Search results for: binding kinetics

Authors: Emine Teke, Soner Kuşlu, Sabri Çolak, Turan Çalban

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The aim of the present study was to investigate the dissolution kinetics of ulexite in sodium dihydrogen phosphate in a mechanical agitation system and also to declare an alternative reactant to produce the boric acid. Reaction temperature, concentration of sodium dihydrogen phosphate, stirring speed, solid-liquid ratio, and ulexite particle size were selected as parameters. The experimental results were successfully correlated by using linear regression and a statistical program. Dissolution curves were evaluated in order to test the shrinking core models for solid-fluid systems. It was observed that increase in the reaction temperature and decrease in the solid/liquid ratio causes an increase in the dissolution rate of ulexite. The activation energy was found to be 36.4 kJ/mol. The leaching of ulexite was controlled by diffusion through the ash (or product) layer.

Keywords: ulexite, sodium dihydrogen phosphate, leaching kinetics, boron

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Authors: Sonam Kumari

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Tuberculosis is the deadliest disease worldwide. Millions of people lose their lives every year due to this disease. It has turned lethal due to the erratic nature of its causative organism, Mycobacterium tuberculosis (Mtb). Mtb tends to enter into an inactive, dormant state and emerge to replicating state upon encountering favorable conditions. The mechanism by which Mtb switches from the dormant state to the replicative form is still poorly characterized. Proteome studies have given us an insight into the role of certain proteins in giving stupendous virulence to Mtb, but numerous dotsremain unconnected and unaccounted. The WhiB family of proteins is one such protein that is associated with developmental processes in actinomycetes. Mtb has seven such proteins (WhiB1 to WhiB7). WhiB proteins are transcriptional regulators; they regulate various essential genes of Mtbby binding to their promoter DNA. Biophysical parameters of the effect of DNA binding on WhiB proteins has not yet been appropriately characterized. Interaction with DNA induces conformational changes in the WhiB proteins, confirmed by steady-state fluorescence and circular dichroism spectroscopy. ITC has deduced thermodynamic parameters and the binding affinity of the interaction. Since these transcription factors are highly unstable in vitro, their stability and solubility were enhanced by the co-expression of molecular chaperones. The present study findings help determine the conditions under which the WhiB proteins interact with their interacting partner and the factors that influence their binding affinity. This is crucial in understanding their role in regulating gene expression in Mtbandin targeting WhiB proteins as a drug target to cure TB.

Keywords: mycobacterium tuberculosis, TB, whiB proteins, ITC

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Authors: Z. V. P. Murthy, Preeti Arunachalam, Sangeeta Balram

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Removal of metal ions from different wastewaters has become important due to their effects on living beings. Cadmium is one of the heavy metals found in different industrial wastewaters. There are many conventional methods available to remove heavy metals from wastewaters like adsorption, membrane separations, precipitation, electrolytic methods, etc. and all of them have their own advantages and disadvantages. The present work deals with the use of natural biosorbents (chitin and chitosan) to separate cadmium ions from aqueous solutions. The adsorption data were fitted with different isotherms and kinetics models. Amongst different adsorption isotherms used to fit the adsorption data, the Freundlich isotherm showed better fits for both the biosorbents. The kinetics data of adsorption of cadmium showed better fit with pseudo-second order model for both the biosorbents. Chitosan, the derivative from chitin, showed better performance than chitin. The separation results are encouraging.

Keywords: chitin, chitosan, cadmium, isotherm, kinetics

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Authors: P. A. Broodryk, A. F. Van Der Merwe, H. W. J. P. Neomagus

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The production of the clear liquid fertilizer ammonium polyphosphate (APP) is best achieved by the pyrolysis of urea phosphate, as it produces a product that is free from any of the impurities present in the raw phosphoric acid it was made from. This is a multiphase, multi-step reaction that produces carbon dioxide and ammonia as gasses and ammonium polyphosphate as liquid products. The polyphosphate chain length affects the solubility and thus the applicability of the product as liquid fertiliser, thus proper control of the reaction conditions is thus required for the use of this reaction in the production of fertilisers. This study investigates the reaction kinetics of the aforementioned reaction, describing a mathematical model for the kinetics of the reaction along with the accompanying rate constants. The reaction is initially exothermic, producing only carbon dioxide as a gas product and ammonium diphosphate, at higher temperatures the reaction becomes endothermic, producing ammonia gas as an additional by-product and longer chain polyphosphates, which when condensed too far becomes highly water insoluble. The aim of this study was to (i) characterise the pyrolysis reaction of urea phosphate by determining the mechanisms and the associated kinetic constants, and (ii) to determine the optimum conditions for ammonium diphosphate production. A qualitative investigation was also done to find the rate of hydrolysis of APP as this provides an estimate of the shelf life of an APP clear liquid fertiliser solution.

Keywords: ammonium polyphosphate, kinetics, pyrolysis, urea phosphate

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Authors: Ulugbek Azimov, Nearchos Stylianidis, Nobuyuki Kawahara, Eiji Tomita

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A chemical kinetics and computational fluid-dynamics (CFD) analysis was performed to evaluate the combustion of syngas derived from biomass and coke-oven solid feedstock in a micro-pilot ignited supercharged dual-fuel engine under lean conditions. For this analysis, a new reduced syngas chemical kinetics mechanism was constructed and validated by comparing the ignition delay and laminar flame speed data with those obtained from experiments and other detail chemical kinetics mechanisms available in the literature. The reaction sensitivity analysis was conducted for ignition delay at elevated pressures in order to identify important chemical reactions that govern the combustion process. The chemical kinetics of NOx formation was analyzed for H2/CO/CO2/CH4 syngas mixtures by using counter flow burner and premixed laminar flame speed reactor models. The new mechanism showed a very good agreement with experimental measurements and accurately reproduced the effect of pressure, temperature and equivalence ratio on NOx formation. In order to identify the species important for NOx formation, a sensitivity analysis was conducted for pressures 4 bar, 10 bar and 16 bar and preheat temperature 300 K. The results show that the NOx formation is driven mostly by hydrogen based species while other species, such as N2, CO2 and CH4, have also important effects on combustion. Finally, the new mechanism was used in a multidimensional CFD simulation to predict the combustion of syngas in a micro-pilot-ignited supercharged dual-fuel engine and results were compared with experiments. The mechanism showed the closest prediction of the in-cylinder pressure and the rate of heat release (ROHR).

Keywords: syngas, chemical kinetics mechanism, internal combustion engine, NOx formation

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Authors: Prasanna Ramachandran, Kareem Graham, Helena Kiefel, Sunit Jain, Todd DeSantis

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Microbes that reside inside the mammalian GI tract, commonly referred to as the gut microbiome, have been shown to have therapeutic effects in animal models of disease. We hypothesize that specific proteins produced by these microbes are responsible for this activity and may be used directly as therapeutics. To speed up the discovery of these key proteins from the big-data metagenomics, we have applied machine learning techniques. Using amino acid sequences of known epitopes and their corresponding binding partners, protein interaction descriptors (PID) were calculated, making a positive interaction set. A negative interaction dataset was calculated using sequences of proteins known not to interact with these same binding partners. Using Random Forest and positive and negative PID, a machine learning model was trained and used to predict interacting versus non-interacting proteins. Furthermore, the continuous variable, cosine similarity in the interaction descriptors was used to rank bacterial therapeutic candidates. Laboratory binding assays were conducted to test the candidates for their potential as therapeutics. Results from binding assays reveal the accuracy of the machine learning prediction and are subsequently used to further improve the model.

Keywords: protein-interactions, machine-learning, metagenomics, microbiome

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Authors: Kakali Bhadra

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Binding of small molecules to DNA and recently to RNA, continues to attract considerable attention for developing effective therapeutic agents for control of gene expression. This work focuses towards understanding interaction of harmalol, a dihydro beta-carboline alkaloid, with different nucleic acid motifs viz. double stranded CT DNA, single stranded A-form poly(A), double-stranded A-form of poly(C)·poly(G) and clover leaf tRNAphe by different spectroscopic, calorimetric and molecular modeling techniques. Results of this study converge to suggest that (i) binding constant varied in the order of CT DNA > poly(C)·poly(G) > tRNAphe > poly(A), (ii) non-cooperative binding of harmalol to poly(C)·poly(G) and poly(A) and cooperative binding with CT DNA and tRNAphe, (iii) significant structural changes of CT DNA, poly(C)·poly(G) and tRNAphe with concomitant induction of optical activity in the bound achiral alkaloid molecules, while with poly(A) no intrinsic CD perturbation was observed, (iv) the binding was predominantly exothermic, enthalpy driven, entropy favoured with CT DNA and poly(C)·poly(G) while it was entropy driven with tRNAphe and poly(A), (v) a hydrophobic contribution and comparatively large role of non-polyelectrolytic forces to Gibbs energy changes with CT DNA, poly(C)·poly(G) and tRNAphe, and (vi) intercalated state of harmalol with CT DNA and poly(C)·poly(G) structure as revealed from molecular docking and supported by the viscometric data. Furthermore, with competition dialysis assay it was shown that harmalol prefers hetero GC sequences. All these findings unequivocally pointed out that harmalol prefers binding with ds CT DNA followed by ds poly(C)·poly(G), clover leaf tRNAphe and least with ss poly(A). The results highlight the importance of structural elements in these natural beta-carboline alkaloids in stabilizing different DNA and RNA of various motifs for developing nucleic acid based better therapeutic agents.

Keywords: calorimetry, docking, DNA/RNA-alkaloid interaction, harmalol, spectroscopy

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Authors: Nidhi Chadha, A. K. Tiwari, Marilyn D. Milton, Anil K. Mishra

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Translocator protein (18 kDa) TSPO is highly expressed during microglia activation in neuroinflammation. Although a number of PET ligands have been developed for the visualization of activated microglia, one of the advantageous approaches is to develop potential optical imaging (OI) probe. Our study involves computational screening, synthesis and evaluation of TSPO ligand through various imaging modalities namely PET/SPECT/Optical. The initial computational screening involves pharmacophore modeling from the library designing having oxo-benzooxazol-3-yl-N-phenyl-acetamide groups and synthesis for visualization of efficacy of these compounds as multimodal imaging probes. Structure modeling of monomer, Ala147Thr mutated, parallel and anti-parallel TSPO dimers was performed and docking analysis was performed for distinct binding sites. Computational analysis showed pattern of variable binding profile of known diagnostic ligands and NBMP via interactions with conserved residues along with TSPO’s natural polymorphism of Ala147→Thr, which showed alteration in the binding affinity due to considerable changes in tertiary structure. Preliminary in vitro binding studies shows binding affinity in the range of 1-5 nm and selectivity was also certified by blocking studies. In summary, this skeleton was found to be potential probe for TSPO imaging due to ease in synthesis, appropriate lipophilicity and reach to specific region of brain.

Keywords: TSPO, molecular modeling, imaging, docking

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Authors: Sirilak Kongkaew, Pathumwadee Yodmanee, Nopporn Kaiyawet, Arthitaya Meeprasert, Thanyada Rungrotmongkol, Toshikatsu Kaburaki, Hiroshi Noguchi, Fujio Takeuch, Nawee Kungwan, Supot Hannongbua

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Behçet’s disease (BD) is a genetic autoimmune expressed by multisystemic inflammatory disorder mostly occurred at the skin, joints, gastrointestinal tract, and genitalia, including ocular, oral, genital, and central nervous systems. Most BD patients in Japan and Korea were strongly indicated by the genetic factor namely HLA-B*51 (especially, HLA-B*51:01) marker in HMC class I, while HLA-A*26:01 allele has been detected from the BD patients in Greek, Japan, and Taiwan. To understand the selective binding of the MICA-TM peptide towards the HLAs associated with BD, the molecular dynamics simulations were applied on the four HLA alleles (B*51:01, B*35:01, A*26:01, and A*11:01) in complex with such peptide. As a result, the key residues in the binding groove of HLA protein which play an important role in the MICA-TM peptide binding and stabilization were revealed. The Van der Waals force was found to be the main protein-protein interaction. Based on the binding free energy prediction by MM/PBSA method, the MICA-TM peptide interacted stronger to the HLA alleles associated to BD in the identical class by 7-12 kcal/mol. The obtained results from the present study could help to differentiate the HLA alleles and explain a source of Behçet’s disease.

Keywords: Behçet’s disease, MD simulations, HMC class I, autoimmune

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Authors: Karolis Leonavičius, Dalius Kučiauskas, Dangiras Lukošius, Arnoldas Jasiūnas, Kostas Zdanys, Rokas Stanislovas, Emilis Gegevičius, Žana Kapustina, Juozas Nainys

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Screening throughput is a common bottleneck in many research areas, including functional genomics, drug discovery, and directed evolution. High-throughput screening techniques can be classified into two main categories: (i) affinity-based screening and (ii) functional screening. The first one relies on binding assays that provide information about the affinity of a test molecule for a target binding site. Binding assays are relatively easy to establish; however, they reveal no functional activity. In contrast, functional assays show an effect triggered by the interaction of a ligand at a target binding site. Functional assays might be based on a broad range of readouts, such as cell proliferation, reporter gene expression, downstream signaling, and other effects that are a consequence of ligand binding. Screening of large cell or gene libraries based on direct activity rather than binding affinity is now a preferred strategy in many areas of research as functional assays more closely resemble the context where entities of interest are anticipated to act. Droplet sorting is the basis of high-throughput functional biological screening, yet its applicability is limited due to the technical complexity of integrating high-performance droplet analysis and manipulation systems. As a solution, the Droplet Genomics Styx platform enables custom droplet sorting workflows, which are necessary for the development of early-stage or complex biological therapeutics or industrially important biocatalysts. The poster will focus on the technical design considerations of Styx in the context of its application spectra.

Keywords: functional screening, droplet microfluidics, droplet sorting, dielectrophoresis

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Authors: A.D. Susanti, W. B. Sediawan, S.K. Wirawan, Budhijanto, Ritmaleni

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Oryzanol content in rice bran oil (RBO) naturally has high antioxidant activity. Its reviewed has several health properties and high interested in pharmacy, cosmetics, and nutrition’s. Because of the low concentration of oryzanol in crude RBO (0.9-2.9%) then its need to be further processed for practical usage, such as via adsorption process. In this study, investigation and adjustment of adsorption equilibrium models were conducted through the kinetic data approachments. Mathematical modeling on kinetics of batch adsorption of oryzanol separation from RBO has been set-up and then applied for equilibrium results. The size of adsorbent particles used in this case are usually relatively small then the concentration in the adsorbent is assumed to be not different. Hence, the adsorption rate is controlled by the rate of oryzanol mass transfer from the bulk fluid of RBO to the surface of silica gel. In this approachments, the rate of mass transfer is assumed to be proportional to the concentration deviation from the equilibrium state. The equilibrium models applied were Langmuir, coefficient distribution, and Freundlich with the values of the parameters obtained from equilibrium results. It turned out that the models set-up can quantitatively describe the experimental kinetics data and the adjustment of the values of equilibrium isotherm parameters significantly improves the accuracy of the model. And then the value of mass transfer coefficient per unit adsorbent mass (kca) is obtained by curve fitting.

Keywords: adsorption equilibrium, adsorption kinetics, oryzanol, rice bran oil

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Authors: Matineh Sadat Hosseini Gheidari, Vahid Reza Yazdanpanah

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In this paper, we used the empirical tight-binding method (ETBM) with sp3s* approximation and considering the first nearest neighbor with spin-orbit interactions in order to model superlattice structure (SLS) of (AlₓGa₁₋ₓAs)ₘ/(GaAs)ₙ grown on GaAs (100) substrate at 300K. In the next step, we investigated the behavior of the energy gap and wavelength of this superlattice in terms of different thicknesses of core materials and Al mole fractions. As a result of this survey, we found out that as the Al composition increases, the energy gap of this superlattice has an upward trend and ranges from 1.42-1.63 eV. Also, according to the wavelength range that we gained from this superlattice in different Al mole fractions and various thicknesses, we can find a suitable semiconductor for a special light-emitting diode (LED) application.

Keywords: energy gap, empirical tight-binding method, light-emitting diode, superlattice, wavelength

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Authors: Kah Yan How, Peh Fern Ong, Keang Peng Song

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Porphyromonas gingivalis is a black-pigmented, anaerobic Gram-negative bacterium that is important in the progression of chronic and severe periodontitis. This organism has an essential requirement for iron, which is usually obtained from hemin, using specific membrane receptors, proteases, and lipoproteins. In this study, we report the characterization of a novel 24 kDa hemin-binding protein, HmuX, in P. gingivalis W50. The hmuX gene is 651 bp long which encodes for a 217 amino acid protein. HmuX was found to be identical at the C-terminus to the previously reported HmuY protein, differing by an additional 74 amino acids at the N-terminus. Recombinant HmuX demonstrated hemin-binding ability by LDS- PAGE and TMBZ staining. Sequence analysis of HmuX revealed a putative lipoprotein attachment site, suggesting its possible role as a lipoprotein. HmuX was also localized to the outer cell surface by transmission electron microscopy. Northern analysis showed hmuX to be transcribed as a single gene and that hmuX mRNA was tightly regulated by the availability of extra-cellular hemin. P. gingivalis isogenic mutant deficient in hmuX gene exhibited significant growth retardation under hemin-limited conditions. Taken together, these results suggest that HmuX is a hemin-binding lipoprotein, important in hemin utilization for the growth of P. gingivalis.

Keywords: Porphyromonas gingivalis, periodontal diseases, HmuX, protein characterization

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Authors: Sinethemba Yakobi, Lindiwe Zuma, Ofentse Pooe

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Gonococcal infections present a notable public health issue, and the major approach for treatment involves using β-lactam antibiotics that specifically target penicillin-binding protein 2 (PBP2) in Neisseria gonorrhoeae. This study examines the influence of flavonoids, namely rutin, on the structural changes of PBP2 in both penicillin-resistant (FA6140) and penicillin-susceptible (FA19) strains. The research clarifies the structural effects of particular mutations, such as inserting an aspartate residue at position 345 (Asp-345a) in the PBP2 protein. The strain FA6140, which is resistant to penicillin, shows specific changes that lead to a decrease in penicillin binding. These mutations, namely P551S and F504L, significantly impact the pace at which acylation occurs and the stability of the strain under high temperatures. Molecular docking analyses investigate the antibacterial activities of rutin and other phytocompounds, emphasizing its exceptional binding affinity and potential as an inhibitor of PBP2. Quercetin and protocatechuic acid have encouraging antibacterial effectiveness, with quercetin displaying characteristics similar to those of drugs. Molecular dynamics simulations offer a detailed comprehension of the interactions between flavonoids and PBP2, highlighting rutin's exceptional antioxidant effects and strong affinity for the substrate binding site. The study's wider ramifications pertain to the pressing requirement for antiviral treatments in the context of the ongoing COVID-19 epidemic. Flavonoids have a strong affinity for binding to PBP2, indicating their potential as inhibitors to impair cell wall formation in N. gonorrhoeae. Ultimately, this study provides extensive knowledge on the interactions between proteins and ligands, the dynamics of the structure, and the ability of flavonoids to combat penicillin-resistant N. gonorrhoeae bacteria. The verified simulation outcomes establish a basis for creating potent inhibitors and medicinal therapies to combat infectious illnesses.

Keywords: phytochemicals, penicillin-binding protein 2, gonococcal infection, ligand-protein interaction, binding energy, neisseria gonorrhoeae FA19, neisseria gonorrhoeae FA6140, flavonoids

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Authors: Karen E. Supan

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Thermal degradation kinetics of switchgrass (Panicum virgatum) from the field, as well as in a pellet form, are presented. Thermogravimetric analysis tests were performed at heating rates of 10-40 K min⁻¹ in an inert atmosphere. The activation energy and the pre-exponential factor were calculated using the Ozawa/Flynn/Wall method as suggested by the ASTM Standard Test Method for Decomposition Kinetics by Thermogravimetry. Four stages were seen in the degradation: dehydration, active pyrolysis of hemicellulose, active pyrolysis of cellulose, and passive pyrolysis. The derivative mass loss peak for active pyrolysis of cellulose in the field-dried sample was much higher than the pelletized. The range of activation energy in the 0.15 – 0.70 conversion interval was 191 – 242 kJ mol⁻¹ for the field-dried and 130-192 kJ mol⁻¹ for the pellets. The highest activation energies were achieved at 0.50 conversion and were 242 kJ mol⁻¹ and 192 kJ mol⁻¹ for the field-dried and pellets, respectively. The thermal degradation and activation energies were comparable to switchgrass and other biomass reported in the literature.

Keywords: biomass, switchgrass, thermal degradation, thermogravimetric analysis

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Authors: C. C. Lin, S. C. Kan, C. W. Yeh, C. I Chen, C. J. Shieh, Y. C. Liu

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In this study, lipid-deprived residuals of microalgae were hydrolyzed for the production of reducing sugars by using the recombinant Bacillus cellulosome, carrying eight genes from the Clostridium thermocellum ATCC27405. The obtained cellulosome was found to exist mostly in the broth supernatant with a cellulosome activity of 2.4 U/mL. Furthermore, the Michaelis-Menten constant (Km) and Vmax of cellulosome were found to be 14.832 g/L and 3.522 U/mL. The activation energy of the cellulosome to hydrolyze microalgae LDRs was calculated as 32.804 kJ/mol.

Keywords: lipid-deprived residuals of microalgae, cellulosome, cellulose, reducing sugars, kinetics

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Authors: Olushola S. Ayanda, Olalekan S. Fatoki, Folahan A. Adekola, Bhekumusa J. Ximba, Cecilia O. Akintayo

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In the present study, the kinetics, equilibrium and thermodynamics of the adsorption of triphenyltin (TPT) from TPT-contaminated water onto nanoSiO2/fly ash/activated carbon composite was investigated in batch adsorption system. Equilibrium adsorption data were analyzed using Langmuir, Freundlich, Temkin and Dubinin–Radushkevich (D-R) isotherm models. Pseudo first- and second-order, Elovich and fractional power models were applied to test the kinetic data and in order to understand the mechanism of adsorption, thermodynamic parameters such as ΔG°, ΔSo and ΔH° were also calculated. The results showed a very good compliance with pseudo second-order equation while the Freundlich and D-R models fit the experiment data. Approximately 99.999 % TPT was removed from the initial concentration of 100 mg/L TPT at 80oC, contact time of 60 min, pH 8 and a stirring speed of 200 rpm. Thus, nanoSiO2/fly ash/activated carbon composite could be used as effective adsorbent for the removal of TPT from contaminated water and wastewater.

Keywords: isotherm, kinetics, nanoSiO₂/fly ash/activated carbon composite, tributyltin

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Authors: Henriette Hammill

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Background: Safe landing in netball is fundamental. Research on the biomechanics of multidirectional landings is lacking, especially among netball players. Furthermore, few studies reporting the associations between lower extremity injuries and landing kinematics and kinetics in university-level netball players have been undertaken. Objectives: The aim is to determine the relationships between lower extremity injuries and landing kinematics and kinetics in university-level netball players that have been undertaken during a single season. Methods: This cross-sectional repeated measure study consisted of ten university-level female netball players. The injury prevalence data was collected during the 2022 netball season. The kinematic and kinetic data were collected during multidirectional single-leg landing trials and was collected. Results: Generally, the ankle strength of netball players was below average. There was evidence of negative correlations between the ankle range of motion (ROM), and muscle activity amplitudes. A lack of evidence precluded the conclusion that lower extremity dominance was a predisposing factor for injury and that any specific body part was most likely to be injured among netball players. Conclusion: Landing forces and muscle activity are direction-dependent, especially for the dominant extremity. Lower extremity strength and neuromuscular control (NMC) across multiple jump-landing directions should be an area of focus for female netball players.

Keywords: netball players, landing kinetics, landing kinematics, lower extremity

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Authors: German Hernandez-Alonso, Antonio Lazcano, Arturo Becerra

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Until today, viruses remain controversial and poorly understood; about their origin, this problem represents an enigma and one of the great challenges for the contemporary biology. Three main theories have tried to explain the origin of viruses: regressive evolution, escaped host gene, and pre-cellular origin. Under the perspective of the escaped host gene theory, it can be assumed a cellular origin of viral components, like protein RNA-binding domains. These universal distributed RNA-binding domains are related to the RNA metabolism processes, including transcription, processing, and modification of transcripts, translation, RNA degradation and its regulation. In the case of viruses, these domains are present in important viral proteins like helicases, nucleases, polymerases, capsid proteins or regulation factors. Therefore, they are implicated in the replicative cycle and parasitic processes of viruses. That is why it is possible to think that those domains present low levels of divergence due to selective pressures. For these reasons, the main goal for this project is to create a catalogue of the RNA-binding domains found in all the available viral proteomes, using bioinformatics tools in order to analyze its evolutionary process, and thus shed light on the general virus evolution. ProDom database was used to obtain larger than six thousand RNA-binding domain families that belong to the three cellular domains of life and some viral groups. From the sequences of these families, protein profiles were created using HMMER 3.1 tools in order to find distant homologous within greater than four thousand viral proteomes available in GenBank. Once accomplished the analysis, almost three thousand hits were obtained in the viral proteomes. The homologous sequences were found in proteomes of the principal Baltimore viral groups, showing interesting distribution patterns that can contribute to understand the evolution of viruses and their host-virus interactions. Presence of cellular RNA-binding domains within virus proteomes seem to be explained by closed interactions between viruses and their hosts. Recruitment of these domains is advantageous for the viral fitness, allowing viruses to be adapted to the host cellular environment.

Keywords: bioinformatics tools, distant homology, RNA-binding domains, viral evolution

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Authors: Nicole C. Valdez, Vincent L. Borromeo, Conrad C. Chong, Ahmad F. Mazahery

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Breast cancer is the most prevalent cancer worldwide, where the majority of cases are estrogen-receptor positive and involve 2 receptor proteins. The binding of estrogen to estrogen receptor alpha (ERα) promotes breast cancer growth, while it's binding to estrogen-receptor beta (ERβ) inhibits tumor growth. While natural products have been a promising source of chemotherapeutic agents, the challenge remains in finding a bioactive compound that specifically targets cancer cells, minimizing side effects on normal cells. Flavonoids are natural products that act as phytoestrogens and induce the same response as estrogen. They are able to compete with estrogen for binding to ERα; however, it has a higher binding affinity for ERβ. Their abundance in nature and low toxicity make them a potential candidate for breast cancer treatment. This study aimed to determine which particular flavonoids can specifically recognize ERβ and potentially be used for breast cancer treatment through molecular docking. A total of 206 flavonoids comprised of 97 isoflavones and 109 flavanones were collected from ZINC15, while the 3D structures of ERβ and ERα were obtained from Protein Data Bank. These flavonoid subclasses were chosen as they bind more strongly to ERs due to their chemical structure. The structures of the flavonoid ligands were converted using Open Babel, while the estrogen receptor protein structures were prepared using Autodock MGL Tools. The optimal binding site was found using BIOVIA Discovery Studio Visualizer before docking all flavonoids on both ERβ and ERα through Autodock Vina. Genistein is a flavonoid that exhibits anticancer effects by binding to ERβ, so its binding affinity was used as a baseline. Eriodictyol and 4”,6”-Di-O-Galloylprunin both exceeded genistein’s binding affinity for ERβ and was lower than its binding affinity for ERα. Of the two, eriodictyol was pursued due to its antitumor properties on a lung cancer cell line and on glioma cells. It is able to arrest the cell cycle at the G2/M phase by inhibiting the mTOR/PI3k/Akt cascade and is able to induce apoptosis via the PI3K/Akt/NF-kB pathway. Protein pathway and gene analysis were also conducted using ChEMBL and PANTHER and it was shown that eriodictyol might induce anticancer effects through the ROS1, CA7, KMO, and KDM1A genes which are involved in cell proliferation in breast cancer, non-small cell lung cancer, and other diseases. The high binding affinity of eriodictyol to ERβ, as well as its potential affected genes and antitumor effects, therefore, make it a candidate for the development of new breast cancer treatment. Verification through in vitro experiments such as checking the upregulation and downregulation of genes through qPCR and checking cell cycle arrest using a flow cytometry assay is recommended.

Keywords: breast cancer, estrogen receptor, flavonoid, molecular docking

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Authors: Swati Tomar, Sunil Kumar Gupta

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Anammox is a promising and cost effective alternative to conventional treatment systems that facilitates direct oxidation of ammonium nitrogen under anaerobic conditions with nitrite as an electron acceptor without addition of any external carbon sources. The present study investigates the process kinetics of laboratory scale anammox hybrid reactor (AHR) which combines the dual advantages of attached and suspended growth. The performance & behaviour of AHR was studied under varying hydraulic retention time (HRTs) and nitrogen loading rate (NLRs). The experimental unit consisted of 4 numbers of 5L capacity anammox hybrid reactor inoculated with mixed seed culture containing anoxic and activated sludge. Pseudo steady state (PSS) ammonium and nitrite removal efficiencies of 90.6% and 95.6%, respectively, were achieved during acclimation phase. After establishment of PSS, the performance of AHR was monitored at seven different HRTs of 3.0, 2.5, 2.0, 1.5, 1.0, 0.5 and 0.25 d with increasing NLR from 0.4 to 4.8 kg N/m3d. The results showed that with increase in NLR and decrease in HRT (3.0 to 0.25 d), AHR registered appreciable decline in nitrogen removal efficiency from 92.9% to 67.4 %, respectively. The HRT of 2.0 d was considered optimal to achieve substantial nitrogen removal of 89%, because on further decrease in HRT below 1.5 days, remarkable decline in the values of nitrogen removal efficiency were observed. Analysis of data indicated that attached growth system contributes an additional 15.4 % ammonium removal and reduced the sludge washout rate (additional 29% reduction). This enhanced performance may be attributed to 25% increase in sludge retention time due to the attached growth media. Three kinetic models, namely, first order, Monod and Modified Stover-Kincannon model were applied to assess the substrate removal kinetics of nitrogen removal in AHR. Validation of the models were carried out by comparing experimental set of data with the predicted values obtained from the respective models. For substrate removal kinetics, model validation revealed that Modified Stover-Kincannon is most precise (R2=0.943) and can be suitably applied to predict the kinetics of nitrogen removal in AHR. Lawrence and McCarty model described the kinetics of bacterial growth. The predicted value of yield coefficient and decay constant were in line with the experimentally observed values.

Keywords: anammox, kinetics, modelling, nitrogen removal, sludge wash out rate, AHR

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Authors: G. Kabir, A. M. Mohammed, M. A. Bawa

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The paper presents corrosion behaviors of Naval Brass, aluminum alloy and carbon steel in simulated seawater under stagnant conditions. The behaviors were characterized on the variation of chloride ions concentration in the range of 3.0wt% and 3.5wt% and exposure time. The weight loss coupon-method immersion technique was employed. The weight loss for the various alloys was measured. Based on the obtained results, the corrosion rate was determined. It was found that the corrosion rates of the various alloys are related to the chloride ions concentrations, exposure time and kinetics of passive film formation of the various alloys. Carbon steel, suffers corrosion many folds more than Naval Brass. This indicated that the alloy exhibited relatively strong resistance to corrosion in the exposure environment of the seawater. Whereas, the aluminum alloy exhibited an excellent and beneficial resistance to corrosion more than the Naval Brass studied. Despite the prohibitive cost, Naval Brass and aluminum alloy, indicated to have beneficial corrosion behavior that can offer wide range of application in seashore operations. The corrosion kinetics parameters indicated that the corrosion reaction is limited by diffusion mass transfer of the corrosion reaction elements and not by reaction controlled.

Keywords: alloys, chloride ions concentration, corrosion kinetics, corrosion rate, diffusion mass transfer, exposure time, seawater, weight loss

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Authors: Han-Bin Kim, Sooim Shin, Moonsung Choi

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There is a growing interest in introducing a desired functional group on enzymes in the field of protein engineering. In here, various redox centers were newly created using histidine tag, which is widely used for protein purification, plus cobalt in one of cupredoxins, amicyanin. The coordination of Cobalt-His tag and reactivity of the Co²⁺ loaded His-tag also were characterized. 3xHis-tag, 6xHis-tag, and 9xHis-tag were introduced on amicyanin by site-directed mutagenesis, and then Co²⁺ was loaded on each His-tagged amicyanin. The spectral changes at 330 nm corresponding to cobalt binding on His-tag site indicated the binding ratio of 3xHis-tag, 6xHis-tag, and 9xHis-tag to cobalt as 1:1, 1:2, 1:3 respectively. Based on kinetic studies of binding cobalt to 3xHis-tag, 6xHis-tag, and 9xHis-tagged amicyanin, the nature of the sites was elucidated. In addition, internal electron transfer properties between Cu¹⁺ site and engineered site of amicyanin were determined. These results provide insight into improvement of metal coordination and alternation of the redox properties of metal as a new catalytic site on proteins.

Keywords: amicyanin, cobalt, histidine, protein engineering

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Authors: Sibashish Baksi, Ujjaini Sarkar, Sudeshna Saha

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In the present study, hydrolysis of Pinus roxburghi wood powder was carried out with Viscozyme, and kinetics of the hydrolysis has been investigated. Finely ground sawdust is submerged into 2% aqueous peroxide solution (pH=11.5) and pretreated through autoclaving, probe sonication, and alkaline peroxide pretreatment. Afterward, the pretreated material is subjected to hydrolysis. A chain of experiments was executed with delignified biomass (50 g/l) and varying enzyme concentrations (24.2–60.5 g/l). In the present study, 14.32 g/l of glucose, along with 7.35 g/l of xylose, have been recovered with a viscozyme concentration of 48.8 g/l and the same condition was treated as optimum condition. Additionally, thermal deactivation of viscozyme has been investigated and found to be gradually decreasing with escalated enzyme loading from 48.4 g/l (dissociation constant= 0.05 h⁻¹) to 60.5 g/l (dissociation constant= 0.02 h⁻¹). The hydrolysis reaction is a pseudo first-order reaction, and therefore, the rate of the hydrolysis can be expressed as a fractal-like kinetic equation that communicates between the product concentration and hydrolytic time t. It is seen that the value of rate constant (K) increases from 0.008 to 0.017 with augmented enzyme concentration from 24.2 g/l to 60.5 g/l. Greater value of K is associated with stronger enzyme binding capacity of the substrate mass. However, escalated concentration of supplied enzyme ensures improved interaction with more substrate molecules resulting in an enhanced de-polymerization of the polymeric sugar chains per unit time which eventually modifies the physiochemical structure of biomass. All fractal dimensions are in between 0 and 1. Lower the value of fractal dimension, more easily the biomass get hydrolyzed. It can be seen that with increased enzyme concentration from 24.2 g/l to 48.4 g/l, the values of fractal dimension go down from 0.1 to 0.044. This indicates that the presence of more enzyme molecules can more easily hydrolyze the substrate. However, an increased value has been observed with a further increment of enzyme concentration to 60.5g/l because of diffusional limitation. It is evident that the hydrolysis reaction system is a heterogeneous organization, and the product formation rate depends strongly on the enzyme diffusion resistances caused by the rate-limiting structures of the substrate-enzyme complex. Value of the rate constant increases from 1.061 to 2.610 with escalated enzyme concentration from 24.2 to 48.4 g/l. As the rate constant is proportional to Fick’s diffusion coefficient, it can be assumed that with a higher concentration of enzyme, a larger amount of enzyme mass dM diffuses into the substrate through the surface dF per unit time dt. Therefore, a higher rate constant value is associated with a faster diffusion of enzyme into the substrate. Regression analysis of time curves with various enzyme concentrations shows that diffusion resistant constant increases from 0.3 to 0.51 for the first two enzyme concentrations and again decreases with enzyme concentration of 60.5 g/l. During diffusion in a differential scale, the enzyme also experiences a greater resistance during diffusion of larger dM through dF in dt.

Keywords: viscozyme, glucose, fractal kinetics, thermal deactivation

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Authors: Kai-Cheng Hsu, Tzu-Ying Sung, Jinn-Moon Yang

Abstract:

Colorectal cancer (CRC) is one of the main causes of cancer death in the world. Although several drugs have been developed to treat colorectal cancer, such as Regorafenib and 5-FU, their efficacy is often limited by the development of drug resistance. Therefore, development of new drugs with new scaffolds is necessary to treat CRC. Here, we used site-moiety maps to identify inhibitors against PIM1, LIMK1, SRC, and mTOR, which are often overexpressed in CRC. A site-moiety map represents physicochemical properties and moiety preferences of a binding site through anchors. An anchor contains three elements: (1) conserved interacting residues of a binding pocket; (2) moiety preference of the binding pocket; and (3) the type (e.g., hydrogen-bonding or van der Waals interactions) of interaction between the moieties and the binding pocket. Then, we performed a structure-based virtual screening of ~260,000 compounds and selected compound candidates with high site-moiety map scores for bioassays. Among these candidates, compound 1 and compound 2 inhibited the growth of CRC cells with IC50 values of <10 μM. The experimental result of enzyme-based assays indicated that compound 1 is a dual inhibitor against PIM1 (IC50 6 μM) and LIMK1(IC50 11 μM). Compound 2 was predicted as a SRC inhibitor and will be further validated. The compounds inhibited different protein targets compared to the current drugs. We believe that the compounds provide a starting point to design new drugs for CRC treatment.

Keywords: colorectal cancer, drug discovery, site-moiety map, virtual screening, PIM1, LIMK1

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Authors: Xing Lu, Yi-ming Wu, Yan-hong Zhu, Zhen-feng Chen, Hong Liang, Yan Peng

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[Eu(BMQ)2(NO3)3(CH3OH)(H2O)] (1),and [Er(BMQ)2(NO3)3(CH3OH)(H2O)] (2),were synthesized. Compounds 1 and 2 exhibit a certain extent cytotoxicity against Hep G2, Hela 229, MGC80-3 and BEL-7404 cell lines invitro, with IC50 values in the14.51±1.41μM to 52.49±4.01μM range. Compound 1 exhibited significantly enhanced cytotoxicity against MGC80-3 cell line, comparing with free 3-(1H-benzimidazol-2-yl)-6-methyl-2(1H)- quinolinone. The binding abilities of 1 to DNA were stronger than that of 2. Intercalation is the most probable binding mode for both the complexes.

Keywords: quinolinone, Eu(II) complex, Er(III) complex, cytotoxicity.

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Authors: Harish Rajak, Swati Singh

Abstract:

A series of novel pyrimidine based semicarbazone were designed and synthesized on the basis of semicarbazone based pharmacophoric model to satisfy the structural prerequisite crucial for antiepileptic activity. The semicarbazones based pharmacophoric model consists of following four essential binding sites: (i) An aryl hydrophobic binding site with halo substituent; (ii) A hydrogen bonding domain; (iii) An electron donor group and (iv) Another hydrophobic-hydrophilic site controlling the pharmacokinetic features of the anticonvulsant. The aryl semicarbazones has been recognized as a structurally novel class of compounds with remarkable anticonvulsant activity. In the present study, all the test semicarbazones were subjected to molecular docking using Glide v5.8. Some of the compounds were found to interact with ARG192, GLU270 and THR353 residues of 1OHV protein, present in GABA-AT receptor. The chemical structures of the synthesized molecules were characterized by elemental and spectral (IR, 1H NMR, 13C NMR and MS) analysis. The anticonvulsant activities of the compounds were investigated using maximal electroshock seizure (MES) and subcutaneous pentylenetrtrazole (scPTZ) models. The neurotoxicity was evaluated in mice by the rotorod test. The attempts were also made to establish structure-activity relationships among synthesized compounds. The results of the present study confirmed that the pharmacophore model with four binding sites is essential for antiepileptic activity.

Keywords: pyrimidine, semicarbazones, anticonvulsant activity, neurotoxicity

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Authors: Agnieszka Krzemińska, Katarzyna Świderek, Vicente Molinier, Piotr Paneth

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In order to understand in details the interactions between ligands and the enzyme isotope effects were studied between clinically used drugs that bind in the active site of Human Immunodeficiency Virus Reverse Transcriptase, HIV-1 RT, as well as triazole-based inhibitor that binds in the allosteric pocket of this enzyme. The magnitudes and origins of the resulting binding isotope effects were analyzed. Subsequently, binding isotope effect of the same triazole-based inhibitor bound in the active site were analyzed and compared. Together, these results show differences in binding origins in two sites of the enzyme and allow to analyze binding mode and place of newly synthesized inhibitors. Typical protocol is described below on the example of triazole ligand in the allosteric pocket. Triazole was docked into allosteric cavity of HIV-1 RT with Glide using extra-precision mode as implemented in Schroedinger software. The structure of HIV-1 RT was obtained from Protein Data Bank as structure of PDB ID 2RKI. The pKa for titratable amino acids was calculated using PROPKA software, and in order to neutralize the system 15 Cl- were added using tLEaP package implemented in AMBERTools ver.1.5. Also N-terminals and C-terminals were build using tLEaP. The system was placed in 144x160x144Å3 orthorhombic box of water molecules using NAMD program. Missing parameters for triazole were obtained at the AM1 level using Antechamber software implemented in AMBERTools. The energy minimizations were carried out by means of a conjugate gradient algorithm using NAMD. Then system was heated from 0 to 300 K with temperature increment 0.001 K. Subsequently 2 ns Langevin−Verlet (NVT) MM MD simulation with AMBER force field implemented in NAMD was carried out. Periodic Boundary Conditions and cut-offs for the nonbonding interactions, range radius from 14.5 to 16 Å, are used. After 2 ns relaxation 200 ps of QM/MM MD at 300 K were simulated. The triazole was treated quantum mechanically at the AM1 level, protein was described using AMBER and water molecules were described using TIP3P, as implemented in fDynamo library. Molecules 20 Å apart from the triazole were kept frozen, with cut-offs established on range radius from 14.5 to 16 Å. In order to describe interactions between triazole and RT free energy of binding using Free Energy Perturbation method was done. The change in frequencies from ligand in solution to ligand bounded in enzyme was used to calculate binding isotope effects.

Keywords: binding isotope effects, molecular dynamics, HIV, reverse transcriptase

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Authors: Bright Chukwunwike Uzuegbunam, Wojciech Paslawski, Hans Agren, Christer Halldin, Wolfgang Weber, Markus Luster, Thomas Arzberger, Behrooz Hooshyar Yousefi

Abstract:

There is a need to develop a PET tracer that will enable to diagnosis and track the progression of Alpha-synucleinopathies (Parkinson’s disease [PD], dementia with Lewy bodies [DLB], multiple system atrophy [MSA]) in living subjects over time. Alpha-synuclein aggregates (a-syn), which are present in all the stages of disease progression, for instance, in PD, are a suitable target for in vivo PET imaging. For this reason, we have developed some promising a-syn tracers based on a disarylbisthiazole (DABTA) scaffold. The precursors are synthesized via a modified Hantzsch thiazole synthesis. The precursors were then radiolabeled via one- or two-step radiofluorination methods. The ligands were initially screened using a combination of molecular dynamics and quantum/molecular mechanics approaches in order to calculate the binding affinity to a-syn (in silico binding experiments). Experimental in vitro binding assays were also performed. The ligands were further screened in other experiments such as log D, in vitro plasma protein binding & plasma stability, biodistribution & brain metabolite analyses in healthy mice. Radiochemical yields were up to 30% - 72% in some cases. Molecular docking revealed possible binding sites in a-syn and also the free energy of binding to those sites (-28.9 - -66.9 kcal/mol), which correlated to the high binding affinity of the DABTAs to a-syn (Ki as low as 0.5 nM) and selectivity (> 100-fold) over Aβ and tau, which usually co-exist with a-synin some pathologies. The log D values range from 2.88 - 2.34, which correlated with free-protein fraction of 0.28% - 0.5%. Biodistribution experiments revealed that the tracers are taken up (5.6 %ID/g - 7.3 %ID/g) in the brain at 5 min (post-injection) p.i., and cleared out (values as low as 0.39 %ID/g were obtained at 120 min p.i. Analyses of the mice brain 20 min p.i. Revealed almost no radiometabolites in the brain in most cases. It can be concluded that in silico study presents a new venue for the rational development of radioligands with suitable features. The results obtained so far are promising and encourage us to further validate the DABTAs in autoradiography, immunohistochemistry, and in vivo imaging in non-human primates and humans.

Keywords: alpha-synuclein aggregates, alpha-synucleinopathies, PET imaging, tracer development

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Authors: E. Balkauskaitė, A. Bučinskas, R. Ivanauskas, M. Kriipsalu, G. Denafas

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Leaching of heavy metals (chromium, zinc, copper) from the fine fraction of the Torma landfill (Estonia) was investigated. The leaching kinetics studies have determined the dependence of some metal’s concentration on the leaching time. Metals were leached with Aqua Regia, distilled water and EDTA (Ethylenediaminetetraacetic acid); process was most intensive 2 hours after the start of the experiment, except for copper with EDTA (0.5 h) and lead with EDTA (4 h). During leaching, steady concentrations of Fe, Mn, Cd and Pb were fully stabilized after 8 h; however concentrations of Cu and Ni were not stabilized after 10 h.

Keywords: fine fraction, landfills, leached metals, leaching kinetics

Procedia PDF Downloads 118