Search results for: relative binding affinity

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.

Procedia PDF Downloads 582

Authors: Markus Bredel, Sindhu Nair, Hoa Q. Trummell, Rajani Rajbhandari, Christopher D. Willey, Lewis Z. Shi, Zhuo Zhang, William J. Placzek, James A. Bonner

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Purpose: EGFR-targeted monoclonal antibodies (mAbs) provide clinical benefit in some patients with H&N squamous cell carcinoma (HNSCC), but others progress with minimal response. Missense mutations in the EGFR ectodomain (ECD) can be acquired under mAb therapy by mimicking the effect of large deletions on receptor untethering and activation. Little is known about the contribution of EGFR ECD mutations to EGFR activation and anti-EGFR response in HNSCC. Methods: We selected patient-derived HNSCC cells (UM-SCC-1) for resistance to mAb Cetuximab (CTX) by repeated, stepwise exposure to mimic what may occur clinically and identified two concurrent EGFR ECD mutations (UM-SCC-1R). We examined the competence of the mutants to bind EGF ligand or CTX. We assessed the potential impact of the mutations through visual analysis of space-filling models of the native sidechains in the original structures vs. their respective side-chain mutations. We performed CRISPR in combination with site-directed mutagenesis to test for the effect of the mutants on ligand-independent EGFR activation and sorting. We determined the effects on receptor internalization, endocytosis, downstream signaling, and radiation sensitivity. Results: UM-SCC-1R cells carried two non-synonymous missense mutations (G33S and N56K) mapping to domain I in or near the EGF binding pocket of the EGFR ECD. Structural modeling predicted that these mutants restrict the adoption of a tethered, inactive EGFR conformation while not permitting association of EGFR with the EGF ligand or CTX. Binding studies confirmed that the mutant, untethered receptor displayed a reduced affinity for both EGF and CTX but demonstrated sustained activation and presence at the cell surface with diminished internalization and sorting for endosomal degradation. Single and double-mutant models demonstrated that the G33S mutant is dominant over the N56K mutant in its effect on EGFR activation and EGF binding. CTX-resistant UM-SCC-1R cells demonstrated cross-resistance to mAb Panitumuab but, paradoxically, remained sensitive to the reversible receptor tyrosine kinase inhibitor Erlotinib. Conclusions: HNSCC cells can select for EGFR ECD mutations under EGFR mAb exposure that converge to trap the receptor in an open, constitutively activated state. These mutants impede the receptor’s competence to bind mAbs and EGF ligand and alter its endosomal trafficking, possibly explaining certain cases of clinical mAb and radiation resistance.

Keywords: head and neck cancer, EGFR mutation, resistance, cetuximab

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Authors: Ria Ghosh, Soumendra Singh, Dipanjan Mukherjee, Susmita Mondal, Monojit Das, Uttam Pal, Aniruddha Adhikari, Aman Bhushan, Surajit Bose, Siddharth Sankar Bhattacharyya, Debasish Pal, Tanusri Saha-Dasgupta, Maitree Bhattacharyya, Debasis Bhattacharyya, Asim Kumar Mallick, Ranjan Das, Samir Kumar Pal

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Drug delivery to a target without adverse effects is one of the major criteria for clinical use. Herein, we have made an attempt to explore the delivery efficacy of SDS surfactant in a monomer and micellar stage during the delivery of the model drug, Toluidine Blue (TB) from the micellar cavity to DNA. Molecular recognition of pre-micellar SDS encapsulated TB with DNA occurs at a rate constant of k1 ~652 s 1. However, no significant release of encapsulated TB at micellar concentration was observed within the experimental time frame. This originated from the higher binding affinity of TB towards the nano-cavity of SDS at micellar concentration which does not allow the delivery of TB from the nano-cavity of SDS micelles to DNA. Thus, molecular recognition controls the extent of DNA recognition by TB which in turn modulates the rate of delivery of TB from SDS in a concentration-dependent manner.

Keywords: DNA, drug delivery, micelle, pre-micelle, SDS, toluidine blue

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Authors: Harish Rajak, Swati Singh

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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: Michal Štros, Eva Polanská, Šárka Pospíšilová

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HMGB1 is an architectural protein in chromatin, acting also as a signaling molecule outside the cell. Recent reports from several laboratories provided evidence that a number of both the intracellular and extracellular functions of HMGB1 may depend on redox-sensitive cysteine residues of the protein. MALDI-TOF analysis revealed that mild oxidization of HMGB1 resulted in a conformational change of the protein due to formation of an intramolecular disulphide bond by opposing Cys23 and Cys45 residues. We have demonstrated that redox state of HMGB1 could significantly modulate the ability of the protein to bind and bend DNA. We have also shown that reduced HMGB1 could easily displace histone H1 from DNA, while oxidized HMGB1 had limited capacity for H1 displacement. Using microscale thermophoresis (MST) we have further studied mechanism of HMGB1 interaction with histone H1 in free solution or when histone H1 was bound to DNA. Our MST analysis indicated that reduced HMGB1 exhibited in free solution > 1000 higher affinity of for H1 (KD ~ 4.5 nM) than oxidized HMGB1 (KD <10 M). Finally, we present a novel mechanism for the HMGB1-mediated modulation of histone H1 binding to DNA.

Keywords: HMGB1, histone H1, redox state, interaction, cross-linking, DNA bending, DNA end-joining, microscale thermophoresis

Procedia PDF Downloads 322

Authors: Moulay Driss Mellaoui, Khadija Zaki, Khalid Abbiche, Abdallah Imjjad, Rachid Boutiddar, Abdelouahid Sbai, Aaziz Jmiai, Souad El Issami, Al Mokhtar Lamsabhi, Hanane Zejli

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This study presents a comprehensive analysis of six isoxazolidine and isoxazoline derivatives, leveraging a multifaceted approach that combines Density Functional Theory (DFT), AdmetSAR analysis, and molecular docking simulations to explore their electronic, pharmacokinetic, and anticancer properties. Through DFT analysis, using the B3LYP-D3BJ functional and the 6-311++G(d,p) basis set, we optimized molecular geometries, analyzed vibrational frequencies, and mapped Molecular Electrostatic Potentials (MEP), identifying key sites for electrophilic attacks and hydrogen bonding. Frontier Molecular Orbital (FMO) analysis and Density of States (DOS) plots revealed varying stability levels among the compounds, with 1b, 2b, and 3b showing slightly higher stability. Chemical potential assessments indicated differences in binding affinities, suggesting stronger potential interactions for compounds 1b and 2b. AdmetSAR analysis predicted favorable human intestinal absorption (HIA) rates for all compounds, highlighting compound 3b superior oral effectiveness. Molecular docking and molecular dynamics simulations were conducted on isoxazolidine and 4-isoxazoline derivatives targeting the EGFR receptor (PDB: 1JU6). Molecular docking simulations confirmed the high affinity of these compounds towards the target protein 1JU6, particularly compound 3b, among the isoxazolidine derivatives, compound 3b exhibited the most favorable binding energy, with a g score of -8.50 kcal/mol. Molecular dynamics simulations over 100 nanoseconds demonstrated the stability and potential of compound 3b as a superior candidate for anticancer applications, further supported by structural analyses including RMSD, RMSF, Rg, and SASA values. This study underscores the promising role of compound 3b in anticancer treatments, providing a solid foundation for future drug development and optimization efforts.

Keywords: isoxazolines, DFT, molecular docking, molecular dynamic, ADMET, drugs.

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Authors: Sonu Gandhi, Neena Capalash, Prince Sharma, C. Raman Suri

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A sensitive chemiluminescence immunoassay (CIA) for heroin and its major metabolites is reported. The method is based on the competitive reaction of horseradish peroxidase (HRP)-labeled anti-MAM antibody and free drug in spiked urine samples. A hapten-protein conjugate was synthesized by using acidic derivative of monoacetyl morphine (MAM) coupled to carrier protein BSA and was used as an immunogen for the generation of anti-MAM (monoacetyl morphine) antibody. A high titer of antibody (1:64,0000) was obtained and the relative affinity constant (Kaff) of antibody was 3.1×107 l/mol. Under the optimal conditions, linear range and reactivity for heroin, mono acetyl morphine (MAM), morphine and codeine were 0.08, 0.09, 0.095 and 0.092 ng/mL respectively. The developed chemiluminescence inhibition assay could detect heroin and its metabolites in standard and urine samples up to 0.01 ng/ml.

Keywords: heroin, metabolites, chemiluminescence immunoassay, horse radish peroxidase

Procedia PDF Downloads 249

Authors: Usha Kiran, M. Z. Abdin

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Osmotin is an abundant cationic multifunctional protein discovered in cells of tobacco (Nicotiana tabacum L. var Wisconsin 38) adapted to an environment of low osmotic potential. It provides plants protection from pathogens, hence placed in the PRP family of proteins. The osmotin induced proline accumulation has been reported in plants including transgenic tomato and strawberry conferring tolerance against both biotic and abiotic stresses. The exact mechanism of induction of proline by osmotin is however, not known till date. These observations have led us to hypothesize that osmotin induced proline accumulation could be due to its involvement as transcription factor and/or cell signal pathway modulator in proline biosynthesis. The present investigation was therefore, undertaken to analyze the osmotin protein as transcription factor /cell signalling modulator using bioinformatics tools. The results of available online DNA binding motif search programs revealed that osmotin does not contain DNA-binding motifs. The alignment results of osmotin protein with the protein sequence from DATF showed the homology in the range of 0-20%, suggesting that it might not contain a DNA binding motif. Further to find unique DNA-binding domain, the superimposition of osmotin 3D structure on modeled Arabidopsis transcription factors using Chimera also suggested absence of the same. We, however, found evidence implicating osmotin in cell signaling. With these results, we concluded that osmotin is not a transcription factor but regulating proline biosynthesis and accumulation through cell signaling during abiotic stresses.

Keywords: osmotin, cell signaling modulator, bioinformatic tools, protein

Procedia PDF Downloads 255

Authors: Monika Kallubai, Shreya Dubey, Rajagopal Subramanyam

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Our study is all about the biological interactions of synthesized 5β-dihydrocortisol (Dhc) and 5β-dihydrocortisol acetate (DhcA) molecules with carrier protein Human Serum Albumin (HSA). The cytotoxic study was performed on breast cancer cell line (MCF-7) normal human embryonic kidney cell line (HEK293), the IC50 values for MCF-7 cells were 28 and 25 µM, respectively, whereas no toxicity in terms of cell viability was observed with HEK293 cell line. The further experiment proved that Dhc and DhcA induced 35.6% and 37.7% early apoptotic cells and 2.5%, 2.9% late apoptotic cells respectively. Morphological observation of cell death through TUNEL assay revealed that Dhc and DhcA induced apoptosis in MCF-7 cells. The complexes of HSA–Dhc and HSA–DhcA were observed as static quenching, and the binding constants (K) was 4.7±0.03×104 M-1 and 3.9±0.05×104 M-1, and their binding free energies were found to be -6.4 and -6.16 kcal/mol, respectively. The displacement studies confirmed that lidocaine 1.4±0.05×104 M-1 replaced Dhc, and phenylbutazone 1.5±0.05×104 M-1 replaced by DhcA, which explains domain I and domain II are the binding sites for Dhc and DhcA. Further, CD results revealed that the secondary structure of HSA was altered in the presence of Dhc and DhcA. Furthermore, the atomic force microscopy and transmission electron microscopy showed that the dimensions like height and molecular sizes of the HSA–Dhc and HSA–DhcA complex were larger compared to HSA alone. Detailed analysis through molecular dynamics simulations also supported the greater stability of HSA–Dhc and HSA–DhcA complexes, and root-mean-square-fluctuation interpreted the binding site of Dhc as domain IB and domain IIA for DhcA. This information is valuable for the further development of steroid derivatives with improved pharmacological significance as novel anti-cancer drugs.

Keywords: apoptosis, dihydrocortisol, fluorescence quenching, protein conformations

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Authors: Jayanthi Sivaraman

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Claudins are the important components of the tight junctions that play a key role in paracellular permeability. Among various members of Claudin family, Claudin 4 (CLDN4) is found to be overexpressed in ovarian, pancreatic carcinomas and other epithelial malignancies. Therefore, in this study, an attempt has been made to identify potent inhibitors for CLDN4 from the ZINC database using virtual screening, molecular docking and molecular dynamics simulations. A well refined molecular model of CLDN4 was built using Prime of Schrodinger v10.2(Template- PDB ID: 4P79). Approximately, 6 million compounds from ZINC database are subjected to high-throughput virtual screening (HTVS) against the active site of CLDN4. Molecular docking using GLIDE predicted ARG31, ASN142, ASP146 and ARG158 as critically important residues. Furthermore, three compounds from ZINC database (ZINC96331839, ZINC36533519 and ZINC75819394) showed highly promising ADME properties and binding affinity with stable conformation. The therapeutic efficiency of these lead compounds is evaluated and confirmed by in-vitro and in-vivo studies which leads to the development of novel anti-cancer drugs.

Keywords: ADME property, inhibitors, molecular docking, virtual screening

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Authors: Qian Li, Shouxiang Lu

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With the rapid increase in electric power use, wire and cable fire occur more and more frequent. The fire smoke has a corrosive effect on the solders, which seriously affects the function of electronic equipment. In this research, the effect of environment relative humidity on corrosion behavior of Sn-0.7Cu solder has been researched under 140 g·m⁻³ polyvinyl chloride (PVC) fire smoke atmosphere. The mass loss of Sn-0.7Cu solder increased with the relative humidity. Furthermore, the microstructures and corrosion mechanism were analyzed by using SEM, EDS, XRD, and XPS. The result shows that Sn₂₁Cl₁₆(OH)₁₄O₆ is the main corrosion products and the corrosion process is an electrochemical reaction. The present work could provide guidance to the risk assessment for electronic equipment rescue after a fire.

Keywords: corrosion, fire smoke, relative humidity, Sn-0.7Cu solder

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Authors: D. Bhowmik, Y. Tian, Q. Yin, F. Zhu

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Cyclic GMP-AMP synthase (cGAS), recognises cytoplasmic double-stranded DNA (dsDNA), indicative of bacterial and viral infections, as well as the leakage of self DNA by cellular dysfunction and stresses, to elicit the host's immune responses. Viruses also have developed numerous strategies to antagonize the cGAS-STING pathway. Kaposi's sarcoma-associated herpesvirus (KSHV) is a human DNA tumor virus that is the causative agent of Kaposi’s sarcoma and several other malignancies. To persist in the host, consequently causing diseases, KSHV must overcome the host innate immune responses, including the cGAS-STING DNA sensing pathway. We already found that ORF52 or KicGAS (KSHV inhibitor of cGAS), an abundant and basic gamma herpesvirus-conserved tegument protein, directly inhibits cGAS enzymatic activity. To better understand the mechanism, we have performed the biochemical and structural characterization of full-length KicGAS and various mutants in regarding binding to DNA. We observed that KicGAS is capable of self-association and identified the critical residues involved in the oligomerization process. We also characterized the DNA-binding of KicGAS and found that KicGAS cooperatively oligomerizes along the length of the double stranded DNA, the highly conserved basic residues at the c-terminal disordered region are crucial for DNA recognition. Deficiency in oligomerization also affects DNA binding. Thus DNA binding by KicGAS sequesters DNA and prevents it from being detected by cGAS, consequently inhibiting cGAS activation. KicGAS homologues also inhibit cGAS efficiently, suggesting inhibition of cGAS is evolutionarily conserved mechanism among gamma herpesvirus. These results highlight the important viral strategy to evade this innate immune sensor.

Keywords: Kaposi's sarcoma-associated herpesvirus, KSHV, cGAS, DNA binding, inhibition

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Authors: Vishal Raj, Noorhan Abbas

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Ambiguity in NLP (Natural language processing) refers to the ability of a word, phrase, sentence, or text to have multiple meanings. This results in various kinds of ambiguities such as lexical, syntactic, semantic, anaphoric and referential am-biguities. This study is focused mainly on solving the issue of Lexical ambiguity. Word Sense Disambiguation (WSD) is an NLP technique that aims to resolve lexical ambiguity by determining the correct meaning of a word within a given context. Most WSD solutions rely on words for training and testing, but we have used lemma and Part of Speech (POS) tokens of words for training and testing. Lemma adds generality and POS adds properties of word into token. We have designed a novel method to create an affinity matrix to calculate the affinity be-tween any pair of lemma_POS (a token where lemma and POS of word are joined by underscore) of given training set. Additionally, we have devised an al-gorithm to create the sense clusters of tokens using affinity matrix under hierar-chy of POS of lemma. Furthermore, three different mechanisms to predict the sense of target word using the affinity/similarity value are devised. Each contex-tual token contributes to the sense of target word with some value and whichever sense gets higher value becomes the sense of target word. So, contextual tokens play a key role in creating sense clusters and predicting the sense of target word, hence, the model is named Contextual SenSe Model (CSM). CSM exhibits a noteworthy simplicity and explication lucidity in contrast to contemporary deep learning models characterized by intricacy, time-intensive processes, and chal-lenging explication. CSM is trained on SemCor training data and evaluated on SemEval test dataset. The results indicate that despite the naivety of the method, it achieves promising results when compared to the Most Frequent Sense (MFS) model.

Keywords: word sense disambiguation (wsd), contextual sense model (csm), most frequent sense (mfs), part of speech (pos), natural language processing (nlp), oov (out of vocabulary), lemma_pos (a token where lemma and pos of word are joined by underscore), information retrieval (ir), machine translation (mt)

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Authors: Fouzia Perveen, Rumana Qureshi

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The presently studied twelve anticancer drugs are the cytotoxic agents which inhibit the replication of DNA and activity of enzymes involved in DNA replication namely topoisomerase-II, polymerase and helicase and have shown remarkable anticancer activity in clinical trials. In this study, we performed molecular docking studies of twelve antitumor drugs against DNA and DNA enzymes in the presence and absence of ascorbic acid (AA) and developed the quantitative structure-activity relationship (QSAR) model for anticancer activity screening. A number of electronic and steric descriptors were calculated using MOE software package. QSAR was established showing a correlation of binding strength with various physicochemical descriptors. Out of these twelve, eight cytotoxic drugs were tested on Non-Small Cell Lung Cancer cell lines (H-157 and H-1299) in the absence and presence of ascorbic acid and experimental IC50 values were calculated. From the docking studies, binding constants were calculated indicating the strength of drug-DNA and drug-enzyme complex formation and it was correlated to the IC50 values (both experimental and theoretical). These results can offer useful references for directing the molecular design of DNA enzyme inhibitor with improved anticancer activity.

Keywords: ascorbic acid, binding constant, cytotoxic agents, cell culture, DNA, DNA enzymes, molecular docking

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Authors: Hamzeh Alipour, Masoumeh Bagheri, Abbasali Raz, Javad Dadgar Pakdel, Kourosh Azizi, Aboozar Soltani, Mohammad Djaefar Moemenbellah-Fard

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Background: Maggot debridement therapy is an appropriate, effective, and controlled method using sterilized larvae of Luciliasericata (L.sericata) to treat wounds. Netrin-A is an enzyme in the Laminins family which secreted from salivary gland of L.sericata with a central role in neural regeneration and angiogenesis. This study aimed to production of new recombinant Netrin-A protein of Luciliasericata larvae by baculovirus expression vector system (BEVS) in SF9. Material and methods: In the first step, gene structure was subjected to the in silico studies, which were include determination of Antibacterial activity, Prion formation risk, homology modeling, Molecular docking analysis, and Optimization of recombinant protein. In the second step, the Netrin-A gene was cloned and amplified in pTG19 vector. After digestion with BamH1 and EcoR1 restriction enzymes, it was cloned in pFastBac HTA vector. It was then transformed into DH10Bac competent cells, and the recombinant Bacmid was subsequently transfected into insect Sf9 cells. The expressed recombinant Netrin-A was thus purified in the Ni-NTA agarose. This protein evaluation was done using SDS-PAGE and western blot, respectively. Finally, its concentration was calculated with the Bradford assay method. Results: The Bacmid vector structure with Netrin-A was successfully constructed and then expressed as Netrin-A protein in the Sf9 cell lane. The molecular weight of this protein was 52 kDa with 404 amino acids. In the in silico studies, fortunately, we predicted that recombinant LSNetrin-A have Antibacterial activity and without any prion formation risk.This molecule hasa high binding affinity to the Neogenin and a lower affinity to the DCC-specific receptors. Signal peptide located between amino acids 24 and 25. The concentration of Netrin-A recombinant protein was calculated to be 48.8 μg/ml. it was confirmed that the characterized gene in our previous study codes L. sericata Netrin-A enzyme. Conclusions: Successful generation of the recombinant Netrin-A, a secreted protein in L.sericata salivary glands, and because Luciliasericata larvae are used in larval therapy. Therefore, the findings of the present study could be useful to researchers in future studies on wound healing.

Keywords: blowfly, BEVS, gene, immature insect, recombinant protein, Sf9

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Authors: Sanja O. Podunavac-Kuzmanović, Strahinja Z. Kovačević, Lidija R. Jevrić, Stela Jokić

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The complexes of transition metals with various organic ligands have been extensively studied as models of some important pharmaceutical molecules. It was found that biological properties of different substituted organic molecules are improved when they are complexed by different metals. Therefore, it is of great importance for the development of coordination chemistry to explore the assembly of functional organic ligands with metal ion and to investigate the relationship between the structure and property. In the present work, we have bioassayed the antibacterial potency of benzimidazoles and their metal salts (Cu or Zn) against yeast Sarcina lutea. In order to validate our in vitro study, we performed in silico studies using molecular docking software. The investigated compounds and their metal complexes (Cu, Zn) showed good to moderate inhibitory activity against Sarcina lutea. In silico docking studies of the synthesized compounds suggested that complexed benzimidazoles have a greater binding affinity and improved antibacterial activity in comparison with non-complexed ligands. These results are part of the CMST COST Action No. 1105 "Functional metal complexes that bind to biomolecules".

Keywords: organometallic complexes, benzimidazoles, chemometric design, Sarcina lutea

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Authors: Laila H. Abdel-Rahman, Mohamed Shaker S. Adam, Ahmed M. Abu-Dief, Hanan El-Sayed Ahmed

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In this investigation, Cu(II), Pd(II) and Ag(I) complexes with the tetra-dentate DSPH Schiff base ligand were synthesized. The DSPH Schiff base and its complexes were characterized by using different physicochemical and spectral analysis. The results revealed that the metal ions coordinated with DSPH ligand through azomethine nitrogen and phenolic oxygen. Cu(II), Pd(II) and Ag(I) complexes are present in a 1:1 molar ratio. Pd(II) and Ag(I) complexes have square planar geometries while, Cu(II) has a distorted octahedral (Oh) geometry. All investigated complexes are nonelectrolytes. The investigated compounds were tested against different strains of bacteria and fungi. Both prepared compounds showed good results of inhibition against the selected pathogenic microorganism. Moreover, the interaction of investigated complexes with CT-DNA was studied via various techniques and the binding modes are mainly intercalative and grooving modes. Operating Environment MOE package was used to do docking studies for the investigated complexes to explore the potential binding mode and energy. Furthermore, the growth inhibitory effect of the investigated compounds was examined on some cancer cells lines.

Keywords: tetradentate, antimicrobial, CT-DNA interaction, docking, anticancer

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Authors: Sudip Mondal, Biswanath Mondal, Sudit S. Mukhopadhyay, Apurba Dey

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Bioactive materials improve devices for a long lifespan but have mechanical limitations. Mechanical characterization is one of the very important characteristics to evaluate the life span and functionality of the scaffold material. After implantation of scaffold material the primary stage rejection of scaffold occurs due to non biocompatible effect of host body system. The second major problems occur due to the effect of mechanical failure. The mechanical and biocompatibility failure of the scaffold materials can be overcome by the prior evaluation of the scaffold materials. In this study chemically treated Labeo rohita scale is used for synthesizing hydroxyapatite (HAp) biomaterial. Thermo-gravimetric and differential thermal analysis (TG-DTA) is carried out to ensure thermal stability. The chemical composition and bond structures of wet ball-milled calcined HAp powder is characterized by Fourier Transform Infrared spectroscopy (FTIR), X-ray Diffraction (XRD), Field Emission Scanning Electron Microscopy (FE-SEM), Transmission Electron Microscopy (TEM), Energy Dispersive X-ray (EDX) analysis. Fish scale derived apatite materials consists of nano-sized particles with Ca/P ratio of 1.71. The biocompatibility through cytotoxicity evaluation and MTT assay are carried out in MG63 osteoblast cell lines. In the cell attachment study, the cells are tightly attached with HAp scaffolds developed in the laboratory. The result clearly suggests that HAp material synthesized in this study do not have any cytotoxic effect, as well as it has a natural binding affinity for mammalian cell lines. The synthesized HAp powder further successfully used to develop porous scaffold material with suitable mechanical property of ~0.8GPa compressive stress, ~1.10 GPa a hardness and ~ 30-35% porosity which is acceptable for implantation in trauma region for animal model. The histological analysis also supports the bio-affinity of processed HAp biomaterials in Wistar rat model for investigating the contact reaction and stability at the artificial or natural prosthesis interface for biomedical function. This study suggests the natural sourced fish scale-derived HAp material could be used as a suitable alternative biomaterial for tissue engineering application in near future.

Keywords: biomaterials, hydroxyapatite, scaffold, mechanical property, tissue engineering

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Authors: Stephy Saavedra, Annsy C. Arredondo, Gisele Monteiro, Adalberto Pessoa Jr, Carol N. Flores-Fernandez, Amparo I. Zavaleta

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L-asparaginase from bacterial sources is used in leukemic treatment and food industry. This enzyme is classified based on its affinity towards L-asparagine and L-glutamine. Likewise, ansZ genes express L-asparaginase with higher affinity to L-asparagine. The aim of this work was to clone and express of ansZ gene from Bacillus sp. CH11 isolated from Chilca salterns in Peru. The gene encoding L-asparaginase was cloned into pET15b vector and transformed in Escherichia coli BL21 (DE3) pLysS. The expression was carried out in a batch culture using LB broth and 0.5 mM IPTG. The recombinant L-asparaginase showed a molecular weight of ~ 39 kDa by SDS PAGE and a specific activity of 3.19 IU/mg of protein. The cloning and expression of ansZ gene from this halotolerant Bacillus sp. CH11 allowed having a biological input to improve a future scaling-up.

Keywords: ansZ gene, Bacillus sp, Chilca salterns, recombinant L-asparaginase

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Authors: Ali M. Elgerbi, Obied A. Alwan, Al-Taher O. Alzwei, Abdurrahim A. Elouzi

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The binding of AFM1 to bacteria in phosphate buffer solution depended on many factors such as: availability of energy, incubation period, species and strain of bacteria. Increase in concentration of sugar showed higher removal of AFM1 and faster than in phosphate buffer alone. With 1.0% glucose lactic acid bacteria and bifidobacteria showed toxin removal ranging from 7.7 to 39.7% whereas with 10.0% glucose the percentage removal was 21.8 to 45.4% at 96 hours of incubation.

Keywords: aflatoxin M1, lactic acid bacteria, bifidobacteria , binding, phosphate buffer

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Authors: Ahmed K. Youssef, Shawkat M. B. Aly

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The interaction between ciprofloxacin and bovine serum albumin (BSA) was investigated by UV-Visible absorption and fluorescence spectroscopy. The influence of Cu²⁺ Ca²⁺, Co²⁺, and Fe³⁺ on the Cip-BSA interaction was investigated. The quenching of the BSA fluorescence emission in presence of ciprofloxacin as well as the influence of metal ions on the interaction was analyzed using the Stern-Volmer equation. The Stern-Volmer quenching constant, Kₛᵥ was calculated in presence and absence of the metal ions at the physiological pH of 7.4 using phosphate buffer. The experimental results showed that interaction mainly static in nature and quenching rate constant is decreased in presence of the studied metal ions with exception of Cu²⁺ ions. The decrease observed in the Kₛᵥ values in presence of Co²⁺, Ca²⁺, and Fe³⁺ can be understood on basis of competition between these metal and Cip when both of them existed in the BSA solution. Cu²⁺ induces interaction between Cip and BSA at faster quenching rates as inferred from the observed increase in the Kₛᵥ value. This allowed us to propose that copper (II) ions are directly involved in the process of Cip binding to BSA. The binding constant for Cip on BSA was determined and the metal ions effect on it was examined as well and their values were in line with the Kₛᵥ values.

Keywords: bovine serum albumin, ciprofloxacin, fluorescence, metal ions effect

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Authors: Mohamed S. Sasi, Adel M. Mlitan, Abdulfattah M. Alkherraz

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This research project aims to investigate difference in relative rates concerning phosphoryl transfer relevant to biological catalysis of DNA and RNA in the pH-independent reactions. Activated Models of DNA and RNA for alkyl-aryl phosphate diesters (with 4-nitrophenyl as a good leaving group) have successfully been prepared to gather kinetic parameters. Eyring plots for the pH–independent hydrolysis of 1 and 2 were established at different temperatures in the range 100–160 °C. These measurements have been used to provide a better estimate for the difference in relative rates between the reactivity of DNA and RNA cleavage. Eyring plot gave an extrapolated rate of kH2O = 1 × 10-10 s -1 for 1 (RNA model) and 2 (DNA model) at 25°C. Comparing the reactivity of RNA model and DNA model shows that the difference in relative rates in the pH-independent reactions is surprisingly very similar at 25°. This allows us to obtain chemical insights into how biological catalysts such as enzymes may have evolved to perform their current functions.

Keywords: DNA and RNA models, relative rates, reactivity, phosphoryl transfe

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Authors: Benarous Khedidja, Yousfi Mohamed

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Infections caused by Candida species manifest in a number of diseases, including candidemia, vulvovaginal candidiasis, endocarditis, and peritonitis. These Candida species have been reported to have lipolytic activity by secretion of lipolytic enzymes such as esterases, lipases and phospholipases. These Extracellular hydrolytic enzymes seem to play an important role in Candida overgrowth. Candidiasis is commonly treated with antimycotics such as clotrimazole and nystatin, which bind to a major component of the fungal cell membrane (ergosterol). This binding forms pores in the membrane that lead to death of the fungus. Due to their secondary effects, scientists have thought of another treatment basing on lipase inhibition but we haven’t found any lipase inhibitors used as candidiasis treatment. In this work, we are interested to lipases inhibitors such as alkaloids as another candidiasis treatment. In the first part, we have proceeded to optimize the alkaloid structures and protein 3D structure using Hyperchem software. Secondly, we have docked inhibitors using Genetic algorithm with GOLD software. The results have shown ten possibilities of binding inhibitor to Candida rugosa lipase (CRL) but only one possibility has been accepted depending on the weakest binding energy.

Keywords: marrubiin, candida rugosa lipase, docking, gold

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Authors: Nigar Kantarci Carsibasi

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Coarse-grained elastic network models, namely Gaussian network model (GNM) and Anisotropic network model (ANM), are utilized in order to investigate the fluctuation dynamics of Murine Double Minute 2 (MDM2), which is the native inhibitor of p53. Conformational dynamics of MDM2 are elucidated in unbound, p53 bound, and non-peptide small molecule inhibitor bound forms. With this, it is aimed to gain insights about the alterations brought to global dynamics of MDM2 by native peptide inhibitor p53, and two small molecule inhibitors (HDM201 and NVP-CGM097) that are undergoing clinical stages in cancer studies. MDM2 undergoes significant conformational changes upon inhibitor binding, carrying pieces of evidence of induced-fit mechanism. Small molecule inhibitors examined in this work exhibit similar fluctuation dynamics and characteristic mode shapes with p53 when complexed with MDM2, which would shed light on the design of novel small molecule inhibitors for cancer therapy. The results showed that residues Phe 19, Trp 23, Leu 26 reside in the minima of slowest modes of p53, pointing to the accepted three-finger binding model. Pro 27 displays the most significant hinge present in p53 and comes out to be another functionally important residue. Three distinct regions are identified in MDM2, for which significant conformational changes are observed upon binding. Regions I (residues 50-77) and III (residues 90-105) correspond to the binding interface of MDM2, including (α2, L2, and α4), which are stabilized during complex formation. Region II (residues 77-90) exhibits a large amplitude motion, being highly flexible, both in the absence and presence of p53 or other inhibitors. MDM2 exhibits a scattered profile in the fastest modes of motion, while binding of p53 and inhibitors puts restraints on MDM2 domains, clearly distinguishing the kinetically hot regions. Mode shape analysis revealed that the α4 domain controls the size of the cleft by keeping the cleft narrow in unbound MDM2; and open in the bound states for proper penetration and binding of p53 and inhibitors, which points to the induced-fit mechanism of p53 binding. P53 interacts with α2 and α4 in a synchronized manner. Collective modes are shifted upon inhibitor binding, i.e., second mode characteristic motion in MDM2-p53 complex is observed in the first mode of apo MDM2; however, apo and bound MDM2 exhibits similar features in the softest modes pointing to pre-existing modes facilitating the ligand binding. Although much higher amplitude motions are attained in the presence of non-peptide small molecule inhibitor molecules as compared to p53, they demonstrate close similarity. Hence, NVP-CGM097 and HDM201 succeed in mimicking the p53 behavior well. Elucidating how drug candidates alter the MDM2 global and conformational dynamics would shed light on the rational design of novel anticancer drugs.

Keywords: cancer, drug design, elastic network model, MDM2

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Authors: Osama K. Abou-Zied, Saba A. Sulaiman

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We studied the spectroscopy of 25-nm diameter gold nanoparticles (AuNPs), coated with human serum albumin (HSA) as a model drug carrier. The morphology and coating of the AuNPs were examined using transmission electron microscopy and dynamic light scattering. Resonance energy transfer from the sole tryptophan of HSA (Trp214) to the AuNPs was observed in which the fluorescence quenching of Trp214 is dominated by a static mechanism. Using fluorescein (FL) to probe the warfarin drug-binding site in HSA revealed the unchanged nature of the binding cavity on the surface of the AuNPs, indicating the stability of the protein structure on the metal surface. The transient absorption results of the surface plasmonic resonance (SPR) band of the AuNPs show three ultrafast dynamics that are involved in the relaxation process after excitation at 460 nm. The three decay components were assigned to the electron-electron (~ 400 fs), electron-phonon (~ 2.0 ps) and phonon-phonon (200–250 ps) interactions. These dynamics were not changed upon coating the AuNPs with HSA which indicates the chemical and physical stability of the AuNPs upon bioconjugation. Binding of FL in HSA did not have any measurable effect on the bleach recovery dynamics of the SPR band, although both FL and AuNPs were excited at 460 nm. The current study is important for a better understanding of the physical and dynamical properties of protein-coated metal nanoparticles which are expected to help in optimizing their properties for critical applications in nanomedicine.

Keywords: gold nanoparticles, human serum albumin, fluorescein, femtosecond transient absorption

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Authors: Ratchaneewan Maneemaroj, Paveena Noisuwan, Chonlada Lakhonphon

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The smoking is one of the major risk factors in Non-Communicable Disease. Free radicals from cigarette smoke can cause oxidative stress. The oxidative insults can lead to red blood cell (RBC) senescence and are involved in the clearance of red blood cells. The objective of the present study is to assess the association between smoke, oxidative stress evaluated with serum Malondialdehyde (MDA) level and phosphatidylserine (PS) externalization (biomarker of RBC senescence) evaluated with annexin V binding. A total of sixty-four male volunteers aged 25-60 years old were recruited in this study. MDA was measured by colorimetric method. Annexin V binding was detected by flow cytometry. Our results show that there was a significant increase in MDA levels in cigarette smokers as compared to non-smokers (p < 0.001). However, there was no significant different between annexin V binding (% gate) in cigarette smokers and non-smokers (p = 0.978). These results provide evidence of free radical from smoking is associated with oxidative damage to erythrocytes. However, our results suggest that PS externalization is unlikely to have a role in RBC senescence pathway of stressed erythrocytes from cigarette smoke. The other biomarker of RBC senescence should be determined on cigarette smoker erythrocytes.

Keywords: malondialdehyde, phosphatidylserine, RBC senescence, annexin V

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Authors: Sudhir Kumar Sharma, Ramesh Jagannathan

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The interaction of organic and inorganic matrices of biological origin resulting in self-assembled structures with unique properties is well established. The development of such self-assembled nanostructures by synthetic and bio-inspired techniques is an established field of active research. Among bio-materials, nacre, a laminar stack of calcium carbonate nanosheets, which are interleaved with organic material, has long been focused research due to its unique mechanical properties. In this paper, we present the development of nacre-like lamellar structures made up of calcium carbonate via a wet chemical route. We used the binding affinity of carboxylate anions and calcium cations using poly (acrylic) acid (PAA) to lead CaCO₃ crystallization. In these experiments, we selected calcium acetate as the precursor molecule along with PAA (Mw ~ 8000 Da). We found that Ca⁺²/COO⁻ ratio provided a tunable control for the morphology and growth of CaCO₃ nanostructures. Drop casting one such formulation on a silicon substrate followed by calcination resulted in co-planner, molecular sheets of CaCO₃, separated by a spacer layer of carbon. The scope of our process could be expanded to produce unit cell thick molecular sheets of other important inorganic materials.

Keywords: self-assembled structures, bio-inspired materials, calcium carbonate, wet chemical route

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Authors: Phillip Kearney, Constantina Lekakou, Stephen Belcher, Alessandro Sordon

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The focus in the automotive industry is to reduce human operator and machine interaction, so manufacturing becomes more automated and safer. The aim is to lower part cost and construction time as well as defects in the parts, sometimes occurring due to the physical limitations of human operators. A move to automate the layup of reinforcement material in composites manufacturing has resulted in the use of tapes that are placed in position by a robotic deposition head, also described as Automated Fibre Placement (AFP). The process of AFP is limited with respect to the finite amount of material that can be loaded into the machine at any one time. Joining two batches of tape material together involves a splice to secure the ends of the finishing tape to the starting edge of the new tape. The splicing method of choice for the majority of prepreg applications is a hand stich method, and as the name suggests requires human input to achieve. This investigation explores three methods for automated splicing, namely, adhesive, binding and stitching. The adhesive technique uses an additional adhesive placed on the tape ends to be joined. Binding uses the binding agent that is already impregnated onto the tape through the application of heat. The stitching method is used as a baseline to compare the new splicing methods to the traditional technique currently in use. As the methods will be used within a High Speed Automated Fibre Placement (HSAFP) process, this meant the parameters of the splices have to meet certain specifications: (a) the splice must be able to endure a load of 50 N in tension applied at a rate of 1 mm/s; (b) the splice must be created in less than 6 seconds, dictated by the capacity of the tape accumulator within the system. The samples for experimentation were manufactured with controlled overlaps, alignment and splicing parameters, these were then tested in tension using a tensile testing machine. Initial analysis explored the use of the impregnated binding agent present on the tape, as in the binding splicing technique. It analysed the effect of temperature and overlap on the strength of the splice. It was found that the optimum splicing temperature was at the higher end of the activation range of the binding agent, 100 °C. The optimum overlap was found to be 25 mm; it was found that there was no improvement in bond strength from 25 mm to 30 mm overlap. The final analysis compared the different splicing methods to the baseline of a stitched bond. It was found that the addition of an adhesive was the best splicing method, achieving a maximum load of over 500 N compared to the 26 N load achieved by a stitching splice and 94 N by the binding method.

Keywords: analysis, automated fibre placement, high speed, splicing

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Authors: Hainan Chen, Jina Qing, Xiao Zhu, Ling Gao, Ampadu O. Jackson, Min Zhang, Kai Yin

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Objective: Editing macrophage activation to dampen inflammatory diseases by promoting the repolarization of inflammatory (M1) macrophages to anti-inflammatory (M2) macrophages is highly associated with mitochondrial respiration. Recent studies have suggested that mitochondrial apolipoprotein A-1 binding protein (APOA1BP) was essential for the cellular metabolite NADHX repair to NADH, which is necessary for the mitochondrial function. The exact role of APOA1BP in the repolarization of M1 to M2, however, is uncertain. Material and method: THP-1-derived macrophages were incubated with LPS (10 ng/ml) or/and IL-4 (100 U/ml) for 24 hours. Biochemical parameters of oxidative phosphorylation and M1/M2 markers were analyzed after overexpression of APOA1BP in cells. Results: Compared with control and IL-4-exposed M2 cells, APOA1BP was downregulated in M1 macrophages. APOA1BP restored the decline in mitochondrial function to improve metabolic and phenotypic reprogramming of M1 to M2 macrophages. Blocking oxidative phosphorylation by oligomycin blunts the effects of APOA1BP on M1 to M2 repolarization. Mechanistically, LPS triggered the hydration of NADH and increased its hydrate NADHX which inhibit cellular NADH dehydrogenases, a key component of electron transport chain for oxidative phosphorylation. APOA1BP decreased the level of NADHX via converting R-NADHX to biologically useful S-NADHX. The mutant of APOA1BP aspartate188, the binding site of NADHX, fail to repair oxidative phosphorylation, thereby preventing repolarization. Conclusions: Restoring mitochondrial function by increasing mitochondrial APOA1BP might be useful to improve the reprogramming of inflammatory macrophages into anti-inflammatory cells to control inflammatory diseases.

Keywords: inflammatory diseases, macrophage repolarization, mitochondrial respiration, apolipoprotein A-1 binding protein, NADHX, NADH

Procedia PDF Downloads 154