Review on the impact of cell phone radiation effects on green plants

The aim of this review is to assess the impact of cell phone radiation effects on green plants. Rapid progress in networking and communication systems has introduced frequency- and amplitude-modulated technologies to the world with higher allowed bands and greater speed by using high-powered radio generators, which facilitate high definition connectivity, rapid transfer of larger data files, and quick multiple accesses. These cause frequent exposure of cellular radiation to the biological world from a number of sources. Key factors like a range of frequencies, time durations, power densities, and electric fields were found to have differential impacts on the growth and development of green plants. As far as the effects on green plants are concerned in this review, alterations in their morphological characteristics like overall growth, canopy density, and pigmentation to physiological variations like chlorophyll fluorescence and change in membrane potential etc. have been found to be affected by cellular radiation. On the other hand, elevated oxidative status of the cell, macromolecular damage, and lipid peroxidation have been found frequently. On the chromosomal level, micronuclei formation, spindle detachments, and increased mitotic indexes etc. have been noticed. Transcription factors were found to be overexpressed in many cases due to the cellular radiation impact, which shows effects at the molecular level.

Induction effect of antiretroviral bictegravir on the expression of Abcb1, Abcg2 and Abcc1 genes associated with P-gp, BCRP and MRP1 transporters present in rat peripheral blood mononuclear cells

BACKGROUND

Antiretrovirals have the potential to cause drug interactions leading to inefficacy or toxicity via induction of efflux transporters through nuclear receptors, altering drug concentrations at their target sites.

RESEARCH DESIGN AND METHODS

This study used molecular dynamic simulations and qRT-PCR to investigate bictegravir's interactions with nuclear receptors PXR and CAR, and its effects on efflux transporters (P-gp, BCRP, MRP1) in rat PBMCs. PBMC/plasma drug concentrations were measured using LC-MS/MS to assess the functional impact of transporter expression.

RESULTS

Bictegravir significantly increased the expression of ABC transporters, with Car identified as a key mediator. This suggests that bictegravir's influence on nuclear receptors could affect drug transport and efficacy at the cellular level.

CONCLUSIONS

Bictegravir activates nuclear receptors enhancing efflux transporter expression. Understanding these interactions is crucial for preventing drug-drug interactions and reducing toxicity in clinical use. Combining CAR antagonists with bictegravir may prevent drug resistance and toxicity. However, these findings are based on preclinical data and necessitate further clinical trials to confirm their applicability in clinical settings.

Pharmacoinformatics approach for type 2 diabetes mellitus therapeutics using phytocompounds from Costus genus: an in-silico investigation

Type 2 Diabetes Mellitus (T2DM), as a significant health concern globally, particularly in India, underscoring the vital need for effective therapeutics. Current drug therapies for T2DM may have limitations, leading researchers to explore natural products as alternatives. In this study. We have investigated the anti-diabetic compounds from the Costus genus, known as the insulin plant, which is abundant in southern India. The bioinformatics tools and software used for in-silico analysis to identify potential therapeutic compounds and hub genes associated with T2DM in the Indian population that could cut short the in-vitro and in-vivo experimental approaches in near future. The systematic review and combinatorial in-silico analysis revealed IGF2BP2, INS and TCF as the key targets that are associated with T2DM. The compounds stigmasterol, cycloartenol, and diosgenone were explored to be potent among all the 38 phytocompounds from genus Costus with binding energies -8.48, -10.07, and -10.31 kcal/mol against IGF2BP2, INS and TCF. The molecular dynamics (MD) simulation studies of these complexes demonstrated stable and consistent dynamic behavior, particularly in the INS-cycloartenol, IGF2BP2-stigmasterol and TCF7L2-diosgenone complexes. The identified compounds and associated targets represent potential candidates for T2DM therapeutics in the Indian population. The pharmacoinformatics approach presented in the study could streamline the drug discovery process by prioritizing compounds for further experimental validation.Communicated by Ramaswamy H. Sarma.

Mechanistic Investigation of Thiazole-Based Pyruvate Kinase M2 Inhibitor Causing Tumor Regression in Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) is a deadly breast cancer with a poor prognosis. Pyruvate kinase M2 (PKM2), a key rate-limiting enzyme in glycolysis, is abnormally highly expressed in TNBC. Overexpressed PKM2 amplifies glucose uptake, enhances lactate production, and suppresses autophagy, thereby expediting the progression of oncogenic processes. A high mortality rate demands novel chemotherapeutic regimens at once. Herein, we report the rational development of an imidazopyridine-based thiazole derivative 7d as an anticancer agent inhibiting PKM2. Nanomolar range PKM2 inhibitors with favorable drug-like properties emerged through enzyme assays. Experiments on two-dimensional (2D)/three-dimensional (3D) cell cultures, lactate release assay, surface plasmon resonance (SPR), and quantitative real-time polymerase chain reaction (qRT-PCR) validated 7d preclinically. In vivo, 7d outperformed lapatinib in tumor regression. This investigation introduces a lead-based approach characterized by its clear-cut chemistry and robust efficacy in designing an exceptionally potent inhibitor targeting PKM2, with a focus on combating TNBC.

In silico mutation of aromatic with aliphatic amino acid residues in Clostridium perfringens epsilon toxin (ETX) reduces its binding efficiency to Caprine Myelin and lymphocyte (MAL) protein receptors

Enterotoxaemia (ET) is a severe disease that affects domestic ruminants, including sheep and goats, and is caused by Clostridium perfringens type B and D strains. The disease is characterized by the production of Epsilon toxin (ETX), which has a significant impact on the farming industry due to its high lethality. The binding of ETX to the host cell receptor is crucial, but still poorly understood. Therefore, the structural features of goat Myelin and lymphocytic (MAL) protein were investigated and defined in this study. We induced the mutations in aromatic amino acid residues of ETX and substituted them with aliphatic residues at domains I and II. Subsequently, protein-protein interactions (PPI) were performed between ETX (wild)-MAL and ETX (mutated)-MAL protein predicting the domain sites of ETX structure. Further, molecular dynamics (MD) simulation studies were performed for both complexes to investigate the dynamic behavior of the proteins. The binding efficiency between 'ETX (wild)-MAL protein' and 'ETX (mutated)-MAL protein complex' interactions were compared and showed that the former had stronger interactions and binding efficiency due to the higher stability of the complex. The MD analysis showed destabilization and higher fluctuations in the PPI of the mutated heterodimeric ETX-MAL complex which is otherwise essential for its functional conformation. Such kind of interactions with mutated functional domains of ligands provided much-needed clarity in understanding the pre-pore complex formation of epsilon toxin with the MAL protein receptor of goats. The findings from this study would provide an impetus for designing a novel vaccine for Enterotoxaemia in goats.Communicated by Ramaswamy H. Sarma.

A comparative proteomic analysis for non-invasive early prediction of hypoxic-ischemic injury in asphyxiated neonates

AIM

Hypoxic Ischemic Encephalopathy (HIE) is one of the principal causes of neonatal mortality and long-term morbidity worldwide. The neonatal signs of mild cerebral injury are subtle, making an early precise diagnosis difficult. Delayed detection, poor prognosis, and lack of specific biomarkers for the disease are increasing mortality rates. In this study, we intended to identify specific biomarkers using comparative proteomic analysis to predict the severity of perinatal asphyxia so that its outcome can also be prevented.

EXPERIMENTAL DESIGN

A case-control study was conducted on 38 neonates, and urine samples were collected within 24 and 72 h of life. A tandem mass spectrometry-based quantitative proteomics approach, followed by validation via sandwich ELISA, was performed.

RESULTS

The LC-MS/MS-based proteomics analysis resulted in the identification of 1201 proteins in urine, with 229, 244, and 426 being differentially expressed in HIE-1, HIE-2, and HIE-3, respectively. Axon guidance, Diseases of programmed cell death, and Detoxification of reactive oxygen species pathways were significantly enriched in mild HIE versus severe HIE. Among the differentially expressed proteins in various stages of HIE, we chose to validate four proteins - APP, AGT, FABP1, and FN1 - via sandwich ELISA. Individual and cumulative ROC curves were plotted. AGT and FABP1 together showed high sensitivity, specificity, and accuracy as potential biomarkers for early diagnosis of HIE.

CONCLUSION

Establishing putative urinary biomarkers will facilitate clinicians to more accurately screen neonates for brain injury and monitor the disease progression. Prompt treatment of neonates may reduce mortality and neurodevelopmental impairment.

Experimental and in silico insights: interaction of dimethyl sulphoxide with 1-hexyl-2-methyl imidazolium bromide/1-octyl-2-methyl imidazolium bromide at different temperatures

Ionic liquids have gained attention as 'designer solvents' since they offer a broad spectrum of properties that can be tuned by altering the constituent ions. In this work, 1-alkyl-2-methyl imidazolium-based ionic liquids with two different alkyl chains (alkyl = hexyl and octyl) have been synthesized and characterized. Since the binary mixture of ionic liquids with molecular solvents can give rise to striking physicochemical properties, the interaction of the synthesized room temperature ionic liquids, 1-hexyl-2-methyl imidazolium bromide [HMIM][Br]/1-octyl-2-methyl imidazolium bromide [OMIM][Br] with DMSO has been examined through density and specific conductance at T = (303.15, 308.15, 313.15 and 318.15) K under atmospheric pressure. The obtained molar volume and excess molar volume are fitted to the Redlich-Kister polynomial equation, and the standard deviation is noted. The positive excess molar volume at elevated temperatures indicates volume expansion due to the mutual loss of dipolar association and differences in the sizes and shapes of the constituent molecules. To have a better understanding of the reactivity and efficacy of 1-hexyl-2-methyl imidazolium bromide and 1-octyl-2-methyl imidazolium bromide with DMSO, the Becke, 3-parameter, Lee-Yang-Parr (B3LYP) correlation function of density functional theory (DFT) has been used. The ORCA Program version 4.0 calculates the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy. The effective reactivities of both the compounds that showed an energy band gap (ΔE), i.e., the difference between ELUMO and EHOMO, are 7.147 and 8.037 kcal mol-1.

Bifunctional backbone modified squaramide dipeptides as amyloid beta (Aβ) aggregation inhibitors

Alzheimer's disease (AD) is a devastating neurodegenerative condition with complex pathophysiology. Aggregated amyloid beta (Aβ) peptide plaques and higher concentrations of bio-metals such as copper (Cu), zinc (Zn), and iron (Fe) are the most significant hallmarks of AD observed in the brains of AD patients. Therefore simultaneous inhibition of Aβ peptide aggregation and reduction of metal stress may serve as an effective therapeutic approach for treating Alzheimer's disease. A series of bifunctional dipeptides bearing squaramide backbone were synthesized and investigated for their ability to chelate metal ions and prevent Aβ peptide aggregation. Dipeptides with Valine (V) and Threonine (T) substitutions at the C-terminus exhibited preferential chelation with Cu(II), Zn(II), and Fe(III) metal ions in the presence of other metal ions. They were also found to inhibit the aggregation of Aβ peptide in-vitro. A further molecular dynamics (MD) simulation study demonstrated that these two dipeptides interact with the Aβ peptide in the hydrophobic core (KLVFF) region. Circular dichroism (CD) study revealed slight conformational change in the Aβ peptide upon the interactions with dipeptides. Apart from metal chelation and inhibition of Aβ peptide aggregation, the selected dipeptides were found to possess anti-oxidant properties. Therefore, the squaramide backbone-modified dipeptides may serve as an active bifunctional scaffold towards the development of new chemical entities for the treatment of Alzheimer's disease.

In Silico Analysis Determining the Binding Interactions of NAD(P)H: Quinone Oxidoreductase 1 and Resveratrol via Docking and Molecular Dynamic Simulations

Objective

NAD(P)H: Quinone oxidoreductase1 (NQO1) plays a crucial role in cellular defense against oxidative stress. Overexpression of NQO1 is linked to various cancer pathways. Despite its potential, the actual mechanisms to inhibit NQO1 and increase the efficacy of standard therapeutic options are not yet established. Resveratrol is an anti-cancer polyphenol found in dietary products and red wine. The objective of this investigation is to employ in silico methods to explore how resveratrol interacts with NQO1.

Materials and Methods

Docking analysis of resveratrol against NQO1 was performed using Glide. The most efficiently docked complex was characterized and analyzed by measuring intermolecular (IM) hydrogen (H)-bonds and binding energy values, additional hydrophobic, and electrostatic interactions. IM interaction between complexed protein and compound was demonstrated using LigPlot+ and the Schrödinger ligand interaction module. Molecular dynamics tools were employed to examine the physical movement of molecules to evaluate how macromolecular structures relate to their functions.

Results

The results of this investigation depicted a strong affinity of resveratrol against NQO1 followed by MD simulations (NQO1-resveratrol complex-binding energy: -2.847kcal/mol). Resveratrol's robust binding affinity through docking and molecular dynamic simulations highlights a significant change around 90 ns. The H-bonds number was inversely linked with the resveratrol-NQO1 complex stability. The NQO1-Resveratrol complex displayed dynamic motion, as revealed by porcupine projections, indicating alterations in its movement and flexibility.

Conclusion

The present in silico analysis suggests a possible alteration in resveratrol's orientation in the protein binding pocket. The findings encourage further investigation, including validation using in vitro and in vivo assays.

Effective voltammetric tool for Nano-detection of triazine herbicide (1-Chloro-3-ethylamino-5-isopropylamino-2,4,6-triazine) by naphthalene derivative

The development and operation of a nanosensor for detecting the poisonous 1-chloro-3-ethylamino-5-isopropylamino-2,4,6-triazine (Atrazine) are described in this study for the first time. The carbon electrode (CE) surface was modified with cysteine-substituted naphthalene diimide to create this sensitive platform. The developed nanosensor (NDI-cys/GCE) was evaluated for its ability to sense Atrazine using differential pulse voltammetry and cyclic voltammetry. To achieve the best response from the target analyte, the effects of several parameters were examined to optimize the conditions. The cysteine-substituted naphthalene diimide significantly improved the signals of the Atrazine compared to bare GCE due to the synergistic activity of substituted naphthalene diimide and cysteine molecules. Under optimal conditions, atrazine detection limits at the (NDI-cys/GCE) were reported to be 94 nM with a linear range of 10-100 μM. The developed sensing platform also showed positive results when used to detect the atrazine herbicide in real tap water, wastewater, and milk samples. Furthermore, a reasonable recovery rate for real-time studies, repeatability, and stability revealed that the developed electrochemical platform could be used for sample analysis.

Instability and fault analysis of arc plasma using advanced signal processing methods

This study focuses on the instability and fault analysis of transferred arc plasma, utilizing advanced signal processing methods. Transferred arc plasma systems find significant applications in various industries, including material processing, metallurgy, and waste management. However, the occurrence of instabilities and fault events can severely impact system performance and reliability. To address instabilities in arc plasma, various conditions were experimented. The operating parameters, such as arc voltage, arc current, acoustic, optical, and spectroscopic signals, were simultaneously recorded at a higher sampling rate. The proposed approach employs advanced signal processing methods, such as the Lyapunov exponent, fast-Fourier transform, short-time-Fourier transform, and power spectral density, to analyze the characteristics and instabilities of the transferred arc plasma process. By capturing and analyzing signals from multiple sensors, it becomes possible to identify deviations, irregularities, and fault patterns that arise during plasma operation. The outcomes of this research will have significant implications for the optimization and control of transferred arc plasma processes. By identifying and characterizing instabilities due to fault events at an early stage, system operators can take timely corrective actions, preventing potential damage and improving the overall system efficiency.

Mining proteomics data to extract post-translational modifications associated with gastric cancer

Gastric cancers are highly heterogeneous, deep-seated tumours associated with late diagnosis and poor prognosis. Post-translational modifications (PTMs) of proteins are known to be well-associated with oncogenesis and metastasis in most cancers. Several enzymes which drive PTMs have also been used as theranostics in cancers of the breast, ovary, prostate and bladder. However, there is limited data on PTMs in gastric cancers. Considering that experimental protocols for simultaneous analysis of multiple PTMs are being explored, a data-driven approach involving reanalysis of mass spectrometry-derived data is useful in cataloguing altered PTMs. We subjected publicly available mass spectrometry data on gastric cancer to an iterative searching strategy for fetching PTMs including phosphorylation, acetylation, citrullination, methylation and crotonylation. These PTMs were catalogued and further analyzed for their functional enrichment through motif analysis. This value-added approach delivered identification of 21,710 unique modification sites on 16,364 modified peptides. Interestingly, we observed 278 peptides corresponding to 184 proteins to be differentially abundant. Using bioinformatics approaches, we observed that majority of these altered PTMs/proteins belonged to cytoskeletal and extracellular matrix proteins, which are known to be perturbed in gastric cancer. The dataset derived by this mutiPTM investigation can provide leads to further investigate the potential role of altered PTMs in gastric cancer management.

Diaryl ether derivative inhibits GPX4 expression levels to induce ferroptosis in thyroid cancer cells

Papillary thyroid carcinoma contributes to about 80% of the total thyroid cancer cases. BRAFV600E is a frequently occurring mutation in PTCs. Although several BRAF inhibitors are available, many thyroid cancer patients acquire resistance to BRAF inhibitors. Therefore, new targets and drugs need to be identified as therapies. Ferroptosis is a recently discovered type of cell death, and inhibiting glutathione peroxidase 4 (GPX4) using small molecules was found to trigger ferroptosis. But it is unknown whether inhibiting GPX4 renders thyroid cancer cells susceptible to ferroptosis. To identify novel GPX4 inhibitors, we focused on our previously reported cohort of diaryl ether and dibenzoxepine molecules. In this study, we asked whether diaryl ether and dibenzoxepine derivatives trigger ferroptosis in thyroid cancer cells. To answer this question, we screened diaryl ether and dibenzoxepine derivatives in cell-based assays and performed mechanism of action studies. We found that a diaryl ether derivative, 16 decreased thyroid cell proliferation and triggered ferroptosis by inhibiting GPX4 expression levels. Molecular modeling and dynamics simulations showed that 16 binds to the active site of GPX4. Upon deciphering the mode of 16-induced ferroptosis, we found that 16 treatments decrease mitochondrial polarization and reduce mitochondrial respiration similar to a ferroptosis inducer, RSL3. We conclude that the diaryl ether derivative, 16 inhibits GPX4 expression levels to induce ferroptosis in thyroid cancer cells. Based on our observations, we suggest that 16 can be lead-optimized and developed as a ferroptosis-inducing agent to treat thyroid cancers.

Structure based virtual screening and molecular dynamics of natural anti-biofilm compounds against SagS response regulator/sensor kinase in Pseudomonas aeruginosa

SagS sensor regulator plays a vital role in biofilm development of Pseudomonas aeruginosa which subsequently makes the cells more tolerant to various antimicrobials. The multidrug resistance (MDR) issue has risen substantially in recent years and is considered a global threat. Therefore, alternative compounds should be unearthed immediately to address the issues related to P. aeruginosa drug resistance for which SagS could be a candidate. The present study is an attempt to screen natural anti-biofilm compounds as the potent inhibitors of SagS. Twenty natural anti-biofilm/quorum sensing inhibiting compounds were retrieved from various literatures with significant inhibitory effects against P. aeruginosa biofilm from in-vitro experiments which were screened using various pharmacokinetic parameters. The screened and three standard drugs were docked against SagS-HisKA using AutoDock 4.2 tool, which were further analysed by MD simulations to understand the binding mode of compounds and dynamic behaviour of the complexes. Two potential anti-biofilm natural compounds, pinocembrin with binding affinity (-7.19 kcal/mol), vestitol (-7.18 kcal/mol) and the standard drug ceftazidime (-8.89 kcal/mol) were selected based on filtered parameters and better binding affinity. The trajectory analysis of MD simulations reflected Pinocembrin in stabilizing the system compared to ceftazidime. The existing reports state that the natural products represent promising source of therapy with least or almost nil adverse effect compared to synthetic drugs which is well collated with our in-silico findings. This investigation can save both time and cost required for in-vitro and in-vivo analysis for designing of a novel anti-biofilm agent against P. aeruginosa biofilm-associated infections.Communicated by Ramaswamy H. Sarma.

Exploring the rare variants associated with Type 2 Diabetes Mellitus in Indian population and its disease-drug association studies: an in-silico approach

The diversified eating habits and religious culture of Indian population may be one of the reasons they largely contribute to the global diabetes burden. In the present investigation, an in-silico approach was carried out to explore hub genes in the Indian population with Type 2 Diabetes Mellitus (T2DM) that are scantily reported in the GWAS catalogue and probable potential anti-diabetic drugs from plants. This computational approach unwrapped LEP (leptin) as the hub gene among 170 genes analyzed with 14 non-synonymous single nucleotide polymorphisms (nsSNPs) with MAF < 0.01. The mutation of the LEP gene leads to a decrease in leptin concentration, which increases the risk of obesity and T2DM. According to the DUET webserver, 11 of 14 mutations examined were found to destabilize the LEP protein. Among 14, four barely reported LEP variants rs781301976 (I45N), rs776443424 (S52F), rs200915360 (D76Y), and rs1191666811 (D162N) were unzipped to be associated with T2DM, which may be the probable potential drug targets. The virtual screening revealed Vescalagin as having the highest binding energy among 336 natural compounds. Molecular docking of Vescalagin depicted higher binding energy (-9.0 kcal/mol) against mutated LEP [rs200915360 (D76Y)] compared to wild (-8.9 kcal/mol) and LEP-Metformin complexes. The trajectory analysis of MD simulations revealed that Vescalagin was more effective than Metformin in stabilizing the system. The present study suggests that the associations of the investigated nsSNPs in LEP [rs200915360 (D76Y)] and others can be key factors in the predominant role of T2DM morbidity in the Indian population that can be used as potential markers and drug targets for T2DM therapeutics.Communicated by Ramaswamy H. Sarma.

Abstract 2169: NAD(P)H: quinone oxidoreductase 1 (NQO1)- A viable biomarker in colorectal cancer

Background/Objective: Colorectal cancer (CRC) is aggressive and widespread (3rd among malignancies) in the United States. NAD(P)H: Quinone Oxidoreductase 1 (NQO1) is an enzyme that contributes to chemoprotection for CRC. The aim of this meta-analysis is to test the connection between NQO1 C609T polymorphisms and CRC risk. Furthermore, the study explores the binding capacity and efficacy of BBI 608 against NQO1 in CRC through molecular docking. The inhibitor will then be tested in vitro.

Methods: PubMed, Web of Science, and Google Scholar were used in bibliographic searches. For the NQO1 C609T analysis, a total of 18 studies were used. Data was gathered and subsequently calculated using the pooled odds ratio (OR) (95% confidence interval, CI). Molecular docking, Western Blot and QRT-PCR were used to determine the molecular function of BBI 608 and NQO1.

Results: The relation between NQO1 polymorphism and CRC risk (TT + CT vs. CC: OR=1.19, 95% CI =1.06-1.34, p&lt;0.001) was significant. Furthermore, stratified investigation based on ethnicity indicated significant association between NQO1 polymorphism and CRC risk (TT + CT vs. CC: OR=1.17, 95% CI =1.08-1.27, p&lt;0.001). This study indicates that the C609T polymorphism of NQO1 is linked with CRC risk in Asians and Caucasians. To observe the molecular properties of BBI 608 (NQO1 inhibitor) and to analyze the exact mechanism of NQO1 on CRC, computational approaches were applied. This investigation provides a detailed understanding of the interaction between NQO1 and BBI 608 and its implication in CRC therapy. To support this computational analysis, in vitro studies were performed. BBI 608 creates higher cytotoxicity in a dose dependent manner in CRC cell lines. BBI 608 treatment significantly (p&lt;0.001) reduced the NQO1 expression at protein and messenger levels in both CRC (HCT 116 and RKO) cell lines.

Conclusion: Based on meta-analysis and computational approach, NQO1 is a viable biomarker and targeted molecule in CRC. In vitro results showed that inhibiting NQO1 with the drug BBI 608 decreased cell proliferation in both CRC cell lines. Knockout or overexpression or site directed mutagenesis is essential for a better understanding about BBI 608 targeted NQO1 and its amino acids.

Citation Format: Chaithanya Ganji, Bhaskar VK Lakkakula, Santosh Kumar Behera, Bassel F. El-Rayes. NAD(P)H: quinone oxidoreductase 1 (NQO1)- A viable biomarker in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2169.

Removal of Pb ions using green Co3O4 nanoparticles: Simulation, modeling, adsorption, and biological studies

Chemical co-precipitation synthesized novel and green cobalt-oxide nanoparticles (Co₃O₄-NPs) utilizing cobalt nitrate as cobalt precursors. FTIR, Raman, scanning electron microscopy, UV visible, X-ray powder diffraction, and BET was used to analyze the surface characteristics, composition, and morphology, of the NPs. These green Co₃O₄-NPs were employed to remove Pb ions from simulated wastewater solutions at various pH, adsorbate, temperature, and dose concentrations. At dose 20 mg/L, pH 6.0, 20 mg/L (Pb(II) solution, 25 °C of temperature, and 45 min for equilibrium, nearly 99.44% of Pb ions were removed. To evaluate the kinetic data, four different kinetic equations were used. The data fit the Elovich rate equation better than the other three models. Thermodynamic and isothermal studies were also evaluated, and the maximum adsorption capacity of 450.45 mg/g was observed at 298.15 K. 0.1 M HNO_3, and 0.1 HCl were used to regenerate used Co₃O₄-NPs. Simulation results show the strong correlation of the Co atom in the Co₃O₄-NPs generates active delocalized surface states, which are energetically most favorable for heavy metal (Pb ions) adsorption and removal, supporting the experimental outcomes. In concluding remarks, green Co₃O₄-NPs can also be used as an adsorbent to remove Pb ions from wastewater bodies.

Applicability of new sustainable and efficient green metal-based nanoparticles for removal of Cr(VI): Adsorption anti-microbial, and DFT studies

Artemisia absinthium leaves were utilized as a reducing agent for green synthesis of Zinc oxide nanoparticles (particle size 17 nm). Synthesized green-ZnO (g-ZnO) were characterized by SEM/EDX, FTIR, XRD, UV, and BET analyses and then further used as an adsorbent to remove Cr(VI) ions from simulated wastewater. Optimal pH, temperature and adsorbent dosage were determined through batch mode studies. High removal efficiency and adsorption capacity were observed at pH 4, 0.25 g L^-1 dosage, and 25 mg L^-1 concentration of Cr(VI). Experimental data were modelled with different adsorption kinetics (Elovich model, PFO, PSO, IDP model) and isotherms (Langmuir, Freundlich, and Temkin), and it was found the adsorption process was well fitted to Langmuir with an R² value greater than>0.99. Computational calculation showed that the g-ZnO nanoparticles became ∼14 times more dynamic with delocalized surface states making them a relevant platform to adsorb Cr with greater work function compatibility supporting the experimental findings. The Q_max adsorption capacity of g-ZnO was 315.46 mg g^-1 from Langmuir calculations. Thermodynamic calculations reveal that the Cr (VI) adsorption process was spontaneous and endothermic, with a positive ΔS value representing the disorder at the solid-solution interface during the adsorption. In addition, the present study has demonstrated that these g-ZnO nanoparticles show strong antibacterial activities against P. aeruginosa (MTCC 1688) and E. coli (MTCC 1687). Also, the novel g-ZnO adsorbent capacity to remove Cr(VI) from simulated water revealed that it could be reused at least six times with higher removal rates during regeneration experiments. The results obtained from adsorption and antimicrobial activities suggest that g-ZnO nanoparticles could be used effectively in real-time wastewater and agricultural safety applications.

Tuning the Red Emission to Instigate Intrinsic White Light Emission in the Single-Phase Phosphor with Excellent Color Rendering Index

There is ever-growing interest to develop intrinsic white light emitting single-phase phosphors that have high CRI, devoid of bluish tinge, ease of synthesis and are scalable. Herein, by manipulating vacuum pressure to instigate white light emission in Cu2+-doped-ZnS phosphors is reported. The detailed X-ray diffraction and electron microscopy confirm the cubic phase of Cu2+-doped-ZnS phosphor having agglomerated particles (~130-150 nm).  The incorporation of Cu2+ in the ZnS lattice is substantiated by the anti-stoke shift of Raman peaks and shifting of XRD peaks to higher 2q values. Upon increasing Cu2+ doping concentration, the resulted decrease in the FWHM of XRD peaks implies shrinkage of the ZnS lattice. Interestingly, by tailoring the excitation wavelength, the stoichiometry of dopant ion, and defect states by varying the vacuum pressure, the optimized ZSC-3 (3% Cu2+-doped-ZnS) displays the origin of clear blue, green and red emission bands, consequently giving rise to white light emission (CIE values:  0.345:0398). The PLQY and average lifetime calculated for ZSC-3 are 5.98% and 1.5 ms, respectively. Such intense white light emission prompted to fabricate a prototype using a 310 nm UV LED. It exhibits high CRI (97) and warm CCT (4538 K)- meeting highly desired values for a white light-emitting phosphor for different lighting and electroluminescence applications.

Computational Biology of BRCA2 in Male Breast Cancer, through Prediction of Probable nsSNPs, and Hit Identification

Male breast cancer (MBC) is a relatively rare disease, but emerging data recommend the development of novel therapeutics considering its alarming threats. Compared to female breast cancer (FBC), MBC is reportedly associated with inferior outcomes (poor survival) owing to their late diagnosis and lack of adequate treatment. Treatment typically correlates with FBC, involving surgical removal of the breast tissue along with chemo/hormonal/radiation therapy, the tamoxifen being a standard adjuvant. Considering the distinct immunophenotypic (implying different pathogenesis and progression) differences from FBC, the identification of diagnostics, prognostics, and therapeutics for MBC is highly desirable. In this context, we have analyzed the most deleterious nsSNPs of BRCA2, a human tumor suppressor gene constituting the potential biomarker for tumors including MBC, to predict the structural changes associated with the mutants hampering the normal protein-protein and protein-ligand interactions, resulting in MBC progression. Among 27 nsSNPs confined to 21 rsIDs pertaining to MBC, the 19 nsSNPs constituting 14 rsIDs have been predicted as highly deleterious. We believe that these nsSNPs could serve as potential biomarkers for diagnostic and prognostic purposes and could be the pivotal target for MBC drug discovery. Subsequently, the study highlights the exploration of the key nsSNPs (of BRCA2 associated with the MBC) and its applications toward the identification of therapeutic hit TIP006136 following the homology modeling, virtual screening of 5284 phytochemicals retrieved from the TIPdb (a database of phytochemicals from indigenous plants in Taiwan) database, molecular docking (against native and mutant BRCA2), dynamic simulations (against native and mutant BRCA2), density functional theory (DFT), and molecular electrostatic potential. To the best of our knowledge, this is the first report to use diverse computational modules to investigate the important nsSNPs of BRCA2 related to MBC, implying that TIP006136 could be a potential hit and must be studied further (in vitro and in vivo) to establish its anticancer property and efficacy against MBC.

Deciphering the signaling mechanisms of β-arrestin1 and β-arrestin2 in regulation of cancer cell cycle and metastasis

β-Arrestins are ubiquitously expressed intracellular proteins with many functions which interact directly and indirectly with a wide number of cellular partners and mediate downstream signaling. Originally, β-arrestins were identified for their contribution to GPCR desensitization to agonist-mediated activation, followed by receptor endocytosis and ubiquitylation. However, current investigations have now recognized that in addition to GPCR arresting (hence the name arrestin). β-Arrestins are adaptor proteins that control the recruitment, activation, and scaffolding of numerous cytoplasmic signaling complexes and assist in G-protein receptor signaling, thus bringing them into close proximity. They have participated in various cellular processes such as cell proliferation, migration, apoptosis, and transcription via canonical and noncanonical pathways. Despite their significant recognition in several physiological processes, these activities are also involved in the onset and progression of various cancers. This review delivers a concise overview of the role of β-arrestins with a primary emphasis on the signaling processes which underlie the mechanism of β-arrestins in the onset of cancer. Understanding these processes has important implications for understanding the therapeutic intervention and treatment of cancer in the future.

Seeking heterocyclic scaffolds as antivirals against dengue virus

Dengue is one of the most typical viral infection categorized in the Neglected Tropical Diseases (NTDs). It is transmitted via the female Aedes aegypti mosquito to humans and majorly puts risk to the lives of more than half of the world. Recent advancements in medicinal chemistry have led to the design and development of numerous potential heterocyclic scaffolds as antiviral drug candidates for the inhibition of the dengue virus (DENV). Thus, in this review, we have discussed the significance of inhibitory and antiviral activities of nitrogen, oxygen, and mixed (nitrogen-sulfur and nitrogen-oxygen) heterocyclic scaffolds that are published in the last seven years (2016–2022). Furthermore, we have also discussed the probable mechanisms of action and the diverse structure-activity relationships (SARs) of the heterocyclic scaffolds. In addition, this review has elaborately outlined the mechanism of viral infection and the life cycle of DENV in the host cells. The wide set of heterocycles and their SARs will aid in the development of pharmaceuticals that will allow the researchers to synthesize the promising anti-dengue drug candidate in the future.

Abstract 5006: Computational analysis of hypoxia-inducible factor 1-alpha and UBS109 in hepatocellular carcinoma

Hypoxia-inducible factor 1-alpha (HIF-1α) is a heterodimeric transcription factor, which is elevated during hypoxic conditions in several malignancies. HIF-1α is known to stimulate hypoxia-responsive genes that are linked with malignant properties viz.: progression, metastasis, and resistance to therapy. The objective of the present study is to target HIF-1α by potential phytodrug, curcumin and its monocarbonyl analog UBS109 in hepatocellular carcinoma (HCC). Curcumin has been known to exhibit therapeutic properties for the management of HCC due to its powerful anti-inflammatory and antioxidant properties as well as its ability to regulate multiple signaling pathways. UBS109 possesses comparable antitumor and anti-inflammatory properties as curcumin without any of its limitations. To analyze the binding capacity and ligand efficacy of HIF-1α against curcumin and UBS109, computational approaches were applied including molecular docking and dynamics simulation that can provide detailed understanding of its implication in HCC treatment and a deeper analysis of the protein-drug interaction.

Citation Format: Neha Bahadur Merchant, Santosh Kumar Behera, Afroz Alam, Ganji Purnachandra Nagaraju, Riyaz Basha. Computational analysis of hypoxia-inducible factor 1-alpha and UBS109 in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5006.

Crystallization induced room-temperature phosphorescence and chiral photoluminescence properties of phosphoramides

We report the design and synthesis of a series of room temperature phosphorescent phosphoramides TPTZPO, TPTZPS, and TPTZPSe with a donor (phenothiazine)-acceptor (P = X, X = O, S, and Se) architecture. All the compounds show structureless fluorescence with a nanosecond lifetime in dilute solutions. However, these compounds show dual fluorescence and room temperature phosphorescence (RTP) in the solid state. Both the intensity and energy of luminescence depend on the heteroatom attached to the phosphorus center. For example, compound TPTZPO with the P[double bond, length as m-dash]O unit exhibits fluorescence at a higher energy region than TPTZPS and TPTZPSe with the P[double bond, length as m-dash]S and P[double bond, length as m-dash]Se groups, respectively. Crystalline samples of TPTZPO, TPTZPS, and TPTZPSe show stronger RTP than the amorphous powder of respective compounds. Detailed steady-state, time-resolved photoluminescence and computational studies established that the 3n-π* state dominated by the phenothiazine moiety is the emissive state of these compounds. Although TPTZPS and TPTZPSe crystallized in the chiral space group, only TPTZPSe showed chiroptical properties in the solid state. The luminescence dissymmetry factor (g lum) value of TPTZPS is small and below the detection limit, and a CPL spectrum could not be observed for this compound.

Biocomputational Assessment of Natural Compounds as a Potent Inhibitor to Quorum Sensors in Ralstonia solanacearum

Ralstonia solanacearum is among the most damaging bacterial phytopathogens with a wide number of hosts and a broad geographic distribution worldwide. The pathway of phenotype conversion (Phc) is operated by quorum-sensing signals and modulated through the (R)-methyl 3-hydroxypalmitate (3-OH PAME) in R. solanacearum. However, the molecular structures of the Phc pathway components are not yet established, and the structural consequences of 3-OH PAME on quorum sensing are not well studied. In this study, 3D structures of quorum-sensing proteins of the Phc pathway (PhcA and PhcR) were computationally modeled, followed by the virtual screening of the natural compounds library against the predicted active site residues of PhcA and PhcR proteins that could be employed in limiting signaling through 3-OH PAME. Two of the best scoring common ligands ZINC000014762512 and ZINC000011865192 for PhcA and PhcR were further analyzed utilizing orbital energies such as HOMO and LUMO, followed by molecular dynamics simulations of the complexes for 100 ns to determine the ligands binding stability. The findings indicate that ZINC000014762512 and ZINC000011865192 may be capable of inhibiting both PhcA and PhcR. We believe that, after further validation, these compounds may have the potential to disrupt bacterial quorum sensing and thus control this devastating phytopathogenic bacterial pathogen.

Towards Phytopathogen Diagnostics? Coconut Bud Rot Pathogen Phytophthora palmivora Mycelial Proteome Analysis Informs Genome Annotation

Planetary agriculture stands to benefit immensely from phytopathogen diagnostics, which would enable early detection of pathogens with harmful effects on crops. For example, Phytophthora palmivora is one of the most destructive phytopathogens affecting many economically important tropical crops such as coconut. P. palmivora causes diseases in over 200 host plants, and notably, the bud rot disease in coconut and oil palm, which is often lethal because it is usually detected at advanced stages of infection. Limited availability of large-scale omics datasets for P. palmivora is an important barrier for progress toward phytopathogen diagnostics. We report here the mycelial proteome of P. palmivora using high-resolution mass spectrometry analysis. We identified 8073 proteins in the mycelium. Gene Ontology-based functional classification of detected proteins revealed 4884, 4981, and 3044 proteins, respectively, with roles in biological processes, molecular functions, and cellular components. Proteins such as P-loop, NTPase, and WD40 domains with key roles in signal transduction pathways were identified. KEGG pathway analysis annotated 2467 proteins to various signaling pathways, such as phosphatidylinositol, Ca²⁺, and mitogen-activated protein kinase, and autophagy and cell cycle. These molecular substrates might possess vital roles in filamentous growth, sporangia formation, degradation of damaged cellular content, and recycling of nutrients in P. palmivora. This large-scale proteomics data and analyses pave the way for new insights on biology, genome annotation, and vegetative growth of the important plant pathogen P. palmivora. They also can help accelerate research on future phytopathogen diagnostics and preventive interventions.

Metabolomics analysis highlights Yashtimadhu (Glycyrrhiza glabra L.)-mediated neuroprotection in a rotenone-induced cellular model of Parkinson's disease by restoring the mTORC1-AMPK1 axis in autophagic regulation

Parkinson's disease (PD) is an age-associated progressive neurodegenerative movement disorder, and its management strategies are known to cause complications with prolonged usage. We aimed to explore the neuroprotective mechanism of the Indian traditional medicine Yashtimadhu, prepared from the dried roots of Glycyrrhiza glabra L. (licorice) in the rotenone-induced cellular model of PD. Retinoic acid-differentiated IMR-32 cells were treated with rotenone (PD model) and Yashtimadhu extract. Mass spectrometry-based untargeted and targeted metabolomic profiling was carried out to discover altered metabolites. The untargeted metabolomics analysis highlighted the rotenone-induced dysregulation and Yashtimadhu-mediated restoration of metabolites involved in the metabolism of nucleic acids, amino acids, lipids, and citric acid cycle. Targeted validation of citric acid cycle metabolites showed decreased α-ketoglutarate and succinate with rotenone treatment and rescued by Yashtimadhu co-treatment. The dysregulation of the citric acid cycle by rotenone-induced energetic stress via dysregulation of the mTORC1-AMPK1 axis was prevented by Yashtimadhu. Yashtimadhu co-treatment restored rotenone-induced ATG7-dependent autophagy and eventually caspases-mediated cell death. Our analysis links the metabolic alterations modulating energy stress and autophagy, which underlies the Yashtimadhu-mediated neuroprotection in the rotenone-induced cellular model of PD.

Synthesis and Characterization of Far-Red Emissive Boron-Based Triads Showing Large Stokes Shifts: Optical, TRANES, and Electrochemical Studies

Herein, we report the design and synthesis of far-red emissive boryl-thiophene-BODIPY triads 1-3. The π-conjugation length and electronic communication between borane and BODIPY moieties are tuned by judiciously varying the size of the oligothiophene spacer in these triads (1, terthiophene; 2, quarterthiophene; and 3, pentathiophene). Conjugates 1-3 showed intriguing triple emissions in the blue to far-red regions. Detailed optical, time-resolved decay kinetics, time-resolved area-normalized emission spectra (TRANES), fluoride binding, and computational studies suggest that the multiple emissions in these triads are due to an inefficient transfer of energy from the boryl-oligothiophene to the BODIPY unit. In addition, all of the conjugates showed a ratiometric fluorescence response to fluoride ions.

Identifying Novel Genes and Proteins Involved in Salt Stress Perception and Signaling of Rice Seedlings

Rice is one of the most important crops worldwide. Crop production is constrained markedly, however, by abiotic stresses such as salinity. To elucidate early stress response signaling networks involved in rice, we report in this study an original quantitative proteomic analysis of the rice seedlings subjected to short-term salt stress. We detected 570 differentially regulated proteins (DRPs) in the root sample. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis demonstrated that DRPs of the root were mainly involved in membrane trafficking, kinase activity, and ion toxicity responses. Interactome analysis revealed the central role of root proteins involved in membrane trafficking in the early response to salinity, such as cell surface receptor-like kinases (RLKs), phosphatidylinositols (PIs), calcium-dependent protein kinases 1 and 5, calcineurin B-like protein-interacting proteins, protein phosphatase 2C (PP2C) inhibitors, and abscisic acid receptors (PYL5/10), indicating activation of S-type anion channel. Furthermore, the proteogenomic analysis revealed 128 unique genome search-specific peptides with high-quality mass spectromety (MS/MS) spectra. We identified 38 novel protein-coding genes, refined the annotation of 17 existing gene models, and suggested several novel stress-responsive proteins, such as RLK5, peroxidase 27, and growth-regulating factor 2. Novel peptides had an ortholog match in the curated protein sequence set of other plant species. In conclusion, this study identifies novel stress-responsive proteins and genes of rice, thus warrant future consideration as candidates for molecular breeding of stress-tolerant crop varieties.

Diabetes Status After Lateral Pancreaticojejunostomy and Frey’s Procedure in Chronic Calcific Pancreatitis: An Observational Study

Introduction

Diabetes secondary to pancreatic diseases is commonly referred to as pancreatogenic diabetes or type 3c diabetes mellitus. This study was conducted to determine the status of diabetes mellitus after Frey’s procedure and lateral pancreaticojejunostomy (LPJ) in diabetic and nondiabetic patients with chronic calcific pancreatitis (CCP) and to discuss the clinicopathological course as well as diabetes in CCP.

Materials and methods

This study was designed as a retrospective observational study consisting of 27 patients with CCP who were surgically treated either with the pancreatic head coring Frey’s procedure or with LPJ. Surgeries were performed in a tertiary care hospital of Eastern India by a team of surgeons following the same surgical principle. The diagnosis of CCP was made by clinical and radiological evaluations. Visual Analog Scale (VAS) scoring was used perioperatively to assess pain. Postoperatively, all the patients were monitored clinically; pain scoring and relevant investigations were done depending upon subjective and objective indications. Special attention was paid to diabetic patients through frequent follow-ups and tight glycemic control. All 27 patients were followed up with at least two outpatient follow-ups.

Results

The trends in fasting blood sugar values in the LPJ group showed a small spike in the early postoperative period (two weeks) with a p-value of >0.05, and later on, it improved over 18 months of follow-up, reaching below the preoperative values (mean 109.38). On the contrary, the fasting blood glucose levels in Frey’s procedure revealed a significant spike in the early postoperative period (two weeks) with a mean sugar value of 148 mg/dl and a p-value of 0.01. The levels stayed well above the preoperative values over 18 months of follow-up. The trends in HbA1c showed marginal improvement in the LPJ group in a six-month follow-up period (p-value 0.008) from the preoperative levels. In Frey’s procedure group, postoperative HbA1c levels at three months revealed an increase, which can be attributed to the minor but significant loss of pancreatic tissue from the head, which continued to be on the higher side at the six-month follow-up. Trends in mean insulin dosage showed a significant spike in the early postoperative period (two weeks) both in the LPJ (p-value 0.01) and Frey’s procedure group (0.01); however, in the LPJ group, the insulin dose showed a reduction over the 18-month follow-up, reaching below the mean preoperative insulin dose. While in the Frey’s procedure group, the postoperative insulin dose remained higher throughout the 18-month follow-up period (p-value <0.05).

Conclusions

LPJ has got a little effect on the diabetic status of nondiabetic patients. Frey’s procedure leads to marginal deterioration of the diabetic status and increases in insulin dosage in both diabetic and nondiabetic patients.

Performance Enhancement of the Unbalanced Text Classification Problem Through a Modified Chi Square-Based Feature Selection Technique

This paper proposes a modified chi square-based feature selection algorithm in conjunction with a random vector functional link network-based text classifier for improving the classification performance of multi-labeled text documents with unbalanced class distributions. In the proposed feature selection method, maximum features are selected from classes that have a great deal of training and testing documents as an improvement towards original chi-square method. On two benchmark datasets that are multi-labeled, multi-class, and unbalanced, a comparison of the model with three conventional selection techniques such as chi-square, term frequency-inverse document frequency, and mutual information is accumulated for assessing its effectiveness. Additionally, the proposed model is compared with four different classifiers. In the study, it was found that the proposed model performs better in terms of precision, recall, f-measure, and hamming losses and is able to select the majority of true positive documents despite an unbalanced class distribution for both the datasets.

Hyperphosphorylation of HDAC2 promotes drug resistance in a novel dual drug resistant mouse melanoma cell line model: an in vitro study

Drug-resistant melanoma is very difficult to treat, and a novel approach is needed to overcome resistance. The present study aims at identifying the alternate pathways utilized in the dual drug-resistant mouse melanoma cells (B16F10R) for their survival and proliferation. The dual drug-resistant mouse melanoma, B16F10R, was established by treating the cells with a combination of U0126 (MEK1/2 inhibitor) and LY294002 (PI3K-AKT kinase inhibitor) in a dose-escalating manner till they attained a resistance fold factor of ≥2. The altered phosphoproteome in the B16F10R, as compared to the parental B16F10C, was analyzed using a high-resolution Orbitrap Fusion Tribrid mass spectrometer. Histone deacetylases 2 (HDAC2) was validated for its role in drug resistance by using its inhibitor, valproic acid (VPA). In the B16F10R cells, 363 altered phosphoproteins were identified, among which 126 were hyperphosphorylated, and 137 were hypophosphorylated (1.5-fold change). Pathway analysis shows the altered phosphoproteins are from RNA metabolism and cell cycle proteins. Inhibition of HDAC2 by VPA induces apoptosis in B16F10C and B16F10R. The present study highlights the role of HDAC2, a cell cycle regulator, in the development of resistance to dual drugs in murine melanoma. Therefore, designing leads for targeting HDAC2 along with key signaling pathways may be explored in treatment strategies.

From LC-MS/MS metabolomics profiling of Kanchanara Guggulu to molecular docking and dynamics simulation of quercetin pentaacetate with aldose reductase

Kanchanara Guggulu (KG) is an important traditional medicine that is prescribed by the Ayurveda physicians for the treatment of swellings in various organs such as the thyroid, and lymph nodes. High-resolution mass-spectrometry-based metabolomics found metabolites in KG. LC-MS/MS-based metabolomics analysis of KG identified 2,579 compounds including quercetin and kaempferol derivatives. The molecular docking and dynamics analysis of quercetin pentaacetate with aldose reductase is documented for further consideration in drug discovery.

Unraveling Toxoplasma gondii GT1 Strain Virulence and New Protein-Coding Genes with Proteogenomic Analyses

Toxoplasma gondii is one of the most widespread parasites of great relevance to planetary health. It infects approximately one-third of the world population. T. gondii establishes itself in warm-blooded animals and causes adverse health outcomes, particularly in immunocompromised patients. T. gondii is also widely used as a model organism to study other related apicomplexan parasites, which requires a deeper understanding of its molecular biology. Type I strains (GT1 and RH) of T. gondii are considered the most virulent forms. The whole-genome sequencing of T. gondii annotated 8460 predicted gene models in the parasite. To this end, the proteogenomics technology allows harnessing of mass spectrometry (MS)-derived proteomic data to unravel new protein-coding genes, not to mention validation and correction of the existing gene models. In this study using the proteogenomic approach, we report the identification of 31 novel protein-coding genes while reannotating 88 existing gene models. Notably, the genome annotations were corrected for genes, such as SAG5C, GRA6, ROP4, ROP5, and ROP26. The associated proteins are known to play important roles in host-parasite interactions, particularly in relation to parasite virulence, suppression of host immune response, and distinctively pertinent for the survival of the parasite inside the host system. These new findings offer new insights, informing planetary health broadly and the knowledge base on T. gondii virulence specifically. The proteogenomics approach also provides a concrete example to study related apicomplexan organisms of relevance to planetary health, and so as to develop new diagnostics and therapeutics against toxoplasmosis and related diseases.

The unique molecular targets associated antioxidant and antifibrotic activity of curcumin in in vitro model of acute lung injury: A proteomic approach

Bleomycin (BLM) injury is associated with the severity of acute lung injury (ALI) leading to fibrosis, a high-morbidity, and high-mortality respiratory disease of unknown etiology. BLM-induced ALI is marked by the activation of a potent fibrogenic cytokine transcription growth factor beta-1 (TGFβ-1), which is considered a critical cytokine in the progression of alveolar injury. Previously, our work demonstrated that a diet-derived compound curcumin (diferuloylmethane), represents its antioxidative and antifibrotic application in TGF-β1-mediated BLM-induced alveolar basal epithelial cells. However, curcumin-specific protein targets, as well as its mechanism using mass spectrometry-based proteomic approach, remain elusive. To elucidate the underlying mechanism, a quantitative proteomics approach and bioinformatics analysis were employed to identify the protein targets of curcumin in BLM or TGF-β1-treated cells. With subsequent in vitro experiments, curcumin-related pathways and cellular processes were predicted and validated. The current study discusses two separate proteomics experiments using BLM and TGF-β1-treated cells with the proteomics approach, various unique target proteins were identified, and proteomic analysis revealed that curcumin reversed the expressions of unique proteins like DNA topoisomerase 2-alpha (TOP2A), kinesin-like protein (KIF11), centromere protein F (CENPF), and so on BLM or TGF-β1 injury. For the first time, the current study reveals that curcumin restores TGF-β1 induced peroxisomes like PEX-13, PEX-14, PEX-19, and ACOX1. This was verified by subsequent in vitro assays. This study generated molecular evidence to deepen our understanding of the therapeutic role of curcumin at the proteomic level and may be useful to identify molecular targets for future drug discovery.

Omics Data Mining for multiPTMs in Oral Cancer: Cellular Proteome and Secretome of Chronic Tobacco-Treated Oral Keratinocytes

Oral cancer is common worldwide but lacks robust diagnostics and therapeutics. Lifestyle factors, such as tobacco chewing and smoking, are significantly associated with oral cancers. Mapping the changes in the global proteome, secretome and post-translational modifications (PTMs) during tobacco exposure of oral keratinocytes hold great potential for understanding the mechanisms of oral carcinogenesis, not to mention for innovation toward clinical interventions in the future. On the other hand, although advances in mass spectrometry (MS)-based techniques have enabled the deep mining of complex proteomes, a large portion of the mass spectrometric data remains unassigned. These unassigned spectral data can be researched for multiple post-translational modifications (multiPTMs). Using data mining of publicly available proteomics data, we report, in this study, a multiPTM analysis of high-resolution MS-derived datasets on cellular proteome and secretome of chronic tobacco-treated oral keratinocytes. We identified 800 PTM sites in 496 proteins. Among them, 43 PTM sites in 37 proteins were found to be differentially expressed, accounting for their protein-level expression. Enrichment analysis of the proteins with altered phosphosite expression and the known kinases of these phosphosites discovered the overrepresentation of certain biological processes such as splicing and hemidesmosome assembly. These findings contribute to a deeper understanding of omics level changes in chronic tobacco-treated oral keratinocytes, and by extension, pathophysiology of oral cancers.

MS2Compound: A User-Friendly Compound Identification Tool for LC-MS/MS-Based Metabolomics Data

Metabolomics is a leading frontier of systems science and biomedical innovation. However, metabolite identification in mass spectrometry (MS)-based global metabolomics investigations remains a formidable challenge. Moreover, lack of comprehensive spectral databases hinders accurate identification of compounds in global MS-based metabolomics. Creating experiment-derived metabolite spectral libraries tailored to each experiment is labor-intensive. Therefore, predicted spectral libraries could serve as a better alternative. User-friendly tools are much needed, as the currently available metabolomic analysis tools do not offer adequate provision for users to create or choose context-specific databases. Here, we introduce the MS2Compound, a metabolite identification tool, which can be used to generate a custom database of predicted spectra using the Competitive Fragmentation Modeling-ID (CFM-ID) algorithm, and identify metabolites or compounds from the generated database. The database generator can create databases of the model/context/species used in the metabolomics study. The MS2Compound is also powered with mS-score, a scoring function for matching raw fragment spectra to a predicted spectra database. We demonstrated that mS-score is robust in par with dot product and hypergeometric score in identifying metabolites using benchmarking datasets. We evaluated and highlight here the unique features of the MS2Compound by a re-analysis of a publicly available metabolomic dataset (MassIVE id: MSV000086784) for a complex traditional drug formulation called Triphala. In conclusion, we believe that the omics systems science and biomedical research and innovation community in the field of metabolomics will find the MS2Compound as a user-friendly analysis tool of choice to accelerate future metabolomic analyses.

Drug repurposing for identification of potential inhibitors against SARS-CoV-2 spike receptor-binding domain: An in silico approach

Background & objectives

The world is currently under the threat of coronavirus disease 2019 (COVID-19) infection, caused by SARS-CoV-2. The objective of the present investigation was to repurpose the drugs with potential antiviral activity against receptor-binding domain (RBD) of SARS-CoV-2 spike (S) protein among 56 commercially available drugs. Therefore, an integrative computational approach, using molecular docking, quantum chemical calculation and molecular dynamics, was performed to unzip the effective drug-target interactions between RBD and 56 commercially available drugs.

Methods

The present in silico approach was based on information of drugs and experimentally derived crystal structure of RBD of SARS-CoV-2 S protein. Molecular docking analysis was performed for RBD against all 56 reported drugs using AutoDock 4.2 tool to screen the drugs with better potential antiviral activity which were further analysed by other computational tools for repurposing potential drug or drugs for COVID-19 therapeutics.

Results

Drugs such as chalcone, grazoprevir, enzaplatovir, dolutegravir, daclatasvir, tideglusib, presatovir, remdesivir and simeprevir were predicted to be potentially effective antiviral drugs against RBD and could have good COVID-19 therapeutic efficacy. Simeprevir displayed the highest binding affinity and reactivity against RBD with the values of -8.52 kcal/mol (binding energy) and 9.254 kcal/mol (band energy gap) among all the 56 drugs under investigation.

Interpretation & conclusions

In the current investigation, simeprevir was identified as the potential antiviral drug based on the in silico findings in comparison to remdesivir, favipiravir and other 53 drugs. Further, laboratory and clinical investigations are needed to be carried out which will aid in the development of quick therapeutics designed for COVID-19.

Effect of the Molecular Conformation on Excitation Energy Transfer in Conformationally Constrained Boryl-BODIPY Dyads

We studied the dual emission characteristics of a series of boryl-BODIPYs (1-6) comprised of triarylborane (TAB) as an energy donor and BODIPY as an energy acceptor. The molecular conformations of dyads 1-6 were systematically tuned by judiciously changing the spacer that bridged the boryl and BODIPY moieties. Frontier molecular orbitals (FMOs) are localized in 3, 4, and 6 with a twisted molecular conformation. In contrast, FMOs are significantly delocalized in 1, 2, and 5 with the least-twisted molecular conformation. Dyads 1-6 showed dual emission features when they were excited at the TAB-dominated absorption band. However, the ratio between the two emission bands in 1-6 significantly varied depending on the molecular conformations. Systematic photoluminescence (PL) studies (both steady-state and time-resolved PL) together with computational, crystal structure, and anion binding studies established that the frustrated excited-state energy transfer from borane to BODIPY is the cause of the dual emission features in these molecular dyads. These studies also revealed that the energy transfer from borane to BODIPY can be elegantly tuned by modulating the dihedral angle between these two moieties.

Assembly and Annotation of the Nuclear and Organellar Genomes of a Dwarf Coconut (Chowghat Green Dwarf) Possessing Enhanced Disease Resistance

Coconut (Cocos nucifera L.), an important source of vegetable oil, nutraceuticals, functional foods, and housing materials, provides raw materials for a repertoire of industries engaged in the manufacture of cosmetics, soaps, detergents, paints, varnishes, and emulsifiers, among other products. The palm plays a vital role in maintaining and promoting the sustainability of farming systems of the fragile ecosystems of islands and coastal regions of the tropics. In this study, we present the genome of a dwarf coconut variety "Chowghat Green Dwarf" (CGD) from India, possessing enhanced resistance to root (wilt) disease. Utilizing short reads from the Illumina HiSeq 4000 platform and long reads from the Pacific Biosciences RSII platform, we have assembled the draft genome assembly of 1.93 Gb. The genome is distributed over 26,855 scaffolds, with ∼81.56% of the assembled genome present in scaffolds of lengths longer than 50 kb. About 77.29% of the genome was composed of transposable elements and repeats. Gene prediction yielded 51,953 genes, which upon stringent filtering, based on Annotation Edit Distance, resulted in 13,707 genes, which coded for 11,181 proteins. Among these, we gathered transcript level evidence for a total of 6828 predicted genes based on the RNA-Seq data from different coconut tissues, since they presented assembled transcripts within the genome annotation coordinates. A total of 112 nucleotide-binding and leucine-rich repeat loci, belonging to six classes, were detected. We have also undertaken the assembly and annotation of the CGD chloroplast and mitochondrial genomes. The availability of the dwarf coconut genome shall prove invaluable for deducing the origin of dwarf coconut cultivars, dissection of genes controlling plant habit and fruit color, and accelerated breeding for improved agronomic traits.