Search results for: phosphinite ligands

Authors: Galina Mamardashvili, Nugzar Mamardashvili, Win Dehaen

Abstract:

The processes of complexation of the Zn-tetraarylporphyrins with eight 4-(4-(3,6-bis(t-butyl)carbazol-9-yl-phenyl)-1,2,3-triazole (ZnP1) and eight 4-(4-(3,6-di-tert-butyl-9-H-carbazol-9-yl)phenoxy)methyl)-2,4,6-trimethylphenyl (ZnP2)with the 1,10-diaza-4,7,13,18tetraoxabicyclo[8.5.5]eicosane (L1),1,10-diaza-4,7,13,16,21,24-hexaoxabicyclo[8.8.8]hexacosane (L2)and 1,10-diaza-5,6,14,15-dibenzo-4,7,13,16,21,24 hexaoxabicyclo[8.8.8] hexacosane (L3) were investigated by the method of spectrophotometric titration and ¹H NMR-spectroscopy. We determined the structures of the host-guest complexes, and their stability constants in toluene were calculated. It was found out that the ZnP1 interacts with the guest molecules L1, L2 with the formation of stable "nest" type complexes and does not form similar complexes with the L3 (presumably due to the fact that the L3 does not match the size of the porphyrin ZnP(1) cavity). On the other hand, the porphyrin ZnP2 binds all of the ligands L1-L3, however complexes thus formed are less stable than complexes ZnP1-L1, ZnP1-L2. In the report, we will also discuss the influence of the alkali cations additives on the stability of the complexes between the porphyrin ZnP1, ZnP2 hosts and guest molecules of the ligands L1-L3.

Keywords: porphyrin, cryptand, cation, complex guest-host

Procedia PDF Downloads 220

Authors: Sh. Sousani, Z. Shadrokh, M. Hofbauerová, J. Kollár, M. Jergel, P. Nádaždy, M. Omastová, E. Majková

Abstract:

Perovskite quantum dots (PQDs) have the potential to increase the performance of the perovskite solar cell (PSCs). The integration of PQDs into PSCs can extend the absorption range and enhance photon harvesting and device efficiency. In addition, PQDs can stabilize the device structure by passivating surface defects and traps in the perovskite layer and enhance its stability. The integration of PQDs into PSCs is strongly affected by the type of ligands on the surface of PQDs. The ligands affect the charge transport properties of PQDs, as well as the formation of well-defined interfaces and stability of PSCs. In this work, the CsPbBr₃ QDs were synthesized by the conventional hot-injection method using cesium oleate, PbBr₂ and two different ligands, namely oleic acid (OA) oleylamine (OAm) and didodecyldimethylammonium bromide (DDAB). The STEM confirmed regular shape and relatively monodisperse cubic structure with an average size of about 10-14 nm of the prepared CsPbBr₃ QDs. Further, the photoluminescent (PL) properties of the PQDs/perovskite bilayer with the ligand OA, OAm and DDAB were studied. For this purpose, ITO/PQDs as well as ITO/PQDs/MAPI perovskite structures were prepared by spin coating and the effect of the ligand and oxygen plasma treatment was analyzed. The plasma treatment of the PQDs layer could be beneficial for the deposition of the MAPI perovskite layer and the formation of a well-defined PQDs/MAPI interface. The absorption edge in UV-Vis absorption spectra for OA, OAm CsPbBr₃ QDs is placed around 513 nm (the band gap 2.38 eV); for DDAB CsPbBr₃ QDs, it is located at 490 nm (the band gap 2.33 eV). The photoluminescence (PL) spectra of CsPbBr₃ QDs show two peaks located around 514 nm (503 nm) and 718 nm (708 nm) for OA, OAm (DDAB). The peak around 500 nm corresponds to the PL of PQDs, and the peak close to 710 nm belongs to the surface states of PQDs for both types of ligands. These surface states are strongly affected by the O₃ plasma treatment. For PQDs with DDAB ligand, the O₃ exposure (5, 10, 15 s) results in the blue shift of the PQDs peak and a non-monotonous change of the amplitude of the surface states' peak. For OA, OAm ligand, the O₃ exposition did not cause any shift of the PQDs peak, and the intensity of the PL peak related to the surface states is lower by one order of magnitude in comparison with DDAB, being affected by O₃ plasma treatment. The PL results indicate the possibility of tuning the position of the PL maximum by the ligand of the PQDs. Similar behavior of the PQDs layer was observed for the ITO/QDs/MAPI samples, where an additional strong PL peak at 770 nm coming from the perovskite layer was observed; for the sample with PQDs with DDAB ligands, a small blue shift of the perovskite PL maximum was observed independently of the plasma treatment. These results suggest the possibility of affecting the PL maximum position and the surface states of the PQDs by the combination of a suitable ligand and the O₃ plasma treatment.

Keywords: perovskite quantum dots, photoluminescence, O₃ plasma., Perovskite Solar Cells

Procedia PDF Downloads 62

Authors: Sh. Sousani, Z. Shadrokh, M. Hofbauerová, J. Kollár, M. Jergel, P. Nádaždy, M. Omastová, E. Majková

Abstract:

Perovskite quantum dots (PQDs) have the potential to increase the performance of the perovskite solar cells (PSCs). The integration of PQDs into PSCs can extend the absorption range and enhance photon harvesting and device efficiency. In addition, PQDs can stabilize the device structure by passivating surface defects and traps in the perovskite layer and enhance its stability. The integration of PQDs into PSCs is strongly affected by the type of ligands on the surface of PQDs. The ligands affect the charge transport properties of PQDs, as well as the formation of well-defined interfaces and stability of PSCs. In this work, the CsPbBr₃ QDs were synthesized by the conventional hot-injection method using cesium oleate, PbBr₂, and two different ligands, namely oleic acid (OA)@oleylamine (OAm) and didodecyldimethylammonium bromide (DDAB). The STEM confirmed regular shape and relatively monodisperse cubic structure with an average size of about 10-14 nm of the prepared CsPbBr₃ QDs. Further, the photoluminescent (PL) properties of the PQDs/perovskite bilayer with the ligand OA@OAm and DDAB were studied. For this purpose, ITO/PQDs, as well as ITO/PQDs/MAPI perovskite structures, were prepared by spin coating, and the effect of the ligand and oxygen plasma treatment was analysed. The plasma treatment of the PQDs layer could be beneficial for the deposition of the MAPI perovskite layer and the formation of a well-defined PQDs/MAPI interface. The absorption edge in UV-Vis absorption spectra for OA@OAm CsPbBr₃ QDs is placed around 513 nm (the band gap 2.38 eV); for DDAB CsPbBr₃ QDs, it is located at 490 nm (the band gap 2.33 eV). The photoluminescence (PL) spectra of CsPbBr₃ QDs show two peaks located around 514 nm (503 nm) and 718 nm (708 nm) for OA@OAm (DDAB). The peak around 500 nm corresponds to the PL of PQDs, and the peak close to 710 nm belongs to the surface states of PQDs for both types of ligands. These surface states are strongly affected by the O₃ plasma treatment. For PQDs with DDAB ligand, the O₃ exposure (5, 10, 15 s) results in the blue shift of the PQDs peak and a non-monotonous change of the amplitude of the surface states' peak. For OA@OAm ligand, the O₃ exposition did not cause any shift of the PQDs peak, and the intensity of the PL peak related to the surface states is lower by one order of magnitude in comparison with DDAB, being affected by O₃ plasma treatment. The PL results indicate the possibility of tuning the position of the PL maximum by the ligand of the PQDs. Similar behaviour of the PQDs layer was observed for the ITO/QDs/MAPI samples, where an additional strong PL peak at 770 nm coming from the perovskite layer was observed; for the sample with PQDs with DDAB ligands, a small blue shift of the perovskite PL maximum was observed independently of the plasma treatment. These results suggest the possibility of affecting the PL maximum position and the surface states of the PQDs by the combination of a suitable ligand and the O₃ plasma treatment.

Keywords: perovskite quantum dots, photoluminescence, O₃ plasma., perovskite solar cells

Procedia PDF Downloads 68

Authors: Abdolamir Allameh, Seyyed Mortaza Haghgoo, Adnan Khosravi, Esmaeil Mortaz, Mihan Pourabdollah-Toutkaboni, Sharareh Seifi

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Non-Small Cell Lung Carcinoma (NSCLC) is associated with a number of gene mutations in epidermal growth factor receptor (EGFR). The prognostic significance of mutations in exons 19 and 21, together with serum levels of EGFR, amphiregulin (AR), and Transforming Growth Factor-alpha (TGF-α) are implicated in diagnosis and treatment. The aim of this study was to examine the relationship of EGFR mutations in selected exons with the expression of relevant ligands in sera samples of NSCLC patients. For this, a group of NSCLC patients (n=98) referred to the hospital for lung surgery with a mean age of 59±10.5 were enrolled (M/F: 75/23). Blood specimen was collected from each patient. Besides, formalin fixed paraffin embedded tissues were processed for DNA extraction. Gene mutations in exons 19 and 21 were detected by direct sequencing, following DNA amplification which was done by PCR (Polymerase Chain Reaction). Also, serum levels of EGFR, AR, and TGF-α were measured by ELISA. The results of our study show that EGFR mutations were present in 37% of Iranian NSCLC patients. The most frequently identified mutations were deletions in exon 19 (72.2%) and substitutions in exon 21 (27.8%). The most frequently identified alteration, which is considered as a rare mutation, was the E872K mutation in exon 21, which was found in 90% (9 out of 10) cases. EGFR mutation detected in exon 21 was significantly (P<0.05) correlated with the levels of its ligands, EGFR and TGF-α in serum samples. Furthermore, it was found that increased serum AR (>3pg/ml) and TGF-α (>10.5 pg/ml) were associated with shorter overall survival (P<0.05). The results clearly showed a close relationship between EGFR mutations and serum EGFR and serum TGF-α. Increased serum EGFR was associated with TGF-α and AR and linked to poor prognosis of NSCLC. These findings are implicated in clinical decision-making related to EGFR-Tyrosine kinase inhibitors (TKIs).

Keywords: lung cancer, Iranian patients, epidermal growth factor, mutation, prognosis

Procedia PDF Downloads 79

Authors: Sujata Sharma, Avinash Singh, Lovely Gautam, Pradeep Sharma, Mau Sinha, Asha Bhushan, Punit Kaur, Tej P. Singh

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Peptidyl-tRNA hydrolase (Pth) Pth is an essential bacterial enzyme that catalyzes the release of free tRNA and peptide moeities from peptidyl tRNAs during stalling of protein synthesis. In order to design inhibitors of Pth from Pseudomonas aeruginosa (PaPth), we have determined the structures of PaPth in its native state and in the bound states with two compounds, amino acylate-tRNA analogue (AAtA) and 5-azacytidine (AZAC). The peptidyl-tRNA hydrolase gene from Pseudomonas aeruginosa was amplified by Phusion High-Fidelity DNA Polymerase using forward and reverse primers, respectively. The E. coliBL21 (λDE3) strain was used for expression of the recombinant peptidyl-tRNA hydrolase from Pseudomonas aeruginosa. The protein was purified using a Ni-NTA superflow column. The crystallization experiments were carried out using hanging drop vapour diffusion method. The crystals diffracted to 1.50 Å resolution. The data were processed using HKL-2000. The polypeptide chain of PaPth consists of 194 amino acid residues from Met1 to Ala194. The centrally located β-structure is surrounded by α-helices from all sides except the side that has entrance to the substrate binding site. The structures of the complexes of PaPth with AAtA and AZAC showed the ligands bound to PaPth in the substrate binding cleft and interacted with protein atoms extensively. The residues that formed intermolecular hydrogen bonds with the atoms of AAtA included Asn12, His22, Asn70, Gly113, Asn116, Ser148, and Glu161 of the symmetry related molecule. The amino acids that were involved in hydrogen bonded interactions in case of AZAC included, His22, Gly113, Asn116, and Ser148. As indicated by fittings of two ligands and the number of interactions made by them with protein atoms, AAtA appears to be a more compatible with the structure of the substrate binding cleft. However, there is a further scope to achieve a better stacking than that of O-tyrosyl moiety because it is not still ideally stacked. These observations about the interactions between the protein and ligands have provided the information about the mode of binding of ligands, nature and number of interactions. This information may be useful for the design of tight inhibitors of Pth enzymes.

Keywords: peptidyl tRNA hydrolase, Acinetobacter baumannii, Pth enzymes, O-tyrosyl

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Authors: Amina Adala, Nadra Debbache, Tahar Sehili

Abstract:

Coordination polymers and uniformly {[Zn(II)(BIPY)(Pht)]n} (1), {[Zn (HYD)(Pht)]n} (2) (BIPY = 4,4’ bipyridine, Pht = terephtalic acid, HYD = 8-hydroxyquinoline) have been successfully synthesized by a hydrothermal process using aqueous zinc solution. The as-prepared compounds phases were characterized by X-ray diffraction (XRD), Fourier Transform Infrared spectroscopy, UV-visible spectroscopy, thermogravimetric analysis (TGA), and the electrochemistry study by the voltammetry cyclic. The results showed a crystalline phase for CP1 however, CP2 requires recrystallization; the FTIR showed the presence of characteristic bands of all ligands; besides that, TGA shows thermal stability up to 300°C. The electrochemistry study showed a good charge transfer between the ligands and Zn metal for the two components. UV-Vis measurement showed strong absorption in a wide range from UV to visible light with a band gap of 2.69 eV for CP1 and 2.56 eV for CP2, smaller than that of ZnO. This represents an alternative to using ZnO. The Ibuprofen IBP decomposition kinetics of 5.10⁻⁵ mol.L⁻¹ under solar and artificial light were studied for different irradiation conditions. Good photocatalytic properties were observed due to their high surface area.

Keywords: metal-organic frameworks, photocatalysis, photodegradation, organic pollutant, ibuprofen

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Authors: Hammed Tanimowo Aiyelabegan, Oluchukwu Franklin Aladi, Mutiu Adewumi Alabi, Raliat Abimbola Aladodo, Emmanuel Oladipupo Ajani, Abdulganiyu Giwa, Esther Owolabi

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The study aimed to evaluate the inhibitory activities of ligands from Enantia chlorantha stem bark on α-amylase and α-glucosidase. In silico pharmacokinetic properties and docking scores were employed to analyse the inhibition using SwissADME and Autodock4.2, respectively. Results revealed that drug-likeness, pharmacokinetics and bioavailability radar of all the ligands except jatrorrhizine and acarbose falls within the radar according to the Lipinski rule of 5. The binding energies of the protein-ligand interactions also show that the ligand fits into the active site. The results obtained from this study show that the chemical constituents from Enantia chlorantha stem bark may bring about positive physiological changes in a patient suffering from diabetes mellitus. Further in vitro studies on diabetes cell lines and in vivo studies on the animal may validate these compounds for diabetes treatment. These phytoconstituents could help in the development of novel anti-diabetic molecules.

Keywords: diabetes mellitus, ?-amylase, ?-glucosidase, in silico, Enantia chlorantha stem bark

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Authors: Hamid Hossein Khezri, Afsaneh Javdani-Mallak

Abstract:

Fast inhibitory neurotransmission in the mammalian nervous system is largely mediated by GABAA receptors, chloride-selective members of the superfamily of pentameric Cys-loop receptors. Cannabidiol (CBD) is one of the members of cannabinoid compounds found in cannabis. CBD and Cannabinol (CBN), as the other extract of plant Cannabis were able to reduce myofascial pain in rats with immunosuppressive and anti-inflammatory activities. In this study, we accomplished protein-protein BLAST, and the sequence was found to be for Gamma-aminobutyric acid receptor subunit alpha-1 (GBRA1) chain A and its 3D structure was subsequently downloaded from Protein Data Bank. The structures of the ligands, cannabinol, and cannabidiol, were obtained from PubChem. After the necessary process of the obtained files, AutoDock Vina was used to perform molecular docking. Docking between the ligands and GBRA1 chain A revealed that cannabinol has a higher affinity to GBRA1 (binding energy = -7.5 kcal/mol) compared to cannabidiol (binding energy = -6.5 kcal/mol). Furthermore, cannabinol seems to be able to interact with 10 residues of the protein, out of which 3 are in the neurotransmitter-gated ion-channel transmembrane domain of GBRA1, whereas cannabidiol interacts with two other residues. Although the results of this project do not indicate the activating /or inhibitory capability of the studied compounds, it suggests that cannabinol can act as a relatively strong ligand for GBRA1.

Keywords: protein-ligand docking, cannabinol, cannabidiol, GBRA1

Procedia PDF Downloads 108

Authors: Indranil Chakraborty, Kalyan Mandal

Abstract:

Three new α-hydroxy carboxylate group functionalized MnFe₂O₄ nanoparticles (NPs) have been developed to explore the microscopic origin of ligand modified fluorescence and magnetic properties of nearly monodispersed MnFe₂O₄ NPs. The surface functionalization has been carried out with three small organic ligands (tartrate, malate, and citrate) having different number of α-hydroxy carboxylate functional group along with steric effect. Detailed study unveils that α-hydroxy carboxylate moiety of the ligands plays key role to generate intrinsic fluorescence in functionalized MnFe₂O₄ NPs through the activation of ligand to metal charge transfer transitions, associated with ligand-Mn²⁺/Fe³⁺ interactions along with d-d transition corresponding to d-orbital energy level splitting of Fe³⁺ ions on NP surface. Further, MnFe₂O₄ NPs show a maximum 140.88% increase in coercivity and 97.95% decrease in magnetization compared to its bare one upon functionalization. The ligands that induce smallest crystal field splitting of d-orbital energy level of transition metal ions are found to result in strongest ferromagnetic activation of the NPs. Finally, our developed tartrate functionalized MnFe₂O₄ (T-MnFe₂O₄) NPs have been utilized for studying DNA binding interaction and nuclease activity for stimulating their beneficial activities toward diverse biomedical applications. The spectroscopic measurements indicate that T-MnFe₂O₄ NPs bind calf thymus DNA by intercalative mode. The ability of T-MnFe₂O₄ NPs to induce DNA cleavage was studied by gel electrophoresis technique where the complex is found to promote the cleavage of pBR322 plasmid DNA from the super coiled form I to linear coiled form II and nicked coiled form III with good efficiency. This may be taken into account for designing new biomolecular detection agents and anti-cancer drug which can open up a new door toward diverse non-invasive biomedical applications.

Keywords: MnFe₂O₄ nanoparticle, α-hydroxy carboxylic acid, comparative fluorescence, magnetism study, DNA interaction, nuclease activity

Procedia PDF Downloads 136

Authors: Laura Bravo-García, Gotzone Barandika, Begoña Bazán, M. Karmele Urtiaga, Luis M. Lezama, María I. Arriortua

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Solid coordination networks (SCNs) are materials consisting of metal ions or clusters that are linked by polyfunctional organic ligands and can be designed to form tridimensional frameworks. Their structural features, as for example high surface areas, thermal stability, and in other cases large cavities, have opened a wide range of applications in fields like drug delivery, host-guest chemistry, biomedical imaging, chemical sensing, heterogeneous catalysis and others referred to greenhouse gases storage or even separation. In this sense, the use of polycarboxylate anions and dipyridyl ligands is an effective strategy to produce extended structures with the needed characteristics for these applications. In this context, a novel compound, [Cu4(m-BDC)4(bpa)2DMF]•DMF has been obtained by microwave synthesis, where m-BDC is 1,3-benzenedicarboxylate and bpa 1,2-bis(4-pyridyl)ethane. The crystal structure can be described as a three dimensional framework formed by two equal, interpenetrated networks. Each network consists of two different CuII dimers. Dimer 1 have two coppers with a square pyramidal coordination, and dimer 2 have one with a square pyramidal coordination and other with octahedral one, the last dimer is unique in literature. Therefore, the combination of both type of dimers is unprecedented. Thus, benzenedicarboxylate ligands form sinusoidal chains between the same type of dimers, and also connect both chains forming these layers in the (100) plane. These layers are connected along the [100] direction through the bpa ligand, giving rise to a 3D network with 10 Å2 voids in average. However, the fact that there are two interpenetrated networks results in a significant reduction of the available volume. Structural analysis was carried out by means of single crystal X-ray diffraction and IR spectroscopy. Thermal and magnetic properties have been measured by means of thermogravimetry (TG), X-ray thermodiffractometry (TDX), and electron paramagnetic resonance (EPR). Additionally, CO2 and CH4 high pressure adsorption measurements have been carried out for this compound.

Keywords: gas adsorption, interpenetrated networks, magnetic measurements, solid coordination network (SCN), thermal stability

Procedia PDF Downloads 323

Authors: V. K. Srivastava

Abstract:

The chemistry of compounds containing transition metals bound to sulfur containing ligands has been actively studied. Interest in these compounds arises from the identification of the biological importance of iron-sulfur containing proteins as well as the unusual behaviour of several types of synthetic metal-sulfur complexes. Metal complexes (C₆H₅)₄P)₂ Pt(Mos₄)₂, (C₆H₅)₄P)₂ Pd(MoS₄)₂, (C₆H₅)₄P)₂ Ni(MoS₄)₂ of bioinorganic relevance were investigated. The complexes [M(M'S₄)₂]²⁻ were prepared with high yield and purity as salts of the variety of organic cations. The diamagnetism and spectroscopic properties of these complexes confirmed that their structures are essentially equivalent with two bidentate M'S₄²⁻ ligands coordinated to the central d⁸ metal in a square planer geometry. The interaction of the complexes with CT-DNA was studied. Results showed that metal complexes increased DNA's relative viscosity and quench the fluorescence intensity of EB bound to DNA. In antimicrobial activities, all complexes showed good antimicrobial activity higher than ligand against gram positive, gram negative bacteria and fungi. The antitumor properties have been tested in vitro against two tumor human cell lines, Hela (derived from cervical cancer) and MCF-7 (derived from breast cancer) using metabolic activity tests. Result showed that the complexes are promising chemotherapeutic alternatives in the search of anticancer agents.

Keywords: anti cancer, biocidal, DNA binding, spectra

Procedia PDF Downloads 158

Authors: Hamid Hossein Khezri, Afsaneh Javdani-Mallak

Abstract:

Fast inhibitory neurotransmission in the mammalian nervous system is largely mediated by GABAA receptors, chloride-selective members of the superfamily of pentameric Cys-loop receptors. Cannabidiol (CBD) is one of the members of cannabinoid compounds found in cannabis. CBD and Cannabinol (CBN), as the other extract of plant Cannabis, were able to reduce myofascial pain in rats with immunosuppressive and anti-inflammatory activities. In this study, we accomplished protein-protein BLAST and the sequence was found to be for Gamma-aminobutyric acid receptor subunit alpha-1 (GBRA1) chain A and its 3D structure was subsequently downloaded from Protein Data Bank. The structures of the ligands cannabinol and cannabidiol were obtained from PubChem. After a necessary process of the obtained files, AutoDock Vina was used to performing molecular docking. Docking between the ligands and GBRA1 chain A revealed that cannabinol has a higher affinity to GBRA1 (binding energy = -7.5 kcal/mol) compared to cannabidiol (binding energy = -6.5 kcal/mol). Furthermore, cannabinol seems to be able to interact with 10 residues of the protein, out of which 3 are in the neurotransmitter-gated ion-channel transmembrane domain of GBRA1, whereas cannabidiol interacts with two other residues. Although the results of this project do not indicate the activating /or inhibitory capability of the studied compounds, it suggests that cannabinol can act as a relatively strong ligand for GBRA1.

Keywords: protein-ligand docking, cannabinol, cannabidiol, GBRA1

Procedia PDF Downloads 116

Authors: Nazli Eslamirad, Peter C. Junk, Jun Wang, Glen B. Deacon

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Since coordination behavior of pyrazoles and pyrazolate ions are widely versatile towards a great range of metals such as d-block, f-block as well as main group elements; they attract interest as ligands for preparing compounds. A variety of rare-earth pyrazolate complexes have been synthesized by redox transmetalation/protolysis (RTP) previously, therefore, a variety of rare-earth pyrazolate complexes using two pyrazoles, 3,5-dimethylpyrazole (Me₂pzH) and 3,5-di-tert -butylpyrazolate (t-Bu₂pzH), in which the structures span the whole La-Lu array beside Sc and Y has been synthesized by RTP reaction. There have been further developments in this study: Synthesizing structure of [Tb(Me₂pz)₃(thf)]₂ which is isomorphous with those of the previously reported [Dy(Me₂pz)₃(thf)]₂ and [Lu(Me₂pz)₃(thf)]₂ analogous that has two µ-1(N):2(Nʹ)-Me2pz ligands (the most common pyrazolate ligation for non-rare-earth complexes). Previously most of the reported compounds using t-Bu2pzH were monomeric compounds however the lanthanum derivative [La(Me₂pz)₃thf₂] ,which has been reported previously without crystal structure, has now been structurally characterized, along with cerium and lutetium analogue. Also a polymeric structure with samarium has now been synthesized which the neodymium analogue has been reported previously and comparing these polymeric structures can support the idea that the geometry of Sm(tBu₂pz)₃ affect the coordination of the solvent. Also, by using 1,2-dimethoxyethane (DME) instead of tetrahydrofuran (THF) new [Er(tBu₂pz)₃ (dme)₂] has now been reported.

Keywords: lanthanoid complexes, pyrazolate, redox transmetalation/protolysis, x-ray crystal structures

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Authors: Romasa Qasim, G. M. Sayedur Rahman, Nahid Hasan, M. Shazzad Hosain

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Millions of people worldwide suffer from Hepatitis C, one of the fatal diseases. Interferon (IFN) and ribavirin are the available treatments for patients with Hepatitis C, but these treatments have their own side-effects. Our research focused on the development of an orally taken small molecule drug targeting the proteins in Hepatitis C Virus (HCV), which has lesser side effects. Our current study aims to the Pharmacophore based drug development of a specific small molecule anti-viral drug for Hepatitis C Virus (HCV). Drug designing using lab experimentation is not only costly but also it takes a lot of time to conduct such experimentation. Instead in this in silico study, we have used computer-aided techniques to propose a Pharmacophore-based anti-viral drug specific for the protein domains of the polyprotein present in the Hepatitis C Virus. This study has used homology modeling and ab initio modeling for protein 3D structure generation followed by pocket identification in the proteins. Drug-able ligands for the pockets were designed using de novo drug design method. For ligand design, pocket geometry is taken into account. Out of several generated ligands, a new Pharmacophore is proposed, specific for each of the protein domains of HCV.

Keywords: pharmacophore-based drug design, anti-viral drug, in-silico drug design, Hepatitis C virus (HCV)

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Authors: Abdul Musaweer Habib, Habibul Hasan Mazumder, Saiful Islam, Sohel Sikder, Omar Faruk Sikder

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The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1499 proteins of Fusobacterium nucleatum, which has no homolog in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the KEGG Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the 3-D structure of these three proteins. Finally, determination of ligand binding sites of the key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against Fusobacterium nucleatum.

Keywords: colorectal cancer, drug target, Fusobacterium nucleatum, homology modeling, ligands

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Authors: Alan Luo, Hunter N. B. Moseley

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Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from x-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for x-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across x-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.

Keywords: biomacromolecular structure, coenzyme, electron density discrepancy analysis, x-ray crystallography

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Authors: Zubair Ahmed, Andrea Barbieri

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The need to reduce energy consumption has prompted a considerable research effort for developing alternative energy-efficient lighting systems to replace conventional light sources (i.e., incandescent and fluorescent lamps). Organic light emitting device (OLED) technology offers the distinctive possibility to fabricate large area flat devices by vacuum or solution processing. Lanthanide β-diketonates complexes, due to unique photophysical properties of Ln(III) ions, have been explored as emitting layers in OLED displays and in solid-state lighting (SSL) in order to achieve high efficiency and color purity. For such applications, the excellent photoluminescence quantum yield (PLQY) and stability are the two key points that can be achieved simply by selecting the proper organic ligands around the Ln ion in a coordination sphere. Regarding the strategies to enhance the PLQY, the most common is the suppression of the radiationless deactivation pathways due to the presence of high-frequency oscillators (e.g., OH, –CH groups) around the Ln centre. Recently, a different approach to maximize the PLQY of Ln(β-DKs) has been proposed (named 'Escalate Coordination Anisotropy', ECA). It is based on the assumption that coordinating the Ln ion with different ligands will break the centrosymmetry of the molecule leading to less forbidden transitions (loosening the constraints of the Laporte rule). The OLEDs based on such complexes are available, but with low efficiency and stability. In order to get efficient devices, there is a need to develop some new Ln complexes with enhanced PLQYs and stabilities. For this purpose, the Ln complexes, both visible and (NIR) emitting, of variant coordination structures based on the various fluorinated/non-fluorinated β-diketones and O/N-donor neutral ligands were synthesized using a one step in situ method. In this method, the β-diketones, base, LnCl₃.nH₂O and neutral ligands were mixed in a 3:3:1:1 M ratio in ethanol that gave air and moisture stable complexes. Further, they were characterized by means of elemental analysis, NMR spectroscopy and single crystal X-ray diffraction. Thereafter, their photophysical properties were studied to select the best complexes for the fabrication of stable and efficient OLEDs. Finally, the OLEDs were fabricated and investigated using these complexes as emitting layers along with other organic layers like NPB,N,N′-Di(1-naphthyl)-N,N′-diphenyl-(1,1′-biphenyl)-4,4′-diamine (hole-transporting layer), BCP, 2,9-Dimethyl-4,7-diphenyl-1,10-phenanthroline (hole-blocker) and Alq3 (electron-transporting layer). The layers were sequentially deposited under high vacuum environment by thermal evaporation onto ITO glass substrates. Moreover, co-deposition techniques were used to improve charge transport in the devices and to avoid quenching phenomena. The devices show strong electroluminescence at 612, 998, 1064 and 1534 nm corresponding to ⁵D₀ →⁷F₂(Eu), ²F₅/₂ → ²F₇/₂ (Yb), ⁴F₃/₂→ ⁴I₉/₂ (Nd) and ⁴I1₃/₂→ ⁴I1₅/₂ (Er). All the devices fabricated show good efficiency as well as stability.

Keywords: electroluminescence, lanthanides, paramagnetic NMR, photoluminescence

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Authors: Zohreh Derikvand

Abstract:

One new 2D metal-organic coordination polymer of Ni(II) namely [Ni2(ndc)2(DMSO)4(H2O)]n, where ndc = naphthalene-1,4-dicarboxylic acid and DMSO= dimethyl sulfoxide has been synthesized and characterized by elemental analysis, spectral (IR, UV-Vis), thermal (TG/DTG) analysis and single crystal X-ray diffraction. Compound 1 possesses a 2D layer structure constructed from dinuclear nickel(II) building blocks in which two crystallographically independent Ni2+ ions are bridged by ndc2– ligands and water molecule. The ndc2– ligands adopt μ3 bridging modes, linking the metal centers into a two-dimensional coordination framework. The two independent NiII cations are surrounded by dimethyl sulfoxide and naphthalene-1,4-dicarboxylate molecules in distorted octahedron geometry. In the crystal structures of 1 there are non-classical hydrogen bonding arrangements and C-H–π stacking interactions. Electrochemical behavior of [Ni2(ndc)2(DMSO)4(H2O)]n, (Ni-NDA) on the surface of carbon nanotube (CNTs) glassy carbon electrode (GCE) was described. The surface structure and composition of the sensor were characterized by scanning electron microscopy (SEM). Oxidation of fructose on the surface of modified electrode was investigated with cyclic voltammetry and electrochemical impedance spectroscopy (EIS) and the results showed that the Ni-NDA/CNTs film displays excellent electrochemical catalytic activities towards fructose oxidation.

Keywords: naphthalene-1, 4-dicarboxylic acid, crystal structure, coordination polymer, electrocatalysis, impedance 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: Iwona Misztalewska-Turkowicz, Agnieszka Z. Wilczewska, Karolina H. Markiewicz

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Carbenes - species which possess neutral carbon atom with two shared and two unshared valence electrons, are known for their high reactivity and instability. Nevertheless, it is also known, that some carbenes i.e. N-heterocyclic carbenes (NHCs), can form stable crystals. The usability of NHCs in organic synthesis was studied. Due to their exceptional properties (high nucleophilicity) NHCs are commonly used as organocatalysts and also as ligands in transition metal complexes. NHC ligands possess better electron-donating properties than phosphines. Moreover, they exhibit lower toxicity. Due to these features, phosphines are frequently replaced by NHC ligands. In this research is discussed the synthesis of five-membered NHCs which are mainly obtained by deprotonation of azolium salts, e.g., imidazolium or imidazolinium salts. Some of them are immobilized on a solid support what leads to formation of heterogeneous, recyclable catalysts. Magnetic nanoparticles (MNPs) are often used as a solid support for catalysts. MNPs can be easily separated from the reaction mixture using an external magnetic field. Due to their low size and high surface to volume ratio, they are a good choice for immobilization of catalysts. Herein is presented synthesis of N-heterocyclic carbene copper complexes directly on the surface of magnetic nanoparticles. Formation of four different catalysts is discussed. They vary in copper oxidation state (Cu(I) and Cu(II)) and structure of NHC ligand. Catalysts were tested in Huisgen reaction, a type of copper catalyzed azide-alkyne cycloaddition (CuAAC) reaction. Huisgen reaction represents one of the few universal and highly efficient reactions in which 1,2,3-triazoles can be obtained. The catalytic activity of all synthesized catalysts was compared with activity of commercially available ones. Different reaction conditions (solvent, temperature, the addition of reductant) and reusability of the obtained catalysts were investigated and are discussed. The project was financially supported by National Science Centre, Poland, grant no. 2016/21/N/ST5/01316. Analyses were performed in Centre of Synthesis and Analyses BioNanoTechno of University of Bialystok. The equipment in the Centre of Synthesis and Analysis BioNanoTechno of University of Bialystok was funded by EU, as a part of the Operational Program Development of Eastern Poland 2007-2013, project: POPW.01.03.00-20-034/09-00 and POPW.01.03.00-20-004/11.

Keywords: N-heterocyclic carbenes, click reaction, magnetic nanoparticles, copper catalysts

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Authors: Juan Antonio Mondragon Sanchez, Ruben Santamaria

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The DNA G-quadruplex is a four-stranded DNA structure conformed by stacked planes of four base paired guanines (G-quartet). The guanine rich DNA sequences are present in many sites of genomic DNA and can potentially lead to the formation of G-quadruplexes, especially at the 3'-terminus of the human telomeric DNA with many TTAGGG repeats. The formation and stabilization of a G-quadruplex by small ligands at the telomeric region can inhibit the telomerase activity. In turn, the ligands can be used to regulate oncogene expression making the G-quadruplex an attractive target for anticancer therapy. Clearly, the G-quadruplex structured in the telomeric DNA is of fundamental importance for rational drug design. In this context, we investigate two G-quadruplex structures, the first follows from the sequence TTAGGG(TTAGGG)3TT (HUT1), and the second from AAAGGG(TTAGGG)3AA (HUT2), both in a K+ solution. We determine the free energy surfaces of the HUT1 and HUT2 structures and investigate their conformations using replica-exchange metadynamics simulations. The carbonyl-carbonyl distances belonging to different guanines residues are selected as the main collective variables to determine the free energy surfaces. The surfaces exhibit two main local minima, compatible with experiments on the conformational transformations of HUT1 and HUT2 under substitution of the K+ ions by the Na+ ions. The conformational transitions are not observed in short MD simulations without the use of the metadynamics approach. The results of this work should be of help to understand the formation and stability of human telomeric G-quadruplex in environments including the presence of K+ and Na+ ions.

Keywords: g-quadruplex, metadynamics, molecular dynamics, replica-exchange

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Authors: Anjani Kumar Tiwari, Neelam Kumari, Anil Mishra

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The 18-kDa translocator protein (TSPO) previously called as peripheral benzodiazepine receptor, is proven biomarker for variety of neuroinflammation. TSPO is tryptophane rich five transmembranal protein found on outer mitochondrial membrane of steroid synthesising and immunomodulatory cells. In case of neuronal damage or inflammation the expression level of TSPO get upregulated as an immunomodulatory response. By utilizing Benzoxazolone as a basic scaffold, series of TSPO ligands have been designed followed by their screening through in silico studies. Synthesis has been planned by employing convergent methodology in six high yielding steps. For the synthesized ligands the ‘in vitro’ assay was performed to determine the binding affinity in term of Ki. On ischemic rat brain, autoradiography studies were also carried to check the specificity and affinity of the designed radiolabelled ligand for TSPO.Screening was performed on the basis of GScore of CADD based schrodinger software. All the modified and better prospective compound were successfully carried out and characterized by spectroscopic techniques (FTIR, NMR and HRMS). In vitro binding assay showed best binding affinity Ki = 6.1+ 0.3 for TSPO over central benzodiazepine receptor (CBR) Ki > 200. ARG studies indicated higher uptake of two analogues on the lesion side compared with that on the non-lesion side of ischemic rat brains. Displacement experiments with unlabelled ligand had minimized the difference in uptake between the two sides which indicates the specificity of the ligand towards TSPO receptor.

Keywords: TSPO, PET, imaging, Acetamidobenzoxazolone

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Authors: Rahul Shrivastava, Manish Tripathi, Mohmmad Yasir, Shailesh Singh

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Life style changes and depletion in atmospheric ozone layer in recent decades lead to increase in skin cancer including both melanoma and nonmelanomas. Natural products which were obtained from different plant species have the potential of anti skin cancer activity. In regard of this, present study focuses the potential effect of Glycosmis pentaphylla against anti skin cancer activity. Different Phytochemical constituents which were present in the roots of Glycosmis pentaphylla were identified and were used as ligands after sketching of their structures with the help of ACD/Chemsketch. These ligands are screened for their anticancer potential with proteins which are involved in skin cancer effects with the help of pyrx software. After performing docking studies, results reveal that Noracronycine secondary metabolite of Glycosmis pentaphylla shows strong affinity of their binding energy with Ribosomal S6 Kinase 2 (2QR8) protein. Ribosomal S6 Kinase 2 (2QR8) has an important role in the cell proliferation and transformation mediated through by N-terminal kinase domain and was induced by the tumour promoters such as epidermal growth factor. It also plays a key role in the neoplastic transformation of human skin cells and in skin cancer growth. Noracronycine interact with THR-493 and MET-496 residue of Ribosomal S6 Kinase 2 protein with binding energy ΔG = -8.68 kcal/mole. Thus on the basis of this study we can say that Noracronycine which present in roots of Glycosmis pentaphylla can be used as lead compound against skin cancer.

Keywords: glycosmis pentaphylla, pyrx, ribosomal s6 kinase, skin cancer

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Authors: Satya Eswari Jujjavarapu, Swast Dhagat

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Contagious diseases enact severe public health problems and have upsetting consequences. The cyclic lipopeptides explained by bacteria Bacillus, Paenibacillus, Pseudomonas, Streptomyces, Serratia, Propionibacterium and fungus Fusarium are very critical in confining the pathogens. As the degree of drug resistance upsurges in unparalleled manner, the perseverance of searching novel cyclic lipopeptides is being professed. The intense study has shown the implication of these bioactive compounds extending beyond antibacterial and antifungal. Lipopeptides, composed of single units of peptide and fatty acyl moiety, show broad spectrum antimicrobial effects. Among the surplus of cyclic lipopeptides, only few have materialized as strong antibiotics. For their functional vigor, polymyxin, daptomycin, surfactin, iturin and bacillomycin have been integrated in mainstream healthcare. In our work daptomycin has been a major part of antimicrobial resource since the past decade. Daptomycin, a cyclic lipopeptide consists of 13-member amino acid with a decanoyl side-chain. This structure of daptomycin confers it the mechanism of action through which it forms pore in the bacterial cell membrane resulting in the death of cell. Daptomycin is produced by Streptococccus roseoporus and acts against Streptococcus pneumonia (PSRP), methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). The PDB structure and ligands of daptomycin are available online. The molecular docking studies of these ligands with the lipopeptides were performed and their docking score and glide energy were recorded.

Keywords: daptomycin, molecular docking, structure-based drug design, lipopeptide

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Authors: Eric Bang

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Interactions between receptors and ligands are crucial for many essential biological processes, including neurotransmission and metabolism. Ligand-receptor analyses that examine cell behavior and interactions often utilize cell type-specific RNA expressions from single-cell RNA sequencing (scRNA-seq) data. Using CellPhoneDB, a public repository consisting of ligands, receptors, and ligand-receptor interactions, the cell-cell interactions were explored in a specific scRNA-seq dataset from kidney tissue and portrayed the results with dot plots and heat maps. Depending on the type of cell, each ligand-receptor pair was aligned with the interacting cell type and calculated the positori probabilities of these associations, with corresponding P values reflecting average expression values between the triads and their significance. Using single-cell data (sample kidney cell references), genes in the dataset were cross-referenced with ones in the existing CellPhoneDB dataset. For example, a gene such as Pleiotrophin (PTN) present in the single-cell data also needed to be present in the CellPhoneDB dataset. Using the single-cell transcriptomics data via slide-seq and reference data, the CellPhoneDB program defines cell types and plots them in different formats, with the two main ones being dot plots and heat map plots. The dot plot displays derived measures of the cell to cell interaction scores and p values. For the dot plot, each row shows a ligand-receptor pair, and each column shows the two interacting cell types. CellPhoneDB defines interactions and interaction levels from the gene expression level, so since the p-value is on a -log10 scale, the larger dots represent more significant interactions. By performing an interaction analysis, a significant interaction was discovered for myeloid and T-cell ligand-receptor pairs, including those between Secreted Phosphoprotein 1 (SPP1) and Fibronectin 1 (FN1), which is consistent with previous findings. It was proposed that an effective protocol would involve a filtration step where cell types would be filtered out, depending on which ligand-receptor pair is activated in that part of the tissue, as well as the incorporation of the CellPhoneDB data in a streamlined workflow pipeline. The filtration step would be in the form of a Python script that expedites the manual process necessary for dataset filtration. Being in Python allows it to be integrated with the CellPhoneDB dataset for future workflow analysis. The manual process involves filtering cell types based on what ligand/receptor pair is activated in kidney cells. One limitation of this would be the fact that some pairings are activated in multiple cells at a time, so the manual manipulation of the data is reflected prior to analysis. Using the filtration script, accurate sorting is incorporated into the CellPhoneDB database rather than waiting until the output is produced and then subsequently applying spatial data. It was envisioned that this would reveal wherein the cell various ligands and receptors are interacting with different cell types, allowing for easier identification of which cells are being impacted and why, for the purpose of disease treatment. The hope is this new computational method utilizing spatially explicit ligand-receptor association data can be used to uncover previously unknown specific interactions within kidney tissue.

Keywords: bioinformatics, Ligands, kidney tissue, receptors, spatial transcriptome

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Authors: Martin Juckel

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Probably no other field of inorganic chemistry has undergone such a rapid development in the past two decades than the low oxidation state chemistry of main group elements. This rapid development has only been possible by the development of new bulky ligands. In case of our research group, super-bulky monodentate amido ligands and β-diketiminate ligands have been used to a great success. We first synthesized the unprecedented magnesium(I) dimer [ᴹᵉˢNacnacMg]₂ (ᴹᵉˢNacnac = [(ᴹᵉˢNCMe)₂CH]-; Mes = mesityl, which has since been used both as reducing agent and also for the synthesis of new metal-magnesium bonds. In case of the zinc bromide precursor [L*ZnBr] (L*=(N(Ar*)(SiPri₃); (Ar* = C₆H₂{C(H)Ph₂}₂Me-2,6,4, the reduction with [ᴹᵉˢNacnacMg]₂ led to such a metal-magnesium bond. This [L*ZnMg(ᴹᵉˢNacnac)] compound can be seen as an ‘inorganic Grignard reagent’, which can be used to transfer the metal fragment onto other functional groups or other metal centers; just like the conventional Grignard reagent. By simple addition of (TBoN)GeCl (TBoN = N(SiMe₃){B(DipNCH)₂) to the aforesaid compound, we were able to transfer the amido-zinc fragment to the Ge center of the germylene starting material and to synthesize the first example of a germanium(II)-zinc bond: [:Ge(TBoN)(ZnL*)]. While these reactions typically led to complex product mixture, [:Ge(TBoN)(ZnL*)] could be isolated as dark blue crystals in a good yield. This new compound shows interesting reactivity towards small molecules, especially dihydrogen gas. This is of special interest as dihydrogen is one of the more difficult small molecules to activate, due to its strong (BDE = 108 kcal/mol) and non-polar bond. In this context, the interaction between H₂ σ-bond with the tetrelylene p-Orbital (LUMO), with concomitant donation of the tetrelylene lone pair (HOMO) into the H₂ σ* orbital are responsible for the activation of dihydrogen gas. Accordingly, the narrower the HOMO-LUMO gap of tertelylene, the more reactivity towards H₂ it typically is. The aim of a narrow HOMO-LUMO gap was reached by transferring electropositive substituents respectively metal substituents with relatively low Pauling electronegativity (zinc: 1.65) onto the Ge center (here: the zinc-amido fragment). In consideration of the unprecedented reactivity of [:Ge(TBoN)(ZnL*)], a computational examination of its frontier orbital energies was undertaken. The energy separation between the HOMO, which has significant Ge lone pair character, and the LUMO, which has predominantly Ge p-orbital character, is narrow (40.8 kcal/mol; cf.∆S-T= 24.8 kcal/mol), and comparable to the HOMO-LUMO gaps calculated for other literature known complexes). The calculated very narrow HOMO-LUMO gap for the [:Ge(TBoN)(ZnL*)] complex is consistent with its high reactivity, and is remarkable considering that it incorporates a π-basic amide ligand, which are known to raise the LUMO of germylenes considerably.

Keywords: activation of dihydrogen gas, narrow HOMO-LUMO gap, first germanium(II)-zinc bond, inorganic Grignard reagent

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Authors: Gajanan M. Sonwane

Abstract:

The computational studies on 2-phenazinamines with their protein targets have been carried out to design compounds with potential anticancer activity. This strategy of designing compounds possessing selectivity over specific tyrosine kinase has been achieved through G-QSAR and molecular docking studies. The objective of this research has been to design newer 2-phenazinamine derivatives as Bcr-Abl tyrosine kinase inhibitors by G-QSAR, molecular docking studies followed by wet-lab studies along with evaluation of their anticancer potential. Computational chemistry was done by using VLife MDS 4.3 and Autodock 4.2 followed by wet-lab experiments for synthesizing 2-phenazinamine derivatives. The chemical structures of ligands in 2D were drawn by employing Chemdraw 2D Ultra 8.0 and were converted into 3D. These were optimized by using a semi-empirical method called MOPAC. The protein structure was retrieved from RCSC protein data bank as a PDB file. The binding interactions of protein and ligands were done by using PYMOL. The molecular properties of the designed compounds were predicted in silico by using Osiris property explorer. The parent compound 2-phenazinamine was synthesized by reduction of 2, 4-dinitro-N-phenyl-benzenamine in the presence of tin chloride followed by cyclization in the presence of nitrobenzene and magnesium sulfate. The derivatization at the amino function of 2-phenazinamine was performed by treating parent compound with various aldehydes in the presence of dicyclohexylcarbodiimide (DCC) and urea to afford 2-(2-chlorophenyl)-3-(phenazine-2-yl) thiazolidine-4-one. Synthesized 39 novel derivatives of 2-phenazinamine and performed antioxidant activity, anti antiproliferative on the bulb of onion and anticancer activity on cell line showing significant competition with marked blockbuster drug imatinib.

Keywords: computer-aided drug design, tyrosin kinases, anticancer, docking

Procedia PDF Downloads 138

Authors: Ayla Roberta Galaco, Juliana Fonseca De Lima, Osvaldo Antonio Serra

Abstract:

Coordination polymers, also known as metal-organic frameworks (MOFs) or lanthanoide organic frameworks (LOFs) have been reported due of their promising applications in gas storage, separation, catalysis, luminescence, magnetism, drug delivery, and so on. As a type of organic–inorganic hybrid materials, the properties of coordination polymers could be chosen by deliberately selecting the organic and inorganic components. LOFs have received considerable attention because of their properties such as porosity, luminescence, and magnetism. Methods such as solvothermal synthesis are important as a strategy to control the structural and morphological properties as well as the composition of the target compounds. In this work the first solvothermal synthesis was employed to obtain the compound [Y0.4,Yb0.4,Er0.2(dmf)(for)(H2O)(tft)], by using terephthalic acid (tft) and oxalic acid, decomposed in formate (for), as ligands; Yttrium, Ytterbium and, Erbium as metal centers, in DMF and water for 4 days under 160 °C. The semi-rigid terephthalic acid (dicarboxylic) coordinates with Ln3+ ions and also is possible to form a polyfunctional bridge. On the other hand, oxalate anion has no high-energy vibrational groups, which benefits the excitation of Yb3+ in upconversion process. It was observed that the compounds with water molecules in the coordination sphere of the lanthanoide ions cause lower crystalline properties and change the structure of the LOF (1D, 2D, 3D). In the FTIR, the bands at 1589 and 1500 cm-1 correspond to the asymmetric stretching vibration of –COO. The band at 1383 cm-1 is assigned to the symmetric stretching vibration of –COO. Single crystal X-ray diffraction study reveals an infinite 3D coordination framework that crystalizes in space group P21/c. The other three products, [TR(chel)(ofd)0,5(H2O)2], where TR= Eu3+, Y3, and Yb3+/Er3+ were obtained by using 1, 2-phenylenedioxydiacetic acid (ofd) and chelidonic acid (chel) as organic ligands. Thermal analysis shows that the lanthanoide organic frameworks do not collapse at temperatures below 250 °C. By the polycrystalline X-ray diffraction patterns (PXRD) it was observed that the compounds with Eu3+, Y3+, and Yb3+/Er3+ ions are isostructural. From PXRD patterns, high crystallinity can be noticed for the complexes. The final products were characterized by single X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), energy dispersive spectroscopy (EDS) and thermogravimetric analysis (TGA). The X-ray diffraction (XRD) is an effective method to investigate crystalline properties of synthesized materials. The solid crystal obtained in the synthesis show peaks at 2θ < 10°, indicating the MOF formation. The chemical composition of LOFs was also confirmed by EDS.

Keywords: isostructural, lanthanoids, lanthanoids organic frameworks (LOFs), metal organic frameworks (MOFs), thermogravimetry, X-Ray diffraction

Procedia PDF Downloads 259

Authors: Mouna Baassi, Mohamed Moussaoui, Hatim Soufi, Sanchaita RajkhowaI, Ashwani Sharma, Subrata Sinha, Said Belaaouad

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Human Immunodeficiency Virus type 1 protease (HIV-1 PR) is one of the most challenging targets of antiretroviral therapy used in the treatment of AIDS-infected people. The performance of protease inhibitors (PIs) is limited by the development of protease mutations that can promote resistance to the treatment. The current study was carried out using statistics and bioinformatics tools. A series of thirty-three compounds with known enzymatic inhibitory activities against HIV-1 protease was used in this paper to build a mathematical model relating the structure to the biological activity. These compounds were designed by software; their descriptors were computed using various tools, such as Gaussian, Chem3D, ChemSketch and MarvinSketch. Computational methods generated the best model based on its statistical parameters. The model’s applicability domain (AD) was elaborated. Furthermore, one compound has been proposed as efficient against HIV-1 protease with comparable biological activity to the existing ones; this drug candidate was evaluated using ADMET properties and Lipinski’s rule. Molecular Docking performed on Wild Type and Mutant Type HIV-1 proteases allowed the investigation of the interaction types displayed between the proteases and the ligands, Darunavir (DRV) and the new drug (ND). Molecular dynamics simulation was also used in order to investigate the complexes’ stability, allowing a comparative study of the performance of both ligands (DRV & ND). Our study suggested that the new molecule showed comparable results to that of Darunavir and may be used for further experimental studies. Our study may also be used as a pipeline to search and design new potential inhibitors of HIV-1 proteases.

Keywords: QSAR, ADMET properties, molecular docking, molecular dynamics simulation.

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Authors: Mahsa Fathollahzadeh

Abstract:

The various nanoparticles employed in drug delivery applications include micelles, liposomes, solid lipid nanoparticles, polymeric nanoparticles, functionalized nanoparticles, nanocrystals, cyclodextrins, dendrimers, and nanotubes. Micelles, composed of amphiphilic block copolymers, can encapsulate hydrophobic molecules, allowing for targeted delivery. Liposomes, vesicular structures made up of phospholipids, can encapsulate both hydrophobic and hydrophilic molecules, providing a flexible platform for delivering therapeutic agents. Solid lipid nanoparticles (SLNs) and nanostructured lipid carriers (NLCs) are designed to improve the stability and bioavailability of lipophilic drugs. Polymeric nanoparticles, such as poly(lactic-co-glycolic acid) (PLGA), are biodegradable and can be engineered to release drugs in a controlled manner. Functionalized nanoparticles, coated with targeting ligands or antibodies, can specifically target diseased cells or tissues. Nanocrystals, engineered to have specific surface properties, can enhance the solubility and bioavailability of poorly soluble drugs. Cyclodextrins, doughnut-shaped molecules with hydrophobic cavities, can be complex with hydrophobic molecules, allowing for improved solubility and bioavailability. Dendrimers, branched polymers with a central core, can be designed to deliver multiple therapeutic agents simultaneously. Nanotubes and metallic nanoparticles, such as gold nanoparticles, offer real-time tracking capabilities and can be used to detect biomolecular interactions. The use of these nanoparticles has revolutionized the field of drug delivery, enabling targeted and controlled release of therapeutic agents, reduced toxicity, and improved patient outcomes.

Keywords: nanotechnology, nanopharmaceuticals, drug-delivery, proteins, ligands, nanoparticles, chemistry

Procedia PDF Downloads 51