Search results for: relative binding affinity

Authors: Christian Fercher, Jiaul Islam, Simon R. Corrie

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Fluorescence-based immunodiagnostics are an emerging field in biosensor development and exhibit several advantages over traditional detection methods. While various affinity biosensors have been developed to generate a fluorescence signal upon sensing varying concentrations of analytes, reagentless, reversible, and continuous monitoring of complex biological samples remains challenging. Here, we aimed to genetically engineer biosensors based on single-chain antibody fragments (scFv) that are site-specifically labeled with environmentally sensitive fluorescent unnatural amino acids (UAA). A rational design approach resulted in quantifiable analyte-dependent changes in peak fluorescence emission wavelength and enabled antigen detection in vitro. Incorporation of a polarity indicator within the topological neighborhood of the antigen-binding interface generated a titratable wavelength blueshift with nanomolar detection limits. In order to ensure continuous analyte monitoring, scFv candidates with fast binding and dissociation kinetics were selected from a genetic library employing a high-throughput phage display and affinity screening approach. Initial rankings were further refined towards rapid dissociation kinetics using bio-layer interferometry (BLI) and surface plasmon resonance (SPR). The most promising candidates were expressed, purified to homogeneity, and tested for their potential to detect biomarkers in a continuous microfluidic-based assay. Variations of dissociation kinetics within an order of magnitude were achieved without compromising the specificity of the antibody fragments. This approach is generally applicable to numerous antibody/antigen combinations and currently awaits integration in a wide range of assay platforms for one-step protein quantification.

Keywords: antibody engineering, biosensor, phage display, unnatural amino acids

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Authors: Mohamad Ammar Ayass, Natalya Griko, Victor Pashkov, Wanying Cao, Kevin Zhu, Jin Zhang, Lina Abi Mosleh

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Respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for coronavirus disease 2019 (COVID-19). Early evidence pointed at the angiotensin-converting enzyme 2 (ACE-2) expressed on the epithelial cells of the lung as the main entry point of SARS-CoV-2 into the cells. The viral entry is mediated by the binding of the Receptor Binding Domain (RBD) of the spike protein that is expressed on the surface of the virus to the ACE-2 receptor. As the number of SARS-CoV-2 variants continues to increase, mutations arising in the RBD of SARS-CoV-2 may lead to the ineffectiveness of RBD targeted neutralizing antibodies. To address this limitation, the objective of this study is to develop a combination of aptamers that target different regions of the RBD, preventing the binding of the spike protein to ACE-2 receptor and subsequent viral entry and replication. A safe and innovative biomedical tool was developed to inhibit viral infection and reduce the harms of COVID-19. In the present study, DNA aptamers were developed against a recombinant trimer S protein using the Systematic Evolution of Ligands by Exponential enrichment (SELEX). Negative selection was introduced at round number 7 to select for aptamers that bind specifically to the RBD domain. A series of 9 aptamers (ADI2010, ADI2011, ADI201L, ADI203L, ADI205L, ADIR68, ADIR74, ADIR80, ADIR83) were selected and characterized with high binding affinity and specificity to the RBD of the spike protein. Aptamers (ADI25, ADI2009, ADI203L) were able to bind and pull down endogenous spike protein expressed on the surface of SARS-CoV-2 virus in COVID-19 positive patient samples and determined by liquid chromatography- tandem mass spectrometry analysis (LC-MS/MS). LC-MS/MS data confirmed that aptamers can bind to the RBD of the spike protein. Furthermore, results indicated that the combination of the 9 best aptamers inhibited the binding of the purified trimer spike protein to the ACE-2 receptor found on the surface of Vero E6 cells. In the same experiment, the combined aptamers displayed a better neutralizing effect than antibodies. The data suggests that the selected aptamers could be used in therapy to neutralize the effect of the SARS-CoV-2 virus by inhibiting the interaction between the RBD and ACE-2 receptor, preventing viral entry into target cells and therefore blocking viral replication.

Keywords: aptamer, ACE-2 receptor, binding inhibitor, COVID-19, spike protein, SARS-CoV-2, treatment

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Authors: A. Jamsheera, F. Arjmand, D. K. Mohapatra

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Small molecules binding to specific sites along DNA molecule are considered as potential chemotherapeutic agents. Their role as mediators of key biological functions and their unique intrinsic properties make them particularly attractive therapeutic agents. Keeping in view, novel dipeptide complexes Cu(II)-Val-Pro (1), Zn(II)-Val-Pro (2), Cu(II)-Ala-Pro (3) and Zn(II)-Ala-Pro (4) were synthesized and thoroughly characterized using different spectroscopic techniques including elemental analyses, IR, NMR, ESI–MS and molar conductance measurements. The solution stability study carried out by UV–vis absorption titration over a broad range of pH proved the stability of the complexes in solution. In vitro DNA binding studies of complexes 1–4 carried out employing absorption, fluorescence, circular dichroism and viscometric studies revealed the binding of complexes to DNA via groove binding. UV–vis titrations of 1–4 with mononucleotides of interest viz., 5´-GMP and 5´-TMP were also carried out. The DNA cleavage activity of the complexes 1 and 2 were ascertained by gel electrophoresis assay which revealed that the complexes are good DNA cleavage agents and the cleavage mechanism involved a hydrolytic pathway. Furthermore, in vitro antitumor activity of complex 1 was screened against human cancer cell lines of different histological origin.

Keywords: dipeptide Cu(II) and Zn(II) complexes, DNA binding profile, pBR322 DNA cleavage, in vitro anticancer activity

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Authors: Ho-Wa Li, Sai-Wing Tsang

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The excitonic effect in organic semiconductors plays a key role in determining the electronic devices performance. Strong exciton binding energy has been regarded as the detrimental factor limiting the further improvement in organic photovoltaic cells. To the best of our knowledge, only limited reported can be found in measuring the exciton binding energy in organic photovoltaic materials. Conventional sophisticated approach using photoemission spectroscopy (UPS and IPES) would limit the wide access of the investigation. Here, we demonstrate a facile approach to study the electrical and optical quantum efficiencies of a series of conjugated photovoltaic polymer, fullerene and non-fullerene materials. Quantitative values of the exciton binding energy in those prototypical materials were obtained with concise photovoltaic device structure. And the extracted binding energies have excellent agreement with those determined by the conventional photoemission technique. More importantly, our findings can provide valuable information on the excitonic dissociation in the first excited state. Particularly, we find that the high binding energy of some non-fullerene acceptors limits the combination of polymer acceptors for efficiency exciton dissociation. The results bring insight into the engineering of excitonic effect for the development of efficient organic photovoltaic cells.

Keywords: organic photovoltaics, quantum efficiency, exciton binding energy, device physics

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Authors: Yaxuan Wang

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It has long been a mystery that why the Mongolian possessive suffix, which is constrained by Condition A of binding theory, has the ability to probe a potential antecedent outside of its binding domain. This squib argues that binding theory alone is not sufficient to explain the linguistic facts and proposes an analysis adopting the Agree operation. The current analysis correctly predicts all the possible and impossible structures, with an additional hypothesis that Mongolian possessive suffixes serve as an antecedent for PROs in adjunct. The findings thus provide insights into how Agree operates in Mongolian language.

Keywords: syntax, Mongolian, agreement, possessive particles

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Authors: Moez Elsaadani, Noel Durand, Brice Sorli, Didier Montet

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Governments and international instances are trying to improve the food safety system to prevent, reduce or avoid the increase of food borne diseases. This food risk is one of the major concerns for the humanity. The contamination by mycotoxins is a threat to the health and life of humans and animals. One of the most common mycotoxin contaminating feed and foodstuffs is Ochratoxin A (OTA), which is a secondary metabolite, produced by Aspergillus and Penicillium strains. OTA has a chronic toxic effect and proved to be mutagenic, nephrotoxic, teratogenic, immunosuppressive, and carcinogenic. On the other side, because of their high stability, specificity, affinity, and their easy chemical synthesis, aptamer based methods are applied to OTA biosensing as alternative to traditional analytical technique. In this work, five aptamers have been tested to confirm qualitatively and quantitatively their binding with OTA. In the same time, three different analytical methods were tested and compared based on their ability to detect and quantify the OTA. The best protocol that was established to quantify free OTA from linked OTA involved an ultrafiltration method in green coffee solution with. OTA was quantified by HPLC-FLD to calculate the binding percentage of all five aptamers. One aptamer (The most effective with 87% binding with OTA) has been selected to be our biorecognition element to study its electrical response (variation of electrical properties) in the presence of OTA in order to be able to make a pairing with a radio frequency identification (RFID). This device, which is characterized by its low cost, speed, and a simple wireless information transmission, will implement the knowledge on the mycotoxins molecular sensors (aptamers), an electronic device that will link the information, the quantification and make it available to operators.

Keywords: aptamer, aptasensor, detection, Ochratoxin A

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Authors: Tivani Phosa Mashamba-Thompson, Mahmoud E. S. Soliman

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To date, the cause of neurodegeneration is not well understood and diseases that stem from neurodegeneration currently have no known cures. Cathepsin B (CB) enzyme is known to be involved in the production of peptide neurotransmitters and toxic peptides in neurodegenerative diseases (NDs). CA-074Me is a membrane-permeable irreversible selective cathepsin B (CB) inhibitor as confirmed by in vivo studies. Due to the lack of the crystal structure, the binding mode of CA-074Me with the human CB at molecular level has not been previously reported. The main aim of this study is to gain an insight into the binding mode of CB CA-074Me to human CB using various computational tools. Herein, molecular dynamics simulations, binding free energy calculations and per-residue energy decomposition analysis were employed to accomplish the aim of the study. Another objective was to identify novel CB inhibitors based on the structure of CA-074Me using fragment based drug design using scaffold hoping drug design approach. Results showed that two of the designed ligands (hit 1 and hit 2) were found to have better binding affinities than the prototype inhibitor, CA-074Me, by ~2-3 kcal/mol. Per-residue energy decomposition showed that amino acid residues Cys29, Gly196, His197 and Val174 contributed the most towards the binding. The Van der Waals binding forces were found to be the major component of the binding interactions. The findings of this study should assist medicinal chemist towards the design of potential irreversible CB inhibitors.

Keywords: cathepsin B, scaffold hopping, docking, molecular dynamics, binding-free energy, neurodegerative diseases

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Authors: Lavinia Ruta, Ileana Farcasanu

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The yeast surface display (YSD) technique enables the expression of proteins on yeast cell surfaces, facilitating the identification and isolation of proteins with targeted binding properties, such as nanobodies. Nanobodies, derived from camelid species, are single-domain antibody fragments renowned for their high affinity and specificity towards target proteins, making them valuable in research and potentially in therapeutics. Their advantages include a compact size (~15 kDa), robust stability, and the ability to target challenging epitopes. The project endeavors to establish and validate a platform for producing Green Fluorescent Protein (GFP) and mCherry nanobodies using the yeast surface display method. mCherry, a prevalent red fluorescent protein sourced from coral species, is commonly utilized as a genetic marker in biological studies due to its vibrant red fluorescence. The GFP-nanobody, a single variable domain of heavy-chain antibodies (VHH), exhibits specific binding to GFP, offering a potent means for isolating and engineering fluorescent protein fusions across various biological research domains. Both GFP and mCherry nanobodies find specific utility in cellular imaging and protein analysis applications.

Keywords: YSD, nanobodies, GFP, Saccharomyces cerevisiae

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Authors: Asma Zaib, Saeed Khan, Ayaz Ahmed Noonari, Sehrish Bint-e-Mohsin

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Breast cancer is the most common cancer among females worldwide and is estimated that more than 450,000 deaths are reported each year. It accounts for about 14% of all female cancer deaths. Angiogenesis plays an essential role in Breast cancer development, invasion, and metastasis. Breast cancer predominantly begins in luminal epithelial cells lining the normal breast ducts. Breast carcinoma likely requires coordinated efforts of both increased proliferation and increased motility to progress to metastatic stages.Resveratrol: a natural stilbenoid, has anti-inflammatory and anticancer effects that inhibits proliferation of variety of human cancer cell lines, including breast, prostate, stomach, colon, pancreatic, and thyroid cancers.The objective of this study is:To investigate anti-neoangiogenesis effects of Resveratrol in breast cancer and to analyze inhibitory effects of resveratrol on aromatase, Erα, HER2/neu, and VEGFR.Docking is the computational determination of binding affinity between molecule (protein structure and ligand).We performed molecular docking using Swiss-Dock and to determine docking effects of (1) Resveratrol with Aromatase, (2) Resveratrol with ERα (3) Resveratrol with HER2/neu and (4) Resveratrol with VEGFR2.Docking results of resveratrol determined inhibitory effects on aromatase with binding energy of -7.28 kcal/mol which shows anticancerous effects on estrogen dependent breast tumors. Resveratrol also show inhibitory effects on ERα and HER2/new with binging energy -8.02, and -6.74 respectively; which revealed anti-cytoproliferative effects upon breast cancer. On the other hand resveratrol v/s VEGFR showed potential inhibitory effects on neo-angiogenesis with binding energy -7.68 kcal/mol, angiogenesis is the important phenomenon that promote tumor development and metastasis. Resveratrol is an anti-breast cancer agent conformed by in silico studies, it has been identified that resveratrol can inhibit breast cancer cells proliferation by acting as competitive inhibitor of aromatase, ERα and HER2 neo, while neo-angiogemesis is restricted by binding to VEGFR which authenticates the anti-carcinogenic effects of resveratrol against breast cancer.

Keywords: angiogenesis, anti-cytoproliferative, molecular docking, resveratrol

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Authors: U. L. Fulco, E. L. Albuquerque, José X. Lima Neto, L. R. Da Silva

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The binding of the nonsteroidal anti-inflammatory drug ibuprofen (IBU) to human serum albumin (HSA) is investigated using density functional theory (DFT) calculations within a fragmentation strategy. Crystallographic data for the IBU–HSA supramolecular complex shows that the ligand is confined to a large cavity at the subdomain IIIA and at the interface between the subdomains IIA and IIB, whose binding sites are FA3/FA4 and FA6, respectively. The interaction energy between the IBU molecule and each amino acid residue of these HSA binding pockets was calculated using the Molecular Fractionation with Conjugate Caps (MFCC) approach employing a dispersion corrected exchange–correlation functional. Our investigation shows that the total interaction energy of IBU bound to HSA at binding sites of the fatty acids FA3/FA4 (FA6) converges only for a pocket radius of at least 8.5 °A, mainly due to the action of residues Arg410, Lys414 and Ser489 (Lys351, Ser480 and Leu481) and residues in nonhydrophobic domains, namely Ile388, Phe395, Phe403, Leu407, Leu430, Val433, and Leu453 (Phe206, Ala210, Ala213, and Leu327), which is unusual. Our simulations are valuable for a better understanding of the binding mechanism of IBU to albumin and can lead to the rational design and the development of novel IBU-derived drugs with improved potency.

Keywords: ibuprofen, human serum albumin, density functional theory, binding energies

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Authors: Tanushree Jaitly, Shailendra Gupta, Leila Taher, Gerold Schuler, Julio Vera

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Genomics-based personalized medicine is a promising approach to fight aggressive tumors based on patient's specific tumor mutation and expression profiles. A remarkable case is, dendritic cell-based immunotherapy, in which tumor epitopes targeting patient's specific mutations are used to design a vaccine that helps in stimulating cytotoxic T cell mediated anticancer immunity. Here we present a computational pipeline for epitope-based personalized cancer vaccines using patient-specific haplotype and cancer mutation profiles. In the workflow proposed, we analyze Whole Exome Sequencing and RNA Sequencing patient data to detect patient-specific mutations and their expression level. Epitopes including the tumor mutations are computationally predicted using patient's haplotype and filtered based on their expression level, binding affinity, and immunogenicity. We calculate binding energy for each filtered major histocompatibility complex (MHC)-peptide complex using docking studies, and use this feature to select good epitope candidates further.

Keywords: cancer immunotherapy, epitope prediction, NGS data, personalized medicine

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Authors: Mariam Mojally, Randa Abdou, Wisal Bokhari, Sultan Sab, Mohammed Dawoud, Amjad Albohy

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Secondary metabolites produced by endophytes are an excellent source of biologically active compounds. In our current study, we evaluated terezine E and 14-hydroxyterezine D for binding to the active site of histone deacetylase (PDB ID: 4CBT) and matrix metalloproteinase 9 (PDB ID: 4H3X) by molecular docking using AutoDock Vina software after having tested their cytotoxic activities on three cell lines (human ductal breast epithelial tumor cells (T47D)-HCC1937), human hepatocarcinoma cell line (HepG2)-HB8065), and human colorectal carcinoma cells (HCT-116)-TCP1006, purchased from ATCC, USA)). Additionally, their antimicrobial activities were investigated, and their minimum inhibitory concentration (MIC) values were determined against P. notatum and S. aureus by the broth microdilution method. Higher cytotoxicity was observed for terezine E against all tested cell lines compared to 14-hydroxyterezine D. Molecular docking results supported the high cytotoxicity of terezine E and showed higher binding affinity with 4CBT with an energy score of 9 kcal/mol. Terezine E showed higher antibacterial and antifungal activities than 14-hydroxyrerezine D: MIC values were 15.45 and 21.73 mg/mL against S. aureus and 8.61 and 11.54 mg/mL against P. notatum, respectively

Keywords: Terezine E, 14-Hydroxyterezine D, cytotoxicity, antimicrobial activity, molecular docking

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Authors: William Thomas Worster

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Diplomatic assurances issued by states declaring that they will not mistreat individuals returned to them occupy a strange middle ground between being legal and non-legal obligations. States assert that they are non-binding, yet at other times that they are binding. However, this assertion may not be the end of the discussion. The International Court of Justice and other tribunals have concluded that similar instruments were binding, states have disagreed that certain similar instruments were binding, and the Vienna Convention on the Law of Treaties and its travaux prépératoires do not appear to contemplate non-binding instruments. This paper is a case study of diplomatic assurances but, by necessity, touches on the delicate question of whether certain texts are treaties, promises, or non-binding political statements. International law, and law in general, requires a binary approach to obligation. All communications must be binding or not, even if the fit is not precise. Through this study, we will find that some of the obligations in certain assurances can be understood as legal and some not. We will attempt to state the current methodology for determining which obligations are legal under the law of treaties and law on binding unilateral promises. The paper begins with some background of the legal environment of diplomatic assurances and their use in cases of expulsion. The paper then turns to discuss the legal nature of diplomatic assurances, proceeding to address various possibilities for legal value as treaties and as binding unilateral statements. This paper will not examine the legal value of diplomatic assurances solely under customary international law other than the way in which customary international law might further refine the treaty definition. In order to identify whether any assurances are contained in legal acts, this study identifies a pool of relevant assurances and qualitatively analyzes whether any of those are contained in treaties or binding unilateral statements. To the author’s best knowledge, this study is the first large-scale, qualitative qualitative analysis of assurances as a group of instruments that accounts for their heterogenous nature. It is also the first study to identify the indicators of whether an instrument is a treaty or promise.

Keywords: diplomatic assurances, deportation, extradition, expulsion, non-refoulement, torture, persecution, death penalty, human rights, memorandum of understanding, promises, secret, monitoring, compliance, enforcement

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Authors: F. Ambreen, A.Naheed

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Osteoarthritis (OA) is a degenerative disorder affecting millions of people worldwide. Nitric oxide (NO) was found to play a catabolic role in the development of osteoarthritis. It is a toxic free radical gas generated during the metabolism of L-arginine by the enzyme Nitric oxide synthase (NOS). Inducible Nitric Oxide Synthase (iNOS) is one of the isoform of NOS, and its overexpression leads to the excessive formation of NO that results in pathophysiological joint conditions. Several synthetic anti-inflammatory drugs and inhibitors are present to date, but all showed side effects and complications. Therefore, the pursuit of natural disease-modifying drugs remains a top priority. Curcumin is an active component of turmeric, and the past few decades have witnessed intense research devoted to the antioxidant and anti-inflammatory properties of curcumin. The present study focused on curcumin and its derivatives in the search for new iNOS inhibitors for the treatment of osteoarthritis. We conducted a molecular docking study on curcumin and its four derivatives; cyclocurcumin, tetrahydrocurcumin, demethoxycurcumin and curcumin monoglucoside with iNOS using CLC Drug discovery work bench 3.02. We selected two co-crystallized ligands for this study; tetrahydrobiopterin and N-omega-propyl-L-arginine present in complex with the enzyme iNOS. Results showed the best binding affinity of N-omega-propyl-L-arginine with cyclocurcumin and curcumin monoglucoside that exhibit binding energies of -65.2 kcal/mol and -68 kcal/mol respectively. Whereas with tetrahydrobiopterin, best binding scores of -64.7 kcal/mol and -62.2 kcal/mol were found with tetrahydrocurcumin and demethoxycurcumin respectively. This information could open doors of research for the designing of novel drugs using herbs such as curcumin for the treatment of inflammatory joint diseases.

Keywords: curcumin, iNOS, molecular docking, osteoarthritis

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Authors: Son Nguyen, Thanh Van, Ly Le

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Ca2+ - dependent calmodulin kinase IIa (CaMKIIa) has recently been found to associate with protein tau missorting and polymerization in Alzheimer’s Disease (AD). However, there has yet inhibitors targeting CaMKIIa to investigate the correlation between CaMKIIa activity and protein tau polymer formation. Combining virtual screening and our statistics in binding contribution scoring function (BCSF), we rationally identified potential compounds that bind to specific CaMKIIa active site and specificity-affinity distribution of the ligand within the active site. Using molecular dynamics simulation, we identified structural stability of CaMKIIa and potent inhibitors, and site-directed bonding, separating non-specific and specific molecular interaction features. Despite of variation in confirmation of simulation time, interactions of the potent inhibitors were found to be strongly associated with the unique chemical features extracted from molecular binding poses. In addition, competitive inhibitors within CaMKIIa showed an important molecular recognition pattern toward specific ligand features. Our approach combining virtual screening with BCSF may provide an universally applicable method for precise identification in the discovery of compounds.

Keywords: Alzheimer’s disease, Ca 2+ -dependent calmodulin kinase IIa, protein tau, molecular docking

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Authors: Katie Kilgour, Brendan Turner, Carly Catella, Michael Daniele, Stefano Menegatti

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In vivo, the extracellular matrix (ECM) provides biochemical and mechanical properties that are instructional to resident cells to form complex tissues with characteristics to develop and support vascular networks. In vitro, the development of vascular networks can be guided by biochemical patterning of substrates via spatial distribution and display of peptides and growth factors to prompt cell adhesion, differentiation, and proliferation. We have developed a technique utilizing peptide ligands that specifically bind vascular endothelial growth factor (VEGF), erythropoietin (EPO), or angiopoietin-1 (ANG1) to spatiotemporally distribute growth factors to cells. This allows for the controlled release of each growth factor, ultimately enhancing the formation of a vascular network. Our engineered tissue constructs (ETCs) are fabricated out of gelatin methacryloyl (GelMA), which is an ideal substrate for tailored stiffness and bio-functionality, and covalently patterned with growth factor specific peptides. These peptides mimic growth factor receptors, facilitating the non-covalent binding of the growth factors to the ETC, allowing for facile uptake by the cells. We have demonstrated in the absence of cells the binding affinity of VEGF, EPO, and ANG1 to their respective peptides and the ability for each to be patterned onto a GelMA substrate. The ability to organize growth factors on an ETC provides different functionality to develop organized vascular networks. Our results demonstrated a method to incorporate biochemical cues into ETCs that enable spatial and temporal control of growth factors. Future efforts will investigate the cellular response by evaluating gene expression, quantifying angiogenic activity, and measuring the speed of growth factor consumption.

Keywords: growth factor, hydrogel, peptide, angiogenesis, vascular, patterning

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Authors: Meltem Betül Sağlam, Halil İbrahim Güler, Aykut Sağlam

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In this work, phthalocyanine compounds containing α-naphtholbenzeinunits have been synthesized. Mutagenicity and DNA binding properties of the compounds were investigated by Salmonella/Microsome Assay and spectrophotometer. According to the results of the preliminary range finding tests, the compounds gave no toxic effect to all tester strain S. typhimurium TA98 and TA100 at doses of 500, 1100, 350, 500 and 750 µg/plate in the presence and absence of S9, respectively. This study showed that all compounds exhibited efficient DNA-binding activity. In conclusion, these non-toxic compounds may be used as effective DNA dyes for molecular biology studies.

Keywords: dye, mutagenicity, phthalocyanine, toxicity

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Authors: Sakshi Piplani, Ajit Kumar

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Valproic acid (VPA) is the first synthetic therapeutic agent used to treat epileptic disorders, which account for affecting nearly 1% world population. Teratogenicity caused by VPA has prompted the search for next generation drug with better efficacy and lower side effects. Recent studies have posed HDAC8 as direct target of VPA that causes the teratogenic effect in foetus. We have employed molecular dynamics (MD) and docking simulations to understand the binding mode of VPA and their analogues onto HDAC8. A total of twenty 3D-structures of human HDAC8 isoforms were selected using BLAST-P search against PDB. Multiple sequence alignment was carried out using ClustalW and PDB-3F07 having least missing and mutated regions was selected for study. The missing residues of loop region were constructed using MODELLER and energy was minimized. A set of 216 structural analogues (>90% identity) of VPA were obtained from Pubchem and ZINC database and their energy was optimized with Chemsketch software using 3-D CHARMM-type force field. Four major neurotransmitters (GABAt, SSADH, α-KGDH, GAD) involved in anticonvulsant activity were docked with VPA and its analogues. Out of 216 analogues, 75 were selected on the basis of lower binding energy and inhibition constant as compared to VPA, thus predicted to have anti-convulsant activity. Selected hHDAC8 structure was then subjected to MD Simulation using licenced version YASARA with AMBER99SB force field. The structure was solvated in rectangular box of TIP3P. The simulation was carried out with periodic boundary conditions and electrostatic interactions and treated with Particle mesh Ewald algorithm. pH of system was set to 7.4, temperature 323K and pressure 1atm respectively. Simulation snapshots were stored every 25ps. The MD simulation was carried out for 20ns and pdb file of HDAC8 structure was saved every 2ns. The structures were analysed using castP and UCSF Chimera and most stabilized structure (20ns) was used for docking study. Molecular docking of 75 selected VPA-analogues with PDB-3F07 was performed using AUTODOCK4.2.6. Lamarckian Genetic Algorithm was used to generate conformations of docked ligand and structure. The docking study revealed that VPA and its analogues have more affinity towards ‘hydrophobic active site channel’, due to its hydrophobic properties and allows VPA and their analogues to take part in van der Waal interactions with TYR24, HIS42, VAL41, TYR20, SER138, TRP137 while TRP137 and SER138 showed hydrogen bonding interaction with VPA-analogues. 14 analogues showed better binding affinity than VPA. ADMET SAR server was used to predict the ADMET properties of selected VPA analogues for predicting their druggability. On the basis of ADMET screening, 09 molecules were selected and are being used for in-vivo evaluation using Danio rerio model.

Keywords: HDAC8, docking, molecular dynamics simulation, valproic acid

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Authors: Sibghat Mansoor Rana, Muhammad Islam, Hamid Saeed, Hummera Rafique, Muhammad Majid, Muhammad Tahir Aqeel, Fariha Imtiaz, Zaman Ashraf

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The 1,3,4-oxadiazole derivatives Ox-6a-f have been synthesized by incorporating flur- biprofen moiety with the aim to explore the potential of target molecules to decrease the oxidative stress. The title compounds Ox-6a-f were prepared by simple reactions in which a flurbiprofen –COOH group was esterified with methanol in an acid-catalyzed medium, which was then reacted with hydrazine to afford the corresponding hydrazide. The acid hydrazide was then cyclized into 1,3,4-oxadiazole-2-thiol by reacting with CS2 in the presence of KOH. The title compounds Ox-6a-f were synthesized by the reaction of an –SH group with various alkyl/aryl chlorides, which involves an S-alkylation reaction. The structures of the synthesized Ox-6a-f derivatives were ascer- tained by spectroscopic data. The in silico molecular docking was performed against target proteins cyclooxygenase-2 COX-2 (PDBID 5KIR) and cyclooxygenase-1 COX-1 (PDBID 6Y3C) to determine the binding affinity of the synthesized compounds with these structures. It has been inferred that most of the synthesized compounds bind well with an active binding site of 5KIR compared to 6Y3C, and especially compound Ox-6f showed excellent binding affinity (7.70 kcal/mol) among all synthesized compounds Ox-6a-f. The molecular dynamic (MD) simulation has also been performed to check the stability of docking complexes of ligands with COX-2 by determining their root mean square deviation and root mean square fluctuation. Little fluctuation was observed in case of Ox-6f, which forms the most stable complex with COX-2. The comprehensive antioxidant potential of the synthesized compounds has been evaluated by determining their free radical scavenging activity, including DPPH, OH, nitric oxide (NO), and iron chelation assay. The derivative Ox-6f showed promising results with 80.23% radical scavenging potential at a dose of 100 μg/mL while ascorbic acid exhibited 87.72% inhibition at the same dose. The anti-inflammatory activity of the final products has also been performed, and inflammatory markers were assayed, such as a thiobarbituric acid-reducing substance, nitric oxide, interleukin-6 (IL-6), and COX-2. The derivatives Ox-6d and Ox-6f displayed higher anti-inflammatory activity, exhibiting 70.56% and 74.16% activity, respectively. The results were compared with standard ibuprofen, which showed 84.31% activity at the same dose, 200 μg/mL. The anti-inflammatory potential has been performed by following the carrageen-induced hind paw edema model, and results showed that derivative Ox-6f exhibited 79.83% reduction in edema volume compared to standard ibuprofen, which reduced 84.31% edema volume. As dry lab and wet lab results confirm each other, it has been deduced that derivative Ox-6f may serve as the lead structure to design potent compounds to address oxidative stress.

Keywords: synthetic chemistry, pharmaceutical chemistry, oxadiazole derivatives, anti-inflammatory, anti-cancer compounds

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Authors: Mala Nath, Nagamani Kompelli, Partha Roy, Snehasish Das

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Two new metal-based anticancer chemotherapeutic agents, [(Ph2Sn)2(HGuO)2(phen)Cl2] 1 and [(Ph3Sn)(HGuO)(phen)]- Cl.CH3OH.H2O 2, were designed, prepared and characterized by analytical and spectral (IR, ESI-Mass, 1H, 13C and 119Sn NMR) techniques. The proposed geometry of Sn(IV) in 1 and 2 is distorted octahedral and distorted trigonal-bipyramidal, respectively. Both 1 and 2 exhibit potential cytotoxicity in vitro against MCF-7, HepG-2 and DU-145 cell lines. The intrinsic binding constant (Kb) values of 1 (2.33 × 105 M-1) and 2 (2.46 × 105 M-1) evaluated from UV-Visible absorption studies suggest non-classical electrostatic mode of interaction via phosphate backbone of DNA double helix. The Stern-Volmer quenching constant (Ksv) of 1 (9.74 × 105 M-1) and 2 (2.9 × 106 M-1) determined by fluorescence studies suggests the groove binding and intercalation mode for 1 and 2, respectively. Effective cleavage of pBR322 DNA is induced by 1. Their interaction with DNA of cancer cells may account for potency.

Keywords: anticancer agents, DNA binding studies, NMR spectroscopy, organotin

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Authors: M. A. Lahmer, K. Guergouri

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The ferromagnetic properties of carbon-doped ZnO (ZnO:CO) and hydrogenated carbon-doped ZnO (ZnO:CO+H) are investigated using the density functional tight binding (DFTB) method. Our results reveal that CO-doped ZnO is a ferromagnetic material with a magnetic moment of 1.3 μB per carbon atom. The presence of hydrogen in the material in the form of CO-H complex decreases the total magnetism of the material without suppressing ferromagnetism. However, the system in this case becomes quickly antiferromagnetic when the C-C separation distance was increased.

Keywords: ZnO, carbon, hydrogen, ferromagnetism, density functional tight binding

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Authors: Boukli Hacene Faiza, Soufi Wassila, Ghalem Said

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The oral antidiabetics drugs such as alpha glucosidase inhibitors present undesirable effects like acarbose. Flavonoids are class of molecules widely distributed in plants, for this reason we are interested in our work to study the inhibition in silico of alpha glucosidase by natural ligands ( flavonoids analogues) using molecular modeling methods using MOE (Molecular Operating Environment) software to predict their interaction with this enzyme with score energy, ADME /T tests and druglikeness properties experiments. Two flavonoids Beicalein and Apigenin have high binding affinity with alpha glucosidase with lower IC50 supposed potent inhibitors.

Keywords: alpha glucosidase, flavonoides analogues, drug research, molecular modeling

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Authors: R. Chanajaree, D. Luanwiset, K. Pongpratea

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Dye removal is an environmental concern because the textile industries have been increasing by world population and industrialization. Adsorption is the technique to find adsorbents to remove dyes from wastewater. This method is low-cost and effective for dye removal. This work tries to develop effective adsorbents using the computational approach because it will be able to predict the possibility of the adsorbents for specific dyes in terms of binding free energies. The computational approach is faster and cheaper than the experimental approach in case of finding the best adsorbents. All starting structures of dyes and adsorbents are optimized by quantum calculation. The complexes between dyes and adsorbents are generated by the docking method. The obtained binding free energies from docking are compared to binding free energies from the experimental data. The calculated energies can be ranked as same as the experimental results. In addition, this work also shows the possible orientation of the complexes. This work used two experimental groups of the complexes of the dyes and adsorbents. In the first group, there are chitosan (adsorbent) and two dyes (reactive red (RR) and direct sun yellow (DY)). In the second group, there are poly(1,2-epoxy-3-phenoxy) propane (PEPP), which is the adsorbent, and 2 dyes of bromocresol green (BCG) and alizarin yellow (AY).

Keywords: dyes removal, binding free energies, quantum calculation, docking

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Authors: Jongwoo Lee, Dae-Eun Kang, Sang-Young Park

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This study presents a precise relative navigational method for satellites flying in formation using laser-based intermittent measurement data. The measurement data for the relative navigation between two satellites consist of a relative distance measured by a laser instrument and relative attitude angles measured by attitude determination. The relative navigation solutions are estimated by both the Extended Kalman filter (EKF) and unscented Kalman filter (UKF). The solutions estimated by the EKF may become inaccurate or even diverge as measurement outage time gets longer because the EKF utilizes a linearization approach. However, this study shows that the UKF with the appropriate scaling parameters provides a stable and accurate relative navigation solutions despite the long measurement outage time and large initial error as compared to the relative navigation solutions of the EKF. Various navigation results have been analyzed by adjusting the scaling parameters of the UKF.

Keywords: satellite relative navigation, laser-based measurement, intermittent measurement, unscented Kalman filter

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Authors: Khwaja Naweed Seddiqi, Shigeo Honma

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Relative permeability is the important parameter controlling the immiscible displacement of multiphase fluids flow in porous medium. The relative permeability for immiscible displacement of two-phase fluids flow (oil and water) in porous medium has been measured in this paper. As a result of the experiment, irreducible water saturation, Swi, residual oil saturation, Sor, and relative permeability curves for Kerosene, Heavy oil and Lubricant oil were determined successfully.

Keywords: relative permeability, two-phase flow, immiscible displacement, porous medium

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Authors: Liang Ming Zhong, Yu Zhong, Wen Zhong, Fei Fei Yin

Abstract:

Trinary affinity is a description of existence: every object exists as it is known and spoken of, in a system of 2 differences (denoted dif1, dif₂) and 1 similarity (Sim), equivalently expressed as dif₁ / Sim / dif₂ and kn / 0 / tkn (kn = the known, tkn = the 'to be known', 0 = the zero point of knowing). They are mathematically verified and illustrated in this paper by the arrangement of all integers onto 3 columns, where each number exists as a difference in relation to another number as another difference, and the 2 difs as arbitrated by a third number as the Sim, resulting in a trinary affinity or trinity of 3 numbers, of which one is the known, the other the 'to be known', and the third the zero (0) from which both the kn and tkn are measured and specified. Consequently, any number is horizontally specified either as 3n, or as '3n – 1' or '3n + 1', and vertically as 'Cn + c', so that any number seems to occur at the intersection of its X and Y axes and represented by its X and Y coordinates, as any point on Earth’s surface by its latitude and longitude. Technically, i) primes are viewed and treated as progenitors, and composites as descending from them, forming families of composites, each capable of being measured and specified from its own zero called in this paper the realistic zero (denoted 0r, as contrasted to the mathematic zero, 0m), which corresponds to the constant c, and the nature of which separates the composite and prime numbers, and ii) any number is considered as having a magnitude as well as a position, so that a number is verified as a prime first by referring to its descriptive formula and then by making sure that no composite number can possibly occur on its position, by dividing it with factors provided by the composite number formulas. The paper consists of 3 parts: 1) a brief explanation of the trinary affinity of things, 2) the 8 formulas that represent ALL the primes, and 3) families of composite numbers, each represented by a formula. A composite number family is described as 3n + f₁‧f₂. Since there are an infinitely large number of composite number families, to verify the primality of a great probable prime, we have to have it divided with several or many a f₁ from a range of composite number formulas, a procedure that is as laborious as it is the surest way to verifying a great number’s primality. (So, it is possible to substitute planned division for trial division.)

Keywords: trinary affinity, difference, similarity, realistic zero

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Authors: Nurudeen Afolami Ayeni, Kasali Adewale Bello

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Study of the effect of dye-resin complexation on the degree of dye absorption were carried out using Procion Blue MX-R to dye cotton fabric in the presence hexamethylol melamine (MR6) and its phosphate derivative (MPR4) for resination. The highest degree of dye exhaustion was obtained at 400C for 1 hour with the resinated fabric showing more affinity for the dye than the ordinary fibre. Improved fastness properties was recorded which show a relatively higher stability of dye-resin complex formed in the fibre.

Keywords: affinity, cotton, dyeing, reactive dye, resination

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Authors: Helio Arthur Reis Irigaray, Fabricio Stocker

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This study aims to discover the extent to which affinity groups effectively act to combat inequalities, promote diversity, and contribute to the inclusion of non-hegemonic groups in the work environment. To this end, we have built empirical research, in which we interviewed 36 leaders and members of the collectives of non-hegemonic groups, namely women, blacks, and LGBTQ. With the proper authorization of the participants, their interviews were transcribed and submitted for critical analysis of the discourse. The field revealed that collectives are the result of the articulation of non-hegemonic groups, which create and participate in legitimate and institutional spaces to promote diversity. We also identified that diversity actions have happened as a market trend and reproduced mimetically. As the largest companies implement these actions, they become benchmarking and thus create a flow that is reproduced by other companies. However, there is no effective change in the structures that could promote inclusion and belonging. We state that a diverse group of employees are not enough to claim that the organization is diverse and inclusive. There remains much more to discuss and delve into deeply, including gender, diversity, and intersectionality.

Keywords: diversity, inclusion, collectives, affinity groups, employee resource groups

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Authors: Opeyemi Elujulo, Aderonke Okoya, Kehinde Awokoya

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Molecularly imprinted polymers (MIP) for the adsorption of pyridine (PYD) was obtained from PYD (the template), styrene (the functional monomer), divinyl benzene (the crosslinker), benzoyl peroxide (the initiator), and water (the porogen). When the template was removed by solvent extraction, imprinted binding sites were left in the polymer material that are capable of selectively rebinding the target molecule. The material was characterized by Fourier transform infrared spectroscopy and differential scanning calorimetry. Batch adsorption experiments were performed to study the adsorption of the material in terms of adsorption kinetics, isotherms, and thermodynamic parameters. The results showed that the imprinted polymer exhibited higher affinity for PYD compared to non-imprinted polymer (NIP).

Keywords: molecularly imprinted polymer, bulk polymerization, environmental pollutant, adsorption

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Authors: Aleksandra Twarda, Dobrosława Krzemień, Grzegorz Dubin, Tad A. Holak

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Stabilin-2 belongs to the group of scavenger receptors and plays a crucial role in clearance of more than 10 ligands from the bloodstream, including hyaluronic acid, products of degradation of extracellular matrix and metabolic products. The Link domain, a defining feature of stabilin-2, has a sequence similar to Link domains in other hyaluronic acid receptors, such as CD44 or TSG-6, and is responsible for most of ligands binding. Present knowledge of signal transduction by stabilin-2, as well as ligands’ recognition and binding mechanism, is limited. Until now, no experimental structures have been solved for any segments of stabilin-2. It has recently been demonstrated that the stabilin-2 knock-out or blocking of the receptor by an antibody effectively opposes cancer metastasis by elevating the level of circulating hyaluronic acid. Moreover, loss of expression of stabilin-2 in a peri-tumourous liver correlates with increased survival. Solving of the crystal structure of stabilin-2 and elucidation of the binding mechanism of hyaluronic acid could enable the precise characterization of the interactions in the binding site. These results may allow for designing specific small-molecule inhibitors of stabilin-2 that could be used in cancer therapy. To carry out screening for crystallization of stabilin-2, we cloned constructs of the Link domain of various lengths with or without surrounding domains. The folding properties of the constructs were checked by nuclear magnetic resonance (NMR). It is planned to show the binding of hyaluronic acid to the Link domain using several biochemical methods, i.a. NMR, isothermal titration calorimetry and fluorescence polarization assay.

Keywords: stabilin-2, Link domain, X-ray crystallography, NMR, hyaluronic acid, cancer

Procedia PDF Downloads 405