatitis B virus (HBV) serological markers. HBsAg, hepatitis B e antigen (HBeAg), anti-HBc total, anti-HBc IgM, and antibody to hepatitis B surface antigen were screened using the ELISA method. Detailed demographic profile including history of previous hepatitis infection, previous blood transfusion, and other related details were collected and documented using a structured questionnaire.

Results:

A total of 87 patients were HBsAg seropositive; among them, 55 (63.2%) were male and 32 (36.9%) were female. Based on the serological markers tested, 24 and 63 were suffering from acute and chronic HBV infections, respectively. Among the acute hepatitis B patients, all samples were seropositive for HBsAg, anti-HBc total, and anti-HBc IgM. HBeAg seromarker was found in 15 patients (62.5%). Among the CHB patients, all samples were seropositive for HBsAg and anti-HBc total. HBeAg seromarker was found in 28 patients with 44.4%. Alcohol consumption was the major risk factor for the transmission of HBV infection.

Conclusion:

An increased sample size and detailed study of high-risk behavior will provide an alarming awareness of their association.

Characterization of virulence factors, antifungal resistance with ERG-11 gene among Candida species isolated from pulmonary samples

BACKGROUND

Candida is a part of the normal oropharyngeal flora and the upper respiratory tract. Candida albicans(C. albicans), is the predominant species causing respiratory tract infections associated with pneumonia. Resistance to azole antifungal agents among the C. albicans may be due to alteration of the target enzymes, which are encoded in ERG11 gene. The biofilm formation may also be a cause to antifungal resistance.

MATERIALS AND METHODS

This study was conducted at Chettinad Hospital and Research Institute. Samples were collected from June 2018-June 2019, for a period of 1 year. After species confirmation, virulence factor among the Candida species were identified by hemolysis test, coagulase test and biofilm formation. Genotypic confirmation of C. albicans and their azole resistance due to ERG 11 gene were done using multiplex PCR.

RESULTS

In our study, 31 (55%) C. albicans, 8 (14%) Candida glabrata(C. glabrata) and 10 (17%) Candida tropicalis(C. tropicalis), three Aspergillus flavus(A. flavus), two Aspergillus fumigatous (A. fumigatous), one Aspergillus niger (A. niger) and one Mucor species were isolated. In C. albicans, 31 were positive for Germ tube and Chalmydospore formation. Six of candida species were isolated along with bacterial co infection. Among the Candida isolates, 17 (55%) C. albicans strains were strongly biofilm positive and 14(45%) were negative. The susceptibility pattern of (n = 31) C. albicans were as follows: fluconazole (21(68%) S, 10(32%) R), voriconazole (22(71%)S),9(21%) R) and Amphotericin B 31(100%) S). Among the 19 C. albicans, four were positive for ERG11 gene.

CONCLUSION

The isolation of C. albicans and non - albicans from respiratory specimens should be reconsidered as these organisms are re-emerging pathogens. Speciation is needed due to variation in species pathogenicity and their susceptibility.

Design of a thrombin resistant human acidic fibroblast growth factor (hFGF1) variant that exhibits enhanced cell proliferation activity

Acidic fibroblast growth factors (FGF1s) are heparin binding proteins that regulate a wide array of key cellular processes and are also candidates for promising biomedical applications. FGF1-based therapeutic applications are currently limited due to their inherent thermal instability and susceptibility to proteases. Using a wide range of biophysical and biochemical techniques, we demonstrate that reversal of charge on a well-conserved positively charged amino acid, R136, in the heparin binding pocket drastically increases the resistance to proteases, thermal stability, and cell proliferation activity of the human acidic fibroblast growth factor (hFGF1). Two-dimensional NMR data suggest that the single point mutations at position-136 (R136G, R136L, R136Q, R136K, and R136E) did not perturb the backbone folding of hFGF1. Results of the differential scanning calorimetry experiments show that of all the designed R136 mutations only the charge reversal mutation, R136E, significantly increases (ΔT_m = 7 °C) the thermal stability of the protein. Limited trypsin and thrombin digestion results reveal that the R136E mutation drastically increases the resistance of hFGF1 to the action of the serine proteases. Isothermal titration calorimetry data show that the R136E mutation markedly decreases the heparin binding affinity of hFGF1. Interestingly, despite lower heparin binding affinity, the cell proliferation activity of the R136E variant is more than double of that exhibited by either the wild type or the other R136 variants. The R136E variant due to its increased thermal stability, resistance to proteases, and enhanced cell proliferation activity are expected to provide valuable clues for the development of hFGF1- based therapeutics for the management of chronic diabetic wounds.

Heat transfer enhancement in the boundary layer flow of hybrid nanofluids due to variable viscosity and natural convection

The aim of the current work is to explore how heat transfer can be enhanced by variations in the basic properties of fluids in the presence of free convection with the aid of suspended hybrid nanofluids. Also, the influence of the Laurentz force on the flow is considered. The mathematical equations are converted into a pair of self-similarity equations by applying appropriate transformations. The reduced similarity equivalences are then solved numerically by Runge-Kutta-Fehlberg 45^th-order method. To gain better perception of the problem, the flow and energy transfer characteristics are explored for distinct values of significant factors such as variable viscosity, convection, magnetic field, and volume fraction. The results acquired are in good agreement with previously published results. The noteworthy finding is that the thermal conductivity is greater in hybrid nanofluid than that of a regular nanofluid in the presence of specified factors. The boundary layer thickness of both hybrid nanofluid and normal nanofluid diminishes due to decrease in variable viscosity. The fluid flow and temperature of the hybrid nanofluid and normal nanofluid increases as there is a rise in volume fraction.

Molecular mechanisms of heparin-induced modulation of human interleukin 12 bioactivity

Human interleukin-12 (hIL-12) is a heparin-binding cytokine whose activity was previously shown to be enhanced by heparin and other sulfated glycosaminoglycans. The current study investigated the mechanisms by which heparin increases hIL-12 activity. Using multiple human cell types, including natural killer cells, an IL-12 indicator cell line, and primary peripheral blood mononuclear and T cells, along with bioactivity, flow cytometry, and isothermal titration calorimetry assays, we found that heparin-dependent modulation of hIL-12 function correlates with several of heparin's biophysical characteristics, including chain length, sulfation level, and concentration. Specifically, only heparin molecules longer than eight saccharide units enhanced hIL-12 activity. Furthermore, heparin molecules with three sulfate groups per disaccharide unit outperformed heparin molecules with one or two sulfate groups per disaccharide unit in terms of enhanced hIL-12 binding and activity. Heparin also significantly reduced the EC₅₀ value of hIL-12 by up to 11.8-fold, depending on the responding cell type. Cytokine-profiling analyses revealed that heparin affected the level, but not the type, of cytokines produced by lymphocytes in response to hIL-12. Interestingly, although murine IL-12 also binds heparin, heparin did not enhance its activity. Using the gathered data, we propose a model of hIL-12 stabilization in which heparin serves as a co-receptor enhancing the interaction between heterodimeric hIL-12 and its receptor subunits. The results of this study provide a foundation for further investigation of heparin's interactions with IL-12 family cytokines and for the use of heparin as an immunomodulatory agent.

Probing the role of proline -135 on the structure, stability, and cell proliferation activity of human acidic fibroblast growth factor

Human acidic fibroblast growth factor 1 (hFGF1) is a protein intricately involved in cell growth and tissue repair. In this study, we investigate the effect(s) of understanding the role of a conserved proline (P135), located in the heparin binding pocket, on the structure, stability, heparin binding affinity, and cell proliferation activity of hFGF1. Substitution of proline-135 with a positively charged lysine (P135K) resulted in partial destabilization of the protein; however, the overall structural integrity of the protein was maintained upon substitution of proline-135 with either a negative charge (P135E) or a polar amino acid (P135Q). Interestingly, upon heparin binding, an increase in thermal stability equivalent to that of wt-hFGF1 was observed when P135 was replaced with a positive (P135K) or a negative charge (P135E), or with a polar amino acid (P135Q). Surprisingly, introduction of negative charge in the heparin-binding pocket at position 135 (P135E) increased hFGF1's affinity for heparin by 3-fold, while the P135K mutation, did not alter the heparin-binding affinity. However, the enhanced heparin-binding affinity of mutant P135E did not translate to an increase in cell proliferation activity. Interestingly, the P135K and P135E double mutations, P135K/R136E and P135/R136E, reduced the heparin binding affinity by ∼3-fold. Furthermore, the cell proliferation activity was increased when the charge reversal mutation R136E was paired with both P135E (P135E/R136E) and P135K (P135K/R136E). Overall, the results of this study suggest that while heparin is useful for stabilizing hFGF1 on the cell surface, this interaction is not mandatory for activation of the FGF receptor.

Identification of avian vasotocin receptor subtype-specific antagonists involved in the stress response of the chicken, Gallus gallus

Vasotocin 1a and 1b receptors (V1aR and V1bR) have been shown to play important roles in the neuroendocrine regulation of stress responses via the anterior pituitary (AP) of birds. To identify effective subtype-specific antagonists for the chicken V1aR (cV1aR) and cV1bR, potential antagonists to the mammalian V1R were screened against the cV1aR and cV1bR 3D structural models by molecular docking analysis with determination of binding pocket/amino acid residues involved in the interaction. The antagonistic effects of the selected ligands were examined by measuring pro-opiomelanocortin (POMC) heteronuclear RNA (hnPOMC) levels following the in vitro stress administration to primary chicken AP cells. Results of in silico analysis showed that the Manning compound and several other antagonists were bound to cV1bR with higher affinity than the natural agonist, arginine vasotocin (AVT). Similarities and differences in the antagonist-receptor binding interface with receptors were characterized for each ligand. Non-peptide mammalian V1bR antagonists, SSR-149415 and L-368899, were shown to be effective and had an additive effect in blocking POMC hnRNA expression in pituitary cell culture studies. SR-49059 antagonized the effect(s) of AVT/CRH on the downregulation of the cV1aR and the upregulation of the cCRH-R2 expression but not the cV1bR and cCRH-R1. The Manning compound antagonized the downregulation of cV1aR, cV1bR and cCRH-R1 and the upregulation of cCRH-R2 expression. The specificity of antagonists apparently resulted from unique differences in the interacting residues and their binding affinities. Collectively, these results provide valuable leads for future development of novel compounds capable of blocking or attenuating the AP stress response of avian species and perhaps other non-mammalian vertebrates as well.

Identification of curcumin derivatives as human LMTK3 inhibitors for breast cancer: a docking, dynamics, and MM/PBSA approach

Human lemur tyrosine kinase-3 (LMTK3) is primarily involved in regulation of estrogen receptor-α (ERα) by phosphorylation activity. LMTK3 acts as key biomarker for ERα positive breast cancer and identified as novel drug target for breast cancer. Due to the absence of experimental reports, the computational approach has been followed to screen LMTK3 inhibitors from natural product curcumin derivatives based on rational inhibitor design. The initial virtual screening and re-docking resulted in identification of top three leads with favorable binding energy and strong interactions in critical residues of ATP-binding cavity. ADME prediction confirmed the pharmacological activity of the leads with various properties. The stability and binding affinity of leads were well refined in dynamic system from 25 ns MD simulations. The behavior of protein motion towards closure of ATP-binding cavity was evaluated based on eigenvectors by PCA. In addition, MM/PBSA calculations also confirmed the relative binding free energy of LMTK3-lead complexes in favor of the effective binding. From our study, novel LMTK3 inhibitors tetrahydrocurcumin, curcumin 4,4'-diacetate, and demethoxycurcumin have been proposed with inhibition mechanism. Further experimental evaluation on reported lead candidates might prove its role in breast cancer therapeutics.

Hemodialysis as a Treatment of Severe Ethanol Poisoning

A 64-year-old woman presented with coma and shock due to severe ethanol intoxication. Her initial, markedly elevated blood alcohol level of 136.5 mM fell only by 16% after a 4-hour period of conservative treatment consisting of mechanical respiration and the administration of intravenous fluids, vasopressors and inotropics. Subsequent hemodialysis rapidly reduced her blood ethanol concentrations to less threatening levels, with prompt restoration of her consciousness. Hemodialysis may be life-saving and should be considered in patients with severe ethanol intoxication.

Effect of extension of the heparin binding pocket on the structure, stability, and cell proliferation activity of the human acidic fibroblast growth factor

Acidic human fibroblast growth factor (hFGF1) plays a key role in cell growth and proliferation. Activation of the cell surface FGF receptor is believed to involve the glycosaminoglycan, heparin. However, the exact role of heparin is a subject of considerable debate. In this context, in this study, the correlation between heparin binding affinity and cell proliferation activity of hFGF1 is examined by extending the heparin binding pocket through selective engineering via charge reversal mutations (D82R, D84R and D82R/D84R). Results of biophysical experiments such as intrinsic tryptophan fluorescence and far UV circular dichroism spectroscopy suggest that the gross native structure of hFGF1 is not significantly perturbed by the engineered mutations. However, results of limited trypsin digestion and ANS binding experiments show that the backbone structure of the D82R variant is more flexible than that of the wild type hFGF1. Results of the temperature and urea-induced equilibrium unfolding experiments suggest that the stability of the charge-reversal mutations increases in the presence of heparin. Isothermal titration calorimetry (ITC) data reveal that the heparin binding affinity is significantly increased when the charge on D82 is reversed but not when the negative charge is reversed at both positions D82 and D84 (D82R/D84R). However, despite the increased affinity of D82R for heparin, the cell proliferation activity of the D82R variant is observed to be reduced compared to the wild type hFGF1. The results of this study clearly demonstrate that heparin binding affinity of hFGF1 is not strongly correlated to its cell proliferation activity.

Distribution of water in the pores of periodic mesoporous organosilicates – a proton solid state MAS NMR study

Proposed model of water layers and pore filling in ethane substituted periodic mesoporous organosilicates (PMO_E) based on analysis of solid state magic angle spinning (MAS) proton NMR spectra.

Stilbenoid prenyltransferases define key steps in the diversification of peanut phytoalexins

Defense responses of peanut (Arachis hypogaea) to biotic and abiotic stresses include the synthesis of prenylated stilbenoids. Members of this compound class show several protective activities in human disease studies, and the list of potential therapeutic targets continues to expand. Despite their medical and biological importance, the biosynthetic pathways of prenylated stilbenoids remain to be elucidated, and the genes encoding stilbenoid-specific prenyltransferases have yet to be identified in any plant species. In this study, we combined targeted transcriptomic and metabolomic analyses to discover prenyltransferase genes in elicitor-treated peanut hairy root cultures. Transcripts encoding five enzymes were identified, and two of these were functionally characterized in a transient expression system consisting of Agrobacterium-infiltrated leaves of Nicotiana benthamiana We observed that one of these prenyltransferases, AhR4DT-1, catalyzes a key reaction in the biosynthesis of prenylated stilbenoids, in which resveratrol is prenylated at its C-4 position to form arachidin-2, whereas another, AhR3'DT-1, added the prenyl group to C-3' of resveratrol. Each of these prenyltransferases was highly specific for stilbenoid substrates, and we confirmed their subcellular location in the plastid by fluorescence microscopy. Structural analysis of the prenylated stilbenoids suggested that these two prenyltransferase activities represent the first committed steps in the biosynthesis of a large number of prenylated stilbenoids and their derivatives in peanut. In summary, we have identified five candidate prenyltransferases in peanut and confirmed that two of them are stilbenoid-specific, advancing our understanding of this specialized enzyme family and shedding critical light onto the biosynthesis of bioactive stilbenoids.

Simple and Efficient Purification of Recombinant Proteins Using the Heparin-Binding Affinity Tag

Heparin, a member of the glycosaminoglycan family, is known to interact with more than 400 different types of proteins. For the past few decades, significant progress has been made to understand the molecular details involved in heparin-protein interactions. Based on the structural knowledge available from the FGF1-heparin interaction studies, we have designed a novel heparin-binding peptide (HBP) affinity tag that can be used for the simple, efficient, and cost-effective purification of recombinant proteins of interest. HBP-tagged fusion proteins can be purified by heparin Sepharose affinity chromatography using a simple sodium chloride gradient to elute the bound fusion protein. In addition, owing to the high density of positive charges on the HBP tag, recombinant target proteins are preferably expressed in their soluble forms. The purification of HBP-fusion proteins can also be achieved in the presence of chemical denaturants, including urea. Additionally, polyclonal antibodies raised against the affinity tag can be used to detect HBP-fused target proteins with high sensitivity. © 2017 by John Wiley & Sons, Inc.

Backbone and side-chain 1H, 15N, and 13C resonance assignments of a novel Staphylococcal inhibitor of myeloperoxidase

The bacterium Staphylococcus aureus produces an array of anti-inflammatory molecules that prevent the innate immune system from recognizing it as a pathogen and clearing it from the host. In the acute phase of inflammation, our immune system relies on neutrophils to clear invading bacteria. Recently, novel classes of secreted proteins from S. aureus, including the Extracellular Adherence Protein (EAP) family (Stapels et al., Proc Natl Acad Sci USA 111:13187-13192, 2014) and the Staphylococcal Peroxidase Inhibitor (SPIN), (unpublished work) have been identified as highly selective inhibitors acting on Neutrophil Serine Proteases (NSPs) and myeloperoxidase (MPO) respectively. SPIN is a protein found only in Staphylococci, with no sequence homology to any known proteins. Solution NMR structural studies of SPIN are therefore expected to provide a deeper understanding of its interaction with MPO. In this study, we report the backbone and side-chain ¹H, ¹⁵N, and ¹³C resonance assignments of SPIN. Furthermore, using the chemical shifts of these resonances, we predicted the secondary structure of SPIN in solution via the TALOS-N server. The assignment data has been deposited in the BMRB data bank under Accession No. 27069.

Modulation of Interleukin-12 activity in the presence of heparin

Glycosaminoglycans (GAGs), especially heparin and heparan sulfate (HS), modulate the functions of numerous cytokines. The aims of this multidisciplinary research were to characterize heparin binding to interleukin-12 (IL-12) and determine the mechanism(s) by which heparin influences IL-12 bioactivity. Heparin and HS were found to bind human IL-12 (hIL-12) with low micromolar affinity and increase hIL-12 bioactivity by more than 6-fold. Conversely, other GAGs did not demonstrate significant binding, nor did their addition affect hIL-12 bioactivity. Biophysical studies demonstrated that heparin induced only minor conformational changes while size-exclusion chromatography and small angle X-ray scattering studies indicated that heparin induced dimerization of hIL-12. Heparin modestly protected hIL-12 from proteolytic degradation, however, this was not a likely mechanism for increased cytokine activity in vitro. Flow cytometry studies revealed that heparin increased the amount of hIL-12 bound to cell surfaces. Heparin also facilitated hIL-12 binding and signaling in cells in which both hIL-12 receptor subunits were functionally deleted. Results of this study demonstrate a new role for heparin in modulating the biological activity of IL-12.

Structure and interactions of RecA: plasticity revealed by molecular dynamics simulations

Eleven independent simulations, each involving three consecutive molecules in the RecA filament, carried out on the protein from Mycobacterium tuberculosis, Mycobacterium smegmatis and Escherichia coli and their Adenosine triphosphate (ATP) complexes, provide valuable information which is complementary to that obtained from crystal structures, in addition to confirming the robust common structural framework within which RecA molecules from different eubacteria function. Functionally important loops, which are largely disordered in crystal structures, appear to adopt in each simulation subsets of conformations from larger ensembles. The simulations indicate the possibility of additional interactions involving the P-loop which remains largely invariant. The phosphate tail of the ATP is firmly anchored on the loop while the nucleoside moiety exhibits substantial structural variability. The most important consequence of ATP binding is the movement of the 'switch' residue. The relevant simulations indicate the feasibility of a second nucleotide binding site, but the pathway between adjacent molecules in the filament involving the two nucleotide binding sites appears to be possible only in the mycobacterial proteins.

Novel Molecular Interactions of Acylcarnitines and Fatty Acids with Myoglobin

Previous research has indicated that long-chain fatty acids can bind myoglobin (Mb) in an oxygen-dependent manner. This suggests that oxy-Mb may play an important role in fuel delivery in Mb-rich muscle fibers (e.g. type I fibers and cardiomyocytes), and raises the possibility that Mb also serves as an acylcarnitine-binding protein. We report for the first time the putative interaction and affinity characteristics for different chain lengths of both fatty acids and acylcarnitines with oxy-Mb using molecular dynamic simulations and isothermal titration calorimetry experiments. We found that short- to medium-chain fatty acids or acylcarnitines (ranging from C2:0 to C10:0) fail to achieve a stable conformation with oxy-Mb. Furthermore, our results indicate that C12:0 is the minimum chain length essential for stable binding of either fatty acids or acylcarnitines with oxy-Mb. Importantly, the empirical lipid binding studies were consistent with structural modeling. These results reveal that: (i) the lipid binding affinity for oxy-Mb increases as the chain length increases (i.e. C12:0 to C18:1), (ii) the binding affinities of acylcarnitines are higher when compared with their respective fatty acid counterparts, and (iii) both fatty acids and acylcarnitines bind to oxy-Mb in 1:1 stoichiometry. Taken together, our results support a model in which oxy-Mb is a novel regulator of long-chain acylcarnitine and fatty acid pools in Mb-rich tissues. This has important implications for physiological fuel management during exercise, and relevance to pathophysiological conditions (e.g. fatty acid oxidation disorders and cardiac ischemia) where long-chain acylcarnitine accumulation is evident.

Domain Organization in the 54-kDa Subunit of the Chloroplast Signal Recognition Particle

Chloroplast signal recognition particle (cpSRP) is a heterodimer composed of an evolutionarily conserved 54-kDa GTPase (cpSRP54) and a unique 43-kDa subunit (cpSRP43) responsible for delivering light-harvesting chlorophyll binding protein to the thylakoid membrane. While a nearly complete three-dimensional structure of cpSRP43 has been determined, no high-resolution structure is yet available for cpSRP54. In this study, we developed and examined an in silico three-dimensional model of the structure of cpSRP54 by homology modeling using cytosolic homologs. Model selection was guided by single-molecule Förster resonance energy transfer experiments, which revealed the presence of at least two distinct conformations. Small angle x-ray scattering showed that the linking region among the GTPase (G-domain) and methionine-rich (M-domain) domains, an M-domain loop, and the cpSRP43 binding C-terminal extension of cpSRP54 are predominantly disordered. Interestingly, the linker and loop segments were observed to play an important role in organizing the domain arrangement of cpSRP54. Further, deletion of the finger loop abolished loading of the cpSRP cargo, light-harvesting chlorophyll binding protein. These data highlight important structural dynamics relevant to cpSRP54's role in the post- and cotranslational signaling processes.

Epigenetics and addiction

Addictions are public health menaces. However, despite advances in addiction research, the cellular or molecular mechanisms that cause transition from recreational use to addiction remain to be elucidated. We have recently suggested that addiction may be secondary to long-term epigenetic modifications that determine the clinical course of substance use disorders. A better understanding of epigenetic mechanisms in animal models that mimic human conditions should help to usher in a new area of drug development against addiction.

Folding of Fibroblast Growth Factor 1 Is Critical for Its Nonclassical Release

Fibroblast growth factor 1 (FGF1), a ubiquitously expressed pro-angiogenic protein that is involved in tissue repair, carcinogenesis, and maintenance of vasculature stability, is released from the cells via a stress-dependent nonclassical secretory pathway. FGF1 secretion is a result of transmembrane translocation of this protein. It correlates with the ability of FGF1 to permeabilize membranes composed of acidic phospholipids. Like several other nonclassically exported proteins, FGF1 exhibits β-barrel folding. To assess the role of folding of FGF1 in its secretion, we applied targeted mutagenesis in combination with a complex of biophysical methods and molecular dynamics studies, followed by artificial membrane permeabilization and stress-induced release experiments. It has been demonstrated that a mutation of proline 135 located in the C-terminus of FGF1 results in (i) partial unfolding of FGF1, (ii) a decrease in FGF1's ability to permeabilize bilayers composed of phosphatidylserine, and (iii) drastic inhibition of stress-induced FGF1 export. Thus, folding of FGF1 is critical for its nonclassical secretion.

Abstract 3058: Oxidative phosphorylation-dependent regulation of cancer cell apoptosis in response to anticancer agents

Although cancer cells develop resistance to multiple types of anticancer agents, whether they adopt similar or differential mechanisms to evade cell death in response to a broad spectrum of cancer therapeutics is not fully defined. We show differential sensitivity, caspase activation, and cytokines/chemokines release in response to multiple anticancer agents. We demonstrated that DNA-damaging agents (etoposide and doxorubicin), ER stressor (thapsigargin), and histone deacetylase inhibitor (apicidin) target oxidative phosphorylation (OXPHOS) for apoptosis induction, whereas other anticancer agents including staurosporine, taxol, and sorafenib induced apoptosis in OXPHOS-independent manner. DNA-damaging agents induced mitochondrial biogenesis accompanied by increased production of cellular and mitochondrial ROS. Mitochondrial biogenesis upregulated both mitochondrial protein-folding machinery and unfolded protein response. Induction of mitochondrial biogenesis occurred in a caspase activation-independent mechanism but was reduced by autophagy inhibition and p53-deficiency. Abrogation of complex-I blocked DNA damage-induced caspase activation, whereas inhibition of complex II or gross complexes did not modulate the caspase activity. Interestingly, DNA damaging agent doxorubicin showed strong binding to mitochondria, which was disrupted upon OXPHOS complex I-deficiency but not by OXPHOS complex II-deficiency. Thapsigargin-induced caspase activation was reduced upon abrogation of complex-I or gross-complexes whereas a reverse trend was observed with apicidin. Together, our findings define the specific targets of apoptosis induction in response to a broad range of anticancer therapeutics, which provide a new strategy for differential mitochondrial targeting for cancer therapy.

Citation Format: Sandeep Kumar, Neelu Yadav, Tim Marlowe, Ajay Chaudhary, Jianmin Wang, Jordan O'Malley, Patrick Boland, Srinivas Jayanthi, Thallapuranam Krishnaswamy Suresh Kumar, Nagendra Yadava, Dhyan Chandra. Oxidative phosphorylation-dependent regulation of cancer cell apoptosis in response to anticancer agents. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3058. doi:10.1158/1538-7445.AM2015-3058

Energy transport mechanism in the form of proton soliton in a one-dimensional hydrogen-bonded polypeptide chain

The dynamics of protons in a one-dimensional hydrogen-bonded (HB) polypeptide chain (PC) is investigated theoretically. A new Hamiltonian is formulated with the inclusion of higher-order molecular interactions between peptide groups (PGs). The wave function of the excitation state of a single particle is replaced by a new wave function of a two-quanta quasi-coherent state. The dynamics is governed by a higher-order nonlinear Schrödinger equation and the energy transport is performed by the proton soliton. A nonlinear multiple-scale perturbation analysis has been performed and the evolution of soliton parameters such as velocity and amplitude is explored numerically. The proton soliton is thermally stable and very robust against these perturbations. The energy transport by the proton soliton is more appropriate to understand the mechanism of energy transfer in biological processes such as muscle contraction, DNA replication, and neuro-electric pulse transfer on biomembranes.

Regulation of Structural Dynamics within a Signal Recognition Particle Promotes Binding of Protein Targeting Substrates

Protein targeting is critical in all living organisms and involves a signal recognition particle (SRP), an SRP receptor, and a translocase. In co-translational targeting, interactions among these proteins are mediated by the ribosome. In chloroplasts, the light-harvesting chlorophyll-binding protein (LHCP) in the thylakoid membrane is targeted post-translationally without a ribosome. A multidomain chloroplast-specific subunit of the SRP, cpSRP43, is proposed to take on the role of coordinating the sequence of targeting events. Here, we demonstrate that cpSRP43 exhibits significant interdomain dynamics that are reduced upon binding its SRP binding partner, cpSRP54. We showed that the affinity of cpSRP43 for the binding motif of LHCP (L18) increases when cpSRP43 is complexed to the binding motif of cpSRP54 (cpSRP54pep). These results support the conclusion that substrate binding to the chloroplast SRP is modulated by protein structural dynamics in which a major role of cpSRP54 is to improve substrate binding efficiency to the cpSRP.

Structural modeling and molecular dynamics studies on the human LMTK3 domain and the mechanism of ATP binding

Estrogen positive breast cancer is a dreadful disease in women worldwide. The human estrogen receptor-α (ERα) pathway plays a critical role in estrogenic signaling and targeting ERα in breast cancer treatment. The key role of Lemur tyrosine kinase-3 (LMTK3) in regulation of ERα has been identified and it is found to be a novel therapeutic target for breast cancer. With lack of structural studies on LMTK3, the breast cancer therapeutics research remains elusive. In this computational study, we performed structural studies on LMTK3 by structural modeling and molecular dynamics (MD) simulations of the apo state and the ATP bound state. The structure of the LMTK3 domain was developed by using I-TASSER server and validated by quality index and Ramachandran plot. MD simulation analysis explained the structural behavior of the LMTK3 domain in the dynamic system and the apo state showed defined protein folding with stable conformation. The mechanism of ATP binding was studied using molecular docking, resulting in the identification of critical residues and the ATP binding cavity. Furthermore, MD simulation of the LMTK3-ATP complex was performed and the trajectory analyses confirmed the stability and effective binding of ATP in the dynamic system. Overall, our computational reports provide more information on the structure-function relationship of LMTK3 with ATP. The critical residues Tyr185 and Asp284 found in the ATP binding cavity may be useful in designing potential inhibitors on human LMTK3.

Fungal peritonitis in continuous ambulatory peritoneal dialysis: The impact of antifungal prophylaxis on patient and technique outcomes

Fungal peritonitis (FP) is a rare, but serious complication of peritoneal dialysis. We analyzed the incidence of FP, associated risk factors and outcome of patients with FP and evaluated the role of prophylactic antifungal agent in reducing its incidence. We studied all patients with FP from January 2005 to January 2012. Study period was divided into two parts, period I (January 2005 to January 2010), when prophylactic antifungal was not used and period II (January 2010 to January 2012), when prophylactic antifungal (fluconazole) was used. A total of 142 episodes of peritonitis were documented during this period of which 20 (14%) were FP. During the study period I, 18 of 102 episodes of peritonitis (17.6%) and in the study period II (with antifungal prophylaxis), only 2 of 40 episodes of peritonitis (5%) were due to fungal infection (P = 0.04). Nine out of 20 patients (45%) had prior exposure to antibiotics. Fungal isolates were Candida albicans in 65%, non-albicans Candida in 25%, Rhizopus species in 5% and Alternaria in 5% of the patients. While 12 out of 20 patients (60%) recovered completely and were re-initiated on continuous ambulatory peritoneal dialysis (CAPD), 4 of them expired (20%) and 4 others (20%) were shifted to hemodialysis. Use of prophylactic antifungal agent significantly reduced the incidence of FP (P = 0.04). We conclude that - fluconazole when used as a prophylactic agent in the setting of bacterial peritonitis significantly reduces the incidence of subsequent FP in CAPD patients.

Copper binding affinity of the C2B domain of synaptotagmin-1 and its potential role in the nonclassical secretion of acidic fibroblast growth factor

Fibroblast growth factor 1 (FGF1) is a heparin-binding proangiogenic protein. FGF1 lacks the conventional N-terminal signal peptide required for secretion through the endoplasmic reticulum (ER)-Golgi secretory pathway. FGF1 is released through a Cu(2+)-mediated nonclassical secretion pathway. The secretion of FGF1 involves the formation of a Cu(2+)-mediated multiprotein release complex (MRC) including FGF1, S100A13 (a calcium-binding protein) and p40 synaptotagmin (Syt1). It is believed that the binding of Cu(2+) to the C2B domain is important for the release of FGF1 into the extracellular medium. In this study, using a variety of biophysical studies, Cu(2+) and lipid interactions of the C2B domain of Syt1 were characterized. Isothermal titration calorimetry (ITC) experiments reveal that the C2B domain binds to Cu(2+) in a biphasic manner involving an initial endothermic and a subsequent exothermic phase. Fluorescence energy transfer experiments using Tb(3+) show that there are two Cu(2+)-binding pockets on the C2B domain, and one of these is also a Ca(2+)-binding site. Lipid-binding studies using ITC demonstrate that the C2B domain preferentially binds to small unilamellar vesicles of phosphatidyl serine (PS). Results of the differential scanning calorimetry and limited trypsin digestion experiments suggest that the C2B domain is marginally destabilized upon binding to PS vesicles. These results, for the first time, suggest that the main role of the C2B domain of Syt1 is to serve as an anchor for the FGF1 MRC on the membrane bilayer. In addition, the binding of the C2B domain to the lipid bilayer is shown to significantly decrease the binding affinity of the protein to Cu(2+). The study provides valuable insights on the sequence of structural events that occur in the nonclassical secretion of FGF1.

Controlling chitosan-based encapsulation for protein and vaccine delivery

Chitosan-based nano/microencapsulation is under increasing investigation for the delivery of drugs, biologics and vaccines. Despite widespread interest, the literature lacks a defined methodology to control chitosan particle size and drug/protein release kinetics. In this study, the effects of precipitation-coacervation formulation parameters on chitosan particle size, protein encapsulation efficiency and protein release were investigated. Chitosan particle sizes, which ranged from 300 nm to 3 μm, were influenced by chitosan concentration, chitosan molecular weight and addition rate of precipitant salt. The composition of precipitant salt played a significant role in particle formation with upper Hofmeister series salts containing strongly hydrated anions yielding particles with a low polydispersity index (PDI) while weaker anions resulted in aggregated particles with high PDIs. Sonication power had minimal effect on mean particle size, however, it significantly reduced polydispersity. Protein loading efficiencies in chitosan nano/microparticles, which ranged from 14.3% to 99.2%, were inversely related to the hydration strength of precipitant salts, protein molecular weight and directly related to the concentration and molecular weight of chitosan. Protein release rates increased with particle size and were generally inversely related to protein molecular weight. This study demonstrates that chitosan nano/microparticles with high protein loading efficiencies can be engineered with well-defined sizes and controllable release kinetics through manipulation of specific formulation parameters.