TY - JOUR A1 - Shityakov, Sergey A1 - Salvador, Ellaine A1 - Pastorin, Giorgia A1 - Förster, Carola T1 - Blood-brain barrier transport studies, aggregation, and molecular dynamics simulation of multiwalled carbon nanotube functionalized with fluorescein isothiocyanate JF - International Journal of Nanomedicine N2 - In this study, the ability of a multiwalled carbon nanotube functionalized with fluorescein isothiocyanate (MWCNT-FITC) was assessed as a prospective central nervous system-targeting drug delivery system to permeate the blood-brain barrier. The results indicated that the MWCNT-FITC conjugate is able to penetrate microvascular cerebral endothelial monolayers; its concentrations in the Transwell® system were fully equilibrated after 48 hours. Cell viability test, together with phase-contrast and fluorescence microscopies, did not detect any signs of MWCNT-FITC toxicity on the cerebral endothelial cells. These microscopic techniques also revealed presumably the intracellular localization of fluorescent MWCNT-FITCs apart from their massive nonfluorescent accumulation on the cellular surface due to nanotube lipophilic properties. In addition, the 1,000 ps molecular dynamics simulation in vacuo discovered the phenomenon of carbon nanotube aggregation driven by van der Waals forces via MWCN-TFITC rapid dissociation as an intermediate phase. KW - endothelial cells KW - cytotoxicity KW - blood-brain barrier KW - fluorescein isothiocyanate KW - aggregation KW - molecular dynamics KW - fluorescence microscopy KW - Transwell® system KW - multiwalled carbon nanotube KW - mice Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-149233 VL - 10 ER - TY - JOUR A1 - Shityakov, Sergey A1 - Dandekar, Thomas A1 - Förster, Carola T1 - Gene expression profiles and protein-protein interaction network analysis in AIDS patients with HIV-associated encephalitis and dementia JF - HIV/AIDS: Research and Palliative Care N2 - Central nervous system dysfunction is an important cause of morbidity and mortality in patients with human immunodeficiency virus type 1 (HIV-1) infection and acquired immunodeficiency virus syndrome (AIDS). Patients with AIDS are usually affected by HIV-associated encephalitis (HIVE) with viral replication limited to cells of monocyte origin. To examine the molecular mechanisms underlying HIVE-induced dementia, the GSE4755 Affymetrix data were obtained from the Gene Expression Omnibus database and the differentially expressed genes (DEGs) between the samples from AIDS patients with and without apparent features of HIVE-induced dementia were identified. In addition, protein–protein interaction networks were constructed by mapping DEGs into protein–protein interaction data to identify the pathways that these DEGs are involved in. The results revealed that the expression of 1,528 DEGs is mainly involved in the immune response, regulation of cell proliferation, cellular response to inflammation, signal transduction, and viral replication cycle. Heat-shock protein alpha, class A member 1 (HSP90AA1), and fibronectin 1 were detected as hub nodes with degree values >130. In conclusion, the results indicate that HSP90A and fibronectin 1 play important roles in HIVE pathogenesis. KW - microarray KW - differentially expressed genes KW - protein-protein interaction network KW - gene ontology KW - encephalitis dementia KW - human immunodeficiency virus Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-149494 VL - 7 ER - TY - JOUR A1 - Shityakov, Sergey A1 - Dandekar, Thomas T1 - Lead expansion and virtual screening of Indinavir derivate HIV-1 protease inhibitors using pharmacophoric - shape similarity scoring function N2 - Indinavir (Crivaxan®) is a potent inhibitor of the HIV (human immunodeficiency virus) protease. This enzyme has an important role in viral replication and is considered to be very attractive target for new antiretroviral drugs. However, it becomes less effective due to highly resistant new viral strains of HIV, which have multiple mutations in their proteases. For this reason, we used a lead expansion method to create a new set of compounds with a new mode of action to protease binding site. 1300 compounds chemically diverse from the initial hit were generated and screened to determine their ability to interact with protease and establish their QSAR properties. Further computational analyses revealed one unique compound with different protease binding ability from the initial hit and its role for possible new class of protease inhibitors is discussed in this report. KW - Proteasen KW - protease; Indinavir; lead expansion; docking; pharmacophore Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-67824 ER - TY - THES A1 - Shityakov, Sergey T1 - Molecular modelling and simulation of retroviral proteins and nanobiocomposites T1 - Simulationen und Interaktionen viraler Proteine sowie von Kohlenstoffenanoröhren mit Membranen und Proteinen N2 - Molecular modelling and simulation are powerful methods in providing important in-formation on different biological systems to elucidate their structural and functional proper-ties, which cannot be determined in experiment. These methods are applied to analyse versa-tile biological systems: lipid membrane bilayers stabilized by an intercalated single wall carbon nanotube and retroviral proteins such as HIV protease and integrase. HIV-1 integrase has nuclear localization signals (NLS) which play a crucial role in nuclear import of viral preintegration complex (PIC). However, the detailed mechanisms of PIC formation and its nuclear transport are not known. Previously it was shown that NLSs bind to the cell transport machinery e.g. proteins of nuclear pore complex such as transportins. I investigated the interaction of this viral protein HIV-1 integrase with proteins of the nuclear pore complex such as transportin-SR2 (Shityakov et al., 2010). I showed that the transportin-SR2 in nuclear import is required due to its interaction with the HIV-1 integrase. I analyzed key domain interaction, and hydrogen bond formation in transportin-SR2. These results were discussed in comparison to other retroviral species such as foamy viruses to better understand this specific and efficient retroviral trafficking route. The retroviral nuclear import was next analyzed in experiments regarding the retroviral ability to infect nondividing cells. To accomplish the gene transfer task successfully, ret-roviruses must efficiently transduce different cell cultures at different phases of cell cycle. However, promising and safe foamy viral vectors used for gene transfer are unable to effi-ciently infect quiescent cells. This drawback was due to their inability to create a preintegra-tion complex (PIC) for nuclear import of retroviral DNA. On the contrary, the lentiviral vec-tors are not dependant on cell cycle. In the course of reverse transcription the polypurine tract (PPT) is believed to be crucial for PIC formation. In this thesis, I compared the transduction frequencies of PPT modified FV vectors with lentiviral vectors in nondividing and dividing alveolar basal epithelial cells from human adenocarcinoma (A549) by using molecular cloning, transfection and transduction techniques and several other methods. In contrast to lentiviral vectors, FV vectors were not able to effi-ciently transduce nondividing cell (Shityakov and Rethwilm, unpublished data). Despite the findings, which support the use of FV vectors as a safe and efficient alternative to lentiviral vectors, major limitation in terms of foamy-based retroviral vector gene transfer in quiescent cells still remains. Many attempts have been made recently to search for the potential molecules as pos-sible drug candidates to treat HIV infection for over decades now. These molecules can be retrieved from chemical libraries or can be designed on a computer screen and then synthe-sized in a laboratory. Most notably, one could use the computerized structure as a reference to determine the types of molecules that might block the enzyme. Such structure-based drug design strategies have the potential to save off years and millions of dollars compared to a more traditional trial-and-error drug development process. After the crystal structure of the HIV-encoded protease enzyme had been elucidated, computer-aided drug design played a pivotal role in the development of new compounds that inhibit this enzyme which is responsible for HIV maturation and infectivity. Promising repre-sentatives of these compounds have recently found their way to patients. Protease inhibitors show a powerful sustained suppression of HIV-1 replication, especially when used in combi-nation therapy regimens. However, these drugs are becoming less effective to more resistant HIV strains due to multiple mutations in the retroviral proteases. In computational drug design I used molecular modelling methods such as lead ex-pansion algorithm (Tripos®) to create a virtual library of compounds with different binding affinities to protease binding site. In addition, I heavily applied computer assisted combinato-rial chemistry approaches to design and optimize virtual libraries of protease inhibitors and performed in silico screening and pharmacophore-similarity scoring of these drug candidates. Further computational analyses revealed one unique compound with different protease bind-ing ability from the initial hit and its role for possible new class of protease inhibitors is dis-cussed (Shityakov and Dandekar, 2009). A number of atomistic models were developed to elucidate the nanotube behaviour in lipid bilayers. However, none of them provided useful information for CNT effect upon the lipid membrane bilayer for implementing all-atom models that will allow us to calculate the deviations of lipid molecules from CNT with atomistic precision. Unfortunately, the direct experimental investigation of nanotube behaviour in lipid bilayer remains quite a tricky prob-lem opening the door before the molecular simulation techniques. In this regard, more de-tailed multi-scale simulations are needed to clearly understand the stabilization characteristics of CNTs in hydrophobic environment. The phenomenon of an intercalated single-wall carbon nanotube in the center of lipid membrane was extensively studied and analyzed. The root mean square deviation and root mean square fluctuation functions were calculated in order to measure stability of lipid mem-branes. The results indicated that an intercalated carbon nanotube restrains the conformational freedom of adjacent lipids and hence has an impact on the membrane stabilization dynamics (Shityakov and Dandekar, 2011). On the other hand, different lipid membranes may have dissimilarities due to the differing abilities to create a bridge formation between the adherent lipid molecules. The results derived from this thesis will help to develop stable nanobiocom-posites for construction of novel biomaterials and delivery of various biomolecules for medi-cine and biology. N2 - Molekulare Modellierung und Simulationen sind leistungsstarke Methoden, um wich-tige Informationen von verschiedenen biologischen Systemen, welche nicht durch Experi-mente erschlossen werden können, darzustellen, und deren strukturelle und funktionelle Ei-genschaften aufzuklären. Diese Arbeit untersucht in Simulationen Interaktionen viraler Proteinen sowie von Kohlenstoffenanoröhren mit Membranen und Proteinen. Die HIV-1 Integrase besitzt Kernlokalisierungssignale („nuclear localization signals [NLS]“), welche eine entscheidende Rolle beim Import des viralen Präintegrationskomplexes („preintegration complex [PIC]“) in den Zellkern spielen. Die Ausbildung des PIC und sein Import in den Zellkern sind im Detail noch nicht bekannt. Es wurde bereits gezeigt, dass die NLS an Moleküle des Zelltransportsystems binden, wie z.B. an Transportinkernporen. Im Rahmen meiner Arbeit untersuchte ich die Interaktionen der viralen HIV-1 Integrase mit Proteinen der Kernporen wie dem Transportin-SR2 Protein (Shityakov et al., 2010). Hierbei wurden die möglichen Interaktionen des Transportin-SR2 Protein mit der HIV-1-Integrase und die Bedeutung dieser Interaktionen mit dem Import in den Kern aufgezeigt. Zudem wur-den die Interaktionen der Schlüsseldomänen und die Ausbildung von Wasserstoffbrücken-bindungen im dem Transportin-SR2 Protein untersucht. Die Ergebnisse wurden mit Protein-komplexen andere retroviralen Spezies, wie z.B. dem humanen Spumaretrovirus („human foamy virus [HFV]“), verglichen, um diesen spezifischen und sehr effizienten retroviralen Transportweg in die Wirtszelle zu entschlüsseln. Der experimentelle Teil dieser Arbeit beschäftigte sich damit, den retroviralen Kern-import zu untersuchen, um die Fähigkeit des Retrovirus, nicht teilende Zellen zu infizieren, besser zu verstehen verstanden wird. Um dies zu bewerkstelligen, müssen Retroviren Zellkul-turen in verschiedenen Stadien des Zellzyklus effizient transduzieren. Vielversprechende und sichere- HFV- Vektoren, welche in der Gentherapie eingesetzt werden könnten, sind nicht in der Lage, diese Effizienz bei ruhenden Zellen zu gewährleisten. Dies rührte daher, dass diese nicht in der Lage waren, einen PIC für den Transport der retroviralen DNA auszubilden. Lentivirale Vektoren sind dagegen nicht auf einen bestimmten Zellzyklus angewiesen. Für die reverse Transkription ist der Polypurinteil („polypurine tract [PPT]“) essentiell für die Ausbildung der PIC. In dieser Doktorarbeit vergleiche ich die Transduktionsfrequenz von PPT-modifizierten HFV-Vektoren mit denen von lentiviralen Vektoren in nichtteilenden und tei-lenden Lungenkarzinomepithelzellen. Hierbei wurden Methoden wie Klonierung, Transfektion, und Transduktion (wie auch weitere Methoden) angewendet. Im Gegensatz zu lentiviralen Vektoren konnten HFV-Vektoren sich nicht teilende Zellen in meinen Versuchen nicht effizient transduzieren (Shityakov und Rethwiln, unveröffentlicht). Trotz der Befunde, dass HFV-Vektoren sichere und effiziente Alternativen zu lentiviralen Vektoren darstellen, bestehen immer noch große Einschränkungen, diese HFV-basierten, retroviralen Vektoren für Gentherapien bei ruhenden Zellen einzusetzen. Viele Versuche wurden unternommen, um mögliche, vielversprechende Moleküle, welche als Wirkstoffe für eine HIV-Therapie eingesetzt werden könnten, zu finden. Diese Moleküle können aus chemischen Substanzbibliotheken bezogen werden oder am Computer in silico entworfen und dann synthetisiert werden. Digitalisierte Strukturen können als Refe-renzen benutzt werden, um besser herauszufinden, wie diese Moleküle Typen diverse Enzy-me blokieren könnten. Strukturbasiertes Wirkstoffdesign hat das Potential, viele Jahre und Geld an Entwicklungskosten einzusparen. Nachdem die Kristallstruktur der HIV-kodierten Proteasen aufgeklärt war, spielte das computergestützte Wirkstoffdesign eine zentrale Rolle bei der Entwicklung neuer Wirkstoffe gegen die Protease. Vielversprechende Vertreter dieser Wirkstoffklasse werden seit kurzem nun auch für die Behandlung von Patienten eingesetzt. Proteaseinhibitoren zeigen eine wir-kungsvolle und langanhaltende Inhibition der HIV-1-Replikation; besonders dann, wenn sie in Kombinationstherapien eingesetzt werden. Aber diese Wirkstoffe werden immer weniger effektiv, je resistenter die HIV-Stämme durch Mutationen in den retroviralen Proteasen wer-den. Im Rahmen meiner Arbeit mit computergestütztem Wirkstoffdesign nutzte ich Model-lierungsmethoden wie den „lead expansion algorithm“ (Tripos®) um virtuelle Wirkstoffbibli-otheken mit verschiedenen Affinitäten zur Proteasebindungsstelle zu erstellen. Zusätzlich wandte ich Verfahren der computergestützten, kombinatorischen Chemie an, um virtuelle Bibliotheken von Proteaseinhibitoren zu designen, und zu verbessern. Parallel dazu wurde eine in silico Selektion sowie eine Einteilung nach Pharmakophorähnlichkeiten für diese Kandidaten vorgenommen. Weiterführende computergestützte Analysen förderten einen ein-zigartigen Wirkstoff zu Tage, welcher neuartige Proteasebindungseigenschaften aufweist, und dessen Rolle für eine potentiell neuartige Klasse von Proteaseinhibitoren schon beschrieben wurde (Shityakov und Dandekar, 2009). Eine Reihe von Modellen mit atomarer Auflösung wurden bereits entwickelt, um das Verhalten von Nanoröhren in Lipid-Doppelschichten aufzuklären. Die Auswirkungen auf die molekular Dynamik einer einschichtigen Karbonnanoröhre, welche in das Zentrum einer Lipid-Doppelschicht eingefügt wurde, wurden intensiv studiert und analysiert. Die Normalabweichung und Fluktuationen wurden berechnet, um eine Aussage über die Stabilität der Lipid-Doppelschichten treffen zu können. Die Ergebnisse weisen darauf hin, dass eine eingefügte Karbonnanoröhre die Freiheit für Konformationsänderungen bei nahegelegenen Lipiden einschränkt und dadurch einen Einfluss auf die Membranstabilität hat (Shityakov und Dandekar, 2011). Es kann aber außer-dem sein, dass verschiedene Lipid-Doppelschichten Unterschiede in ihrer Fähigkeit, Brücken zwischen benachbarten Lipiden auszubilden, aufweisen. Viren und Karbonnanoröhren werden damit in verschiedenen dynamischen Simulati-onen untersucht, um mehr über ihre Interaktionen mit Proteinen und Membranen zu erfahren. KW - Kohlenstoff KW - Nanoröhre KW - Retroviren KW - Proteine KW - virale Proteine KW - retroviral proteins KW - nanobiocomposites Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-56960 ER - TY - JOUR A1 - Shityakov, Sergey A1 - Sohajda, Tamás A1 - Puskas, Istaván A1 - Roewer, Norbert A1 - Förster, Carola A1 - Broscheit, Jens-Albert T1 - Ionization States, Cellular Toxicity and Molecular Modeling Studies of Midazolam Complexed with Trimethyl-β-Cyclodextrin JF - Molecules N2 - We investigated the ionization profiles for open-ring (OR) and closed-ring (CR) forms of midazolam and drug-binding modes with heptakis-(2,3,6-tri-O-methyl)-β-cyclodextrin (trimethyl-β-cyclodextrin; TRIMEB) using molecular modeling techniques and quantum mechanics methods. The results indicated that the total net charges for different molecular forms of midazolam tend to be cationic for OR and neutral for CR at physiological pH levels. The thermodynamic calculations demonstrated that CR is less water-soluble than OR, mainly due to the maximal solvation energy (ΔG(CR)(solv = -9.98 kcal·mol ⁻¹), which has a minimal ΔG(OR)(solv) of -67.01 kcal·mol⁻¹. A cell viability assay did not detect any signs of TRIMEB and OR/CR-TRIMEB complex toxicity on the cEND cells after 24 h of incubation in either Dulbecco's Modified Eagles Medium or in heat-inactivated human serum. The molecular docking studies identified the more flexible OR form of midazolam as being a better binder to TRIMEB with the fluorophenyl ring introduced inside the amphiphilic cavity of the host molecule. The OR binding affinity was confirmed by a minimal Gibbs free energy of binding (ΔG(bind)) value of -5.57 ± 0.02 kcal·mol⁻¹, an equilibrium binding constant (K(b)) of 79.89 ± 2.706 μM, and a ligand efficiency index (LE(lig)) of -0.21 ± 0.001. Our current data suggest that in order to improve the clinical applications of midazolam via its complexation with trimethyl-β-cyclodextrin to increase drug's overall aqueous solubility, it is important to concern the different forms and ionization states of this anesthetic. All mean values are indicated with their standard deviations. KW - quantum mechanics KW - free energy of solvation KW - torsional energy KW - trimethyl-β-cyclodextrin KW - midazolam KW - transition state KW - molecular docking KW - Gibbs free energy of binding Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-119186 VL - 19 IS - 10 ER - TY - JOUR A1 - Shityakov, Sergey A1 - Förster, Carola T1 - In silico predictive model to determine vector-mediated transport properties for the blood-brain barrier choline transporter JF - Advances and Applications in Bioinformatics and Chemistry N2 - The blood–brain barrier choline transporter (BBB-ChT) may have utility as a drug delivery vector to the central nervous system (CNS). We therefore initiated molecular docking studies with the AutoDock and AutoDock Vina (ADVina) algorithms to develop predictive models for compound screening and to identify structural features important for binding to this transporter. The binding energy predictions were highly correlated with r2=0.88, F=692.4, standard error of estimate =0.775, and P-value<0.0001 for selected BBB-ChT-active/inactive compounds (n=93). Both programs were able to cluster active (Gibbs free energy of binding <−6.0 kcal*mol-1) and inactive (Gibbs free energy of binding >−6.0 kcal*mol-1) molecules and dock them significantly better than at random with an area under the curve value of 0.86 and 0.84, respectively. In ranking smaller molecules with few torsional bonds, a size-related bias in scoring producing false-negative outcomes was detected. Finally, important blood–brain barrier parameters, such as the logBBpassive and logBBactive values, were assessed to predict compound transport to the CNS accurately. Knowledge gained from this study is useful to better understand the binding requirements in BBB-ChT, and until such time as its crystal structure becomes available, it may have significant utility in developing a highly predictive model for the rational design of drug-like compounds targeted to the brain. KW - virtual screening KW - Gibbs free energy of binding KW - diffusion KW - molecular docking KW - drug delivery vector KW - central nervous system KW - blood–brain barrier choline transporter Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-120200 VL - 7 ER - TY - JOUR A1 - Shityakov, Sergey A1 - Förster, Carola T1 - In silico structure-based screening of versatile P-glycoprotein inhibitors using polynomial empirical scoring functions JF - Advances and Applications in Bioinformatics and Chemistry N2 - P-glycoprotein (P-gp) is an ATP (adenosine triphosphate)-binding cassette transporter that causes multidrug resistance of various chemotherapeutic substances by active efflux from mammalian cells. P-gp plays a pivotal role in limiting drug absorption and distribution in different organs, including the intestines and brain. Thus, the prediction of P-gp–drug interactions is of vital importance in assessing drug pharmacokinetic and pharmacodynamic properties. To find the strongest P-gp blockers, we performed an in silico structure-based screening of P-gp inhibitor library (1,300 molecules) by the gradient optimization method, using polynomial empirical scoring (POLSCORE) functions. We report a strong correlation (r2=0.80, F=16.27, n=6, P<0.0157) of inhibition constants (Kiexp or pKiexp; experimental Ki or negative decimal logarithm of Kiexp) converted from experimental IC50 (half maximal inhibitory concentration) values with POLSCORE-predicted constants (KiPOLSCORE or pKiPOLSCORE), using a linear regression fitting technique. The hydrophobic interactions between P-gp and selected drug substances were detected as the main forces responsible for the inhibition effect. The results showed that this scoring technique might be useful in the virtual screening and filtering of databases of drug-like compounds at the early stage of drug development processes. KW - multidrug resistance KW - molecular docking KW - POLSCORE KW - P-gp inhibitors KW - ATP-binding cassette transporter Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-120214 VL - 7 ER - TY - JOUR A1 - Shityakov, Sergey A1 - Puskás, István A1 - Roewer, Norbert A1 - Förster, Carola A1 - Broscheit, Jens T1 - Three-dimensional quantitative structure-activity relationship and docking studies in a series of anthocyanin derivatives as cytochrome P450 3A4 inhibitors JF - Advances and Applications in Bioinformatics and Chemistry N2 - The cytochrome P450 (CYP)3A4 enzyme affects the metabolism of most drug-like substances, and its inhibition may influence drug safety. Modulation of CYP3A4 by flavonoids, such as anthocyanins, has been shown to inhibit the mutagenic activity of mammalian cells. Considering the previous investigations addressing CYP3A4 inhibition by these substances, we studied the three-dimensional quantitative structure-activity relationship (3D-QSAR) in a series of anthocyanin derivatives as CYP3A4 inhibitors. For the training dataset (n=12), comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) yielded crossvalidated and non-crossvalidated models with a q (2) of 0.795 (0.687) and r (2) of 0.962 (0.948), respectively. The models were also validated by an external test set of four compounds with r (2) of 0.821 (CoMFA) and r (2) of 0.812 (CoMSIA). The binding affinity modes associated with experimentally derived IC50 (half maximal inhibitory concentration) values were confirmed by molecular docking into the CYP3A4 active site with r (2) of 0.66. The results obtained from this study are useful for a better understanding of the effects of anthocyanin derivatives on inhibition of carcinogen activation and cellular DNA damage. KW - molecular docking KW - three-dimensional quantitative structure–activity relationship KW - cytochrome P450 3A4 KW - comparative molecular similarity index analysis KW - comparative molecular field analysis KW - carcinogen activation KW - anthocyanin derivatives Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-120226 VL - 7 ER - TY - JOUR A1 - Shityakov, Sergey A1 - Hayashi, Kentaro A1 - Störk, Stefan A1 - Scheper, Verena A1 - Lenarz, Thomas A1 - Förster, Carola Y. T1 - The conspicuous link between ear, brain and heart − Could neurotrophin-treatment of age-related hearing loss help prevent Alzheimer's disease and associated amyloid cardiomyopathy? JF - Biomolecules N2 - Alzheimer's disease (AD), the most common cause of dementia in the elderly, is a neurodegenerative disorder associated with neurovascular dysfunction and cognitive decline. While the deposition of amyloid β peptide (Aβ) and the formation of neurofibrillary tangles (NFTs) are the pathological hallmarks of AD-affected brains, the majority of cases exhibits a combination of comorbidities that ultimately lead to multi-organ failure. Of particular interest, it can be demonstrated that Aβ pathology is present in the hearts of patients with AD, while the formation of NFT in the auditory system can be detected much earlier than the onset of symptoms. Progressive hearing impairment may beget social isolation and accelerate cognitive decline and increase the risk of developing dementia. The current review discusses the concept of a brain–ear–heart axis by which Aβ and NFT inhibition could be achieved through targeted supplementation of neurotrophic factors to the cochlea and the brain. Such amyloid inhibition might also indirectly affect amyloid accumulation in the heart, thus reducing the risk of developing AD-associated amyloid cardiomyopathy and cardiovascular disease. KW - Alzheimer's disease KW - amyloid cardiomyopathy KW - heart failure KW - age-related hearing loss KW - neurotrophins KW - blood–brain barrier KW - blood–labyrinth barrier KW - spiral ganglion neuron KW - BDNF KW - GDNF Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-241084 SN - 2218-273X VL - 11 IS - 6 ER - TY - JOUR A1 - Shityakov, Sergey A1 - Broscheit, Jens A1 - Förster, Carola T1 - Multidrug resistance protein P-gp interaction with nanoparticles (fullerenes and carbon nanotube) to assess their drug delivery potential: a theoretical molecular docking study. JF - International journal of computational biology and drug design N2 - P-glycoprotein (P-gp)-mediated efflux system plays an important role to maintain chemical balance in mammalian cells for endogenous and exogenous chemical compounds. However, despite the extensive characterisation of P-gp potential interaction with drug-like molecules, the interaction of carbon nanoparticles with this type of protein molecule is poorly understood. Thus, carbon nanoparticles were analysed, such as buckminsterfullerenes (C20, C60, C70), capped armchair single-walled carbon nanotube (SWCNT or C168), and P-gp interactions using different molecular docking techniques, such as gradient optimisation algorithm (ADVina), Lamarckian genetic algorithm (FastDock), and shape-based approach (PatchDock) to estimate the binding affinities between these structures. The theoretical results represented in this work show that fullerenes might be P-gp binders because of low levels of Gibbs free energy of binding (ΔG) and potential of mean force (PMF) values. Furthermore, the SWCNT binding is energetically unfavourable, leading to a total decrease in binding affinity by elevation of the residual area (Ares), which also affects the π-π stacking mechanisms. Further, the obtained data could potentially call experimental studies using carbon nanostructures, such as SWCNT for development of drug delivery vehicles, to administer and assess drug-like chemical compounds to the target cells since organisms probably did not develop molecular sensing elements to detect these types of carbon molecules. KW - SWCNT CNTs KW - pi-pi stacking KW - mean force potential KW - Gibbs free energy of binding KW - molecular docking KW - shape-based approach KW - Lamarckian genetic algorithms KW - gradient optimisation KW - drug delivery KW - multidrug resistance KW - P-glycoprotein KW - carbon nanoparticles KW - fullerenes KW - single-walled carbon nanotubes Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-132089 VL - 6 IS - 4 ER - TY - JOUR A1 - Salvador, Ellaine A1 - Shityakov, Sergey A1 - Förster, Carola T1 - Glucocorticoids and endothelial cell barrier function JF - Cell and Tissue Research N2 - Glucocorticoids (GCs) are steroid hormones that have inflammatory and immunosuppressive effects on a wide variety of cells. They are used as therapy for inflammatory disease and as a common agent against edema. The blood brain barrier (BBB), comprising microvascular endothelial cells, serves as a permeability screen between the blood and the brain. As such, it maintains homeostasis of the central nervous system (CNS). In many CNS disorders, BBB integrity is compromised. GC treatment has been demonstrated to improve the tightness of the BBB. The responses and effects of GCs are mediated by the ubiquitous GC receptor (GR). Ligand-bound GR recognizes and binds to the GC response element located within the promoter region of target genes. Transactivation of certain target genes leads to improved barrier properties of endothelial cells. In this review, we deal with the role of GCs in endothelial cell barrier function. First, we describe the mechanisms of GC action at the molecular level. Next, we discuss the regulation of the BBB by GCs, with emphasis on genes targeted by GCs such as occludin, claudins and VE-cadherin. Finally, we present currently available GC therapeutic strategies and their limitations. KW - endothelial cells KW - glucocorticoids KW - glucocorticoid receptor KW - blood brain barrier Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-132091 VL - 355 IS - 3 ER - TY - JOUR A1 - Shityakov, Sergey A1 - Förster, Carola T1 - Pharmacokinetic Delivery and Metabolizing Rate of Nicardipine Incorporated in Hydrophilic and Hydrophobic Cyclodextrins Using Two-Compartment Mathematical Model JF - The Scientific World Journal N2 - The dispersion routes of cyclodextrin complexes with nicardipine (NC), such as hydrophilic hydroxypropyl-\(\beta\)-cyclodextrin (NC/HP\(\beta\)CD) and hydrophobic triacetyl-\(\beta\)-cyclodextrin (NC/TA\(\beta\)CD), through the body for controlled drug delivery and sustained release have been examined. The two-compartment pharmacokinetic model described the mechanisms of how the human body handles with ingestion of NC-cyclodextrin complexes in gastrointestinal tract (GI), distribution in plasma, and their metabolism in the liver. The model showed that drug bioavailability was significantly improved after oral administration of cyclodextrin complexes. The mathematical significance of this study to predict nicardipine delivery using pharmacokinetic two-compartment mathematical model with linear ordinary differential equations (ODE) approach represents a valuable tool to emphasize its effectiveness and metabolizing rate and diminish the side effects. KW - pharmacokinetic delivery KW - metabolizing rate KW - Nicardipine Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-130519 VL - 2013 IS - 131358 ER - TY - JOUR A1 - Shityakov, Sergey A1 - Förster, Carola A1 - Rethwilm, Axel A1 - Dandekar, Thomas T1 - Evaluation and Prediction of the HIV-1 Central Polypurine Tract Influence on Foamy Viral Vectors to Transduce Dividing and Growth-Arrested Cells N2 - Retroviral vectors are potent tools for gene delivery and various biomedical applications. To accomplish a gene transfer task successfully, retroviral vectors must effectively transduce diverse cell cultures at different phases of a cell cycle. However, very promising retroviral vectors based on the foamy viral (FV) backbone lack the capacity to efficiently transduce quiescent cells. It is hypothesized that this phenomenon might be explained as the inability of foamy viruses to form a pre-integration complex (PIC) with nuclear import activity in growth-arrested cells, which is the characteristic for lentiviruses (HIV-1). In this process, the HIV-1 central polypurine tract (cPPT) serves as a primer for plus-strand synthesis to produce a “flap” element and is believed to be crucial for the subsequent double-stranded cDNA formation of all retroviral RNA genomes. In this study, the effects of the lentiviral cPPT element on the FV transduction potential in dividing and growth-arrested (G1/S phase) adenocarcinomic human alveolar basal epithelial (A549) cells are investigated by experimental and theoretical methods. The results indicated that the HIV-1 cPPT element in a foamy viral vector background will lead to a significant reduction of the FV transduction and viral titre in growth-arrested cells due to the absence of PICs with nuclear import activity. KW - Evaluation KW - Prognose KW - HIV KW - Spumaviren KW - Einfluss Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-112763 ER - TY - JOUR A1 - Shityakov, Sergey A1 - Puskás, István A1 - Pápai, Katalin A1 - Salvador, Ellaine A1 - Roewer, Norbert A1 - Förster, Carola A1 - Broscheit, Jens-Albert T1 - Sevoflurane-sulfobutylether-\(\beta\)-cyclodextrin complex: preparation, characterization, cellular toxicity, molecular modeling and blood-brain barrier transport studies JF - Molecules N2 - The objective of the present investigation was to study the ability of sulfobutylether-\(\beta\)-cyclodextrin (SBECD) to form an inclusion complex with sevoflurane (SEV), a volatile anesthetic with poor water solubility. The inclusion complex was prepared, characterized and its cellular toxicity and blood-brain barrier (BBB) permeation potential of the formulated SEV have also been examined for the purpose of controlled drug delivery. The SEV-SBE\(\beta\)CD complex was nontoxic to the primary brain microvascular endothelial (pEND) cells at a clinically relevant concentration of sevoflurane. The inclusion complex exhibited significantly higher BBB permeation profiles as compared with the reference substance (propranolol) concerning calculated apparent permeability values (P\(_{app}\)). In addition, SEV binding affinity to SBE\(\beta\)CD was confirmed by a minimal Gibbs free energy of binding (ΔG\(_{bind}\)) value of -1.727 ± 0.042 kcal・mol\(^{-1}\) and an average binding constant (K\(_{b}\)) of 53.66 ± 9.24 mM indicating rapid drug liberation from the cyclodextrin amphiphilic cavity. KW - pharmaceutical applications KW - in vitro KW - propranolol KW - water KW - primary microvascular endothelial cells KW - molecular liphophilicity potential KW - molecular docking KW - blood-brain barrier KW - ulfobutylether-\(\beta\)-cyclodextrin KW - sevoflurane KW - cyclodextrin formulations KW - safety KW - etomidate KW - formulations KW - hydrochloride KW - ether KW - intestinal absorption Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148543 VL - 20 ER - TY - JOUR A1 - Bencurova, Elena A1 - Shityakov, Sergey A1 - Schaack, Dominik A1 - Kaltdorf, Martin A1 - Sarukhanyan, Edita A1 - Hilgarth, Alexander A1 - Rath, Christin A1 - Montenegro, Sergio A1 - Roth, Günter A1 - Lopez, Daniel A1 - Dandekar, Thomas T1 - Nanocellulose composites as smart devices with chassis, light-directed DNA Storage, engineered electronic properties, and chip integration JF - Frontiers in Bioengineering and Biotechnology N2 - The rapid development of green and sustainable materials opens up new possibilities in the field of applied research. Such materials include nanocellulose composites that can integrate many components into composites and provide a good chassis for smart devices. In our study, we evaluate four approaches for turning a nanocellulose composite into an information storage or processing device: 1) nanocellulose can be a suitable carrier material and protect information stored in DNA. 2) Nucleotide-processing enzymes (polymerase and exonuclease) can be controlled by light after fusing them with light-gating domains; nucleotide substrate specificity can be changed by mutation or pH change (read-in and read-out of the information). 3) Semiconductors and electronic capabilities can be achieved: we show that nanocellulose is rendered electronic by iodine treatment replacing silicon including microstructures. Nanocellulose semiconductor properties are measured, and the resulting potential including single-electron transistors (SET) and their properties are modeled. Electric current can also be transported by DNA through G-quadruplex DNA molecules; these as well as classical silicon semiconductors can easily be integrated into the nanocellulose composite. 4) To elaborate upon miniaturization and integration for a smart nanocellulose chip device, we demonstrate pH-sensitive dyes in nanocellulose, nanopore creation, and kinase micropatterning on bacterial membranes as well as digital PCR micro-wells. Future application potential includes nano-3D printing and fast molecular processors (e.g., SETs) integrated with DNA storage and conventional electronics. This would also lead to environment-friendly nanocellulose chips for information processing as well as smart nanocellulose composites for biomedical applications and nano-factories. KW - nanocellulose KW - DNA storage KW - light-gated proteins KW - single-electron transistors KW - protein chip Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-283033 SN - 2296-4185 VL - 10 ER - TY - JOUR A1 - Isaacs, Darren A1 - Mikasi, Sello Given A1 - Obasa, Adetayo Emmanuel A1 - Ikomey, George Mondinde A1 - Shityakov, Sergey A1 - Cloete, Ruben A1 - Jacobs, Graeme Brendon T1 - Structural comparison of diverse HIV-1 subtypes using molecular modelling and docking analyses of integrase inhibitors JF - Viruses N2 - The process of viral integration into the host genome is an essential step of the HIV-1 life cycle. The viral integrase (IN) enzyme catalyzes integration. IN is an ideal therapeutic enzyme targeted by several drugs; raltegravir (RAL), elvitegravir (EVG), dolutegravir (DTG), and bictegravir (BIC) having been approved by the USA Food and Drug Administration (FDA). Due to high HIV-1 diversity, it is not well understood how specific naturally occurring polymorphisms (NOPs) in IN may affect the structure/function and binding affinity of integrase strand transfer inhibitors (INSTIs). We applied computational methods of molecular modelling and docking to analyze the effect of NOPs on the full-length IN structure and INSTI binding. We identified 13 NOPs within the Cameroonian-derived CRF02_AG IN sequences and further identified 17 NOPs within HIV-1C South African sequences. The NOPs in the IN structures did not show any differences in INSTI binding affinity. However, linear regression analysis revealed a positive correlation between the Ki and EC50 values for DTG and BIC as strong inhibitors of HIV-1 IN subtypes. All INSTIs are clinically effective against diverse HIV-1 strains from INSTI treatment-naïve populations. This study supports the use of second-generation INSTIs such as DTG and BIC as part of first-line combination antiretroviral therapy (cART) regimens, due to a stronger genetic barrier to the emergence of drug resistance. KW - integrase KW - naturally occurring polymorphisms KW - HIV-1 KW - molecular modelling KW - molecular docking KW - diversity Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-211170 SN - 1999-4915 VL - 12 IS - 9 ER - TY - JOUR A1 - Shityakov, Sergey A1 - Roewer, Norbert A1 - Förster, Carola A1 - Broscheit, Jens-Albert T1 - In silico modeling of indigo and Tyrian purple single-electron nano-transistors using density functional theory approach JF - Nanoscale Research Letters N2 - The purpose of this study was to develop and implement an in silico model of indigoid-based single-electron transistor (SET) nanodevices, which consist of indigoid molecules from natural dye weakly coupled to gold electrodes that function in a Coulomb blockade regime. The electronic properties of the indigoid molecules were investigated using the optimized density-functional theory (DFT) with a continuum model. Higher electron transport characteristics were determined for Tyrian purple, consistent with experimentally derived data. Overall, these results can be used to correctly predict and emphasize the electron transport functions of organic SETs, demonstrating their potential for sustainable nanoelectronics comprising the biodegradable and biocompatible materials. KW - density functional theory KW - indigo KW - Tyrian purple KW - single-electron transistor Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-158332 VL - 12 IS - 439 ER - TY - JOUR A1 - Shityakov, Sergey A1 - Bencurova, Elena A1 - Förster, Carola A1 - Dandekar, Thomas T1 - Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches JF - BMC Bioinformatics N2 - Background Processing and analysis of DNA sequences obtained from next-generation sequencing (NGS) face some difficulties in terms of the correct prediction of DNA sequencing outcomes without the implementation of bioinformatics approaches. However, algorithms based on NGS perform inefficiently due to the generation of long DNA fragments, the difficulty of assembling them and the complexity of the used genomes. On the other hand, the Sanger DNA sequencing method is still considered to be the most reliable; it is a reliable choice for virtual modeling to build all possible consensus sequences from smaller DNA fragments. Results In silico and in vitro experiments were conducted: (1) to implement and test our novel sequencing algorithm, using the standard cloning vectors of different length and (2) to validate experimentally virtual shotgun sequencing using the PCR technique with the number of cycles from 1 to 9 for each reaction. Conclusions We applied a novel algorithm based on Sanger methodology to correctly predict and emphasize the performance of DNA sequencing techniques as well as in de novo DNA sequencing and its further application in synthetic biology. We demonstrate the statistical significance of our results. KW - Shotgun method KW - Sanger sequencing KW - Virtual sequencing KW - Polymerase chain reaction KW - Gene expression vectors KW - Synthetic biology Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-229169 VL - 2020 ER - TY - JOUR A1 - Sarukhanyan, Edita A1 - Shityakov, Sergey A1 - Dandekar, Thomas T1 - Rational drug design of Axl tyrosine kinase type I inhibitors as promising candidates against cancer JF - Frontiers in Chemistry N2 - The high level of Axl tyrosine kinase expression in various cancer cell lines makes it an attractive target for the development of anti-cancer drugs. In this study, we carried out several sets of in silico screening for the ATP-competitive Axl kinase inhibitors based on different molecular docking protocols. The best drug-like candidates were identified, after parental structure modifications, by their highest affinity to the target protein. We found that our newly designed compound R5, a derivative of the R428 patented analog, is the most promising inhibitor of the Axl kinase according to the three molecular docking algorithms applied in the study. The molecular docking results are in agreement with the molecular dynamics simulations using the MM-PBSA/GBSA implicit solvation models, which confirm the high affinity of R5 toward the protein receptor. Additionally, the selectivity test against other kinases also reveals a high affinity of R5 toward ABL1 and Tyro3 kinases, emphasizing its promising potential for the treatment of malignant tumors. KW - Axl tyrosine kinase KW - anti-cancer drug-like molecules KW - rational drug design KW - molecular docking KW - molecular dynamics Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-199505 SN - 2296-2646 VL - 7 IS - 920 ER - TY - JOUR A1 - Shityakov, Sergey A1 - Skorb, Ekaterina V. A1 - Förster, Carola Y. A1 - Dandekar, Thomas T1 - Scaffold Searching of FDA and EMA-Approved Drugs Identifies Lead Candidates for Drug Repurposing in Alzheimer’s Disease JF - Frontiers in Chemistry N2 - Clinical trials of novel therapeutics for Alzheimer’s Disease (AD) have consumed a significant amount of time and resources with largely negative results. Repurposing drugs already approved by the Food and Drug Administration (FDA), European Medicines Agency (EMA), or Worldwide for another indication is a more rapid and less expensive option. Therefore, we apply the scaffold searching approach based on known amyloid-beta (Aβ) inhibitor tramiprosate to screen the DrugCentral database (n = 4,642) of clinically tested drugs. As a result, menadione bisulfite and camphotamide substances with protrombogenic and neurostimulation/cardioprotection effects were identified as promising Aβ inhibitors with an improved binding affinity (ΔGbind) and blood-brain barrier permeation (logBB). Finally, the data was also confirmed by molecular dynamics simulations using implicit solvation, in particular as Molecular Mechanics Generalized Born Surface Area (MM-GBSA) model. Overall, the proposed in silico pipeline can be implemented through the early stage rational drug design to nominate some lead candidates for AD, which will be further validated in vitro and in vivo, and, finally, in a clinical trial. KW - scaffold search KW - approved drugs KW - drug repurposing KW - alzheimer's disease KW - chemical similarity KW - molecular modeling Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-248703 SN - 2296-2646 VL - 9 ER - TY - JOUR A1 - Khan, Muhammad Usman A1 - Pirzadeh, Maryam A1 - Förster, Carola Yvette A1 - Shityakov, Sergey A1 - Shariati, Mohammad Ali T1 - Role of milk-derived antibacterial peptides in modern food biotechnology: their synthesis, applications and future perspectives JF - Biomolecules N2 - Milk-derived antibacterial peptides (ABPs) are protein fragments with a positive influence on the functions and conditions of a living organism. Milk-derived ABPs have several useful properties important for human health, comprising a significant antibacterial effect against various pathogens, but contain toxic side-effects. These compounds are mainly produced from milk proteins via fermentation and protein hydrolysis. However, they can also be produced using recombinant DNA techniques or organic synthesis. This review describes the role of milk-derived ABPs in modern food biotechnology with an emphasis on their synthesis and applications. Additionally, we also discuss the mechanisms of action and the main bioproperties of ABPs. Finally, we explore future perspectives for improving ABP physicochemical properties and diminishing their toxic side-effects. KW - milk proteins KW - bioactive peptide KW - antibacterial activity KW - fermentation KW - protein hydrolysis KW - recombinant DNA KW - peptide synthesis Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-197610 SN - 2218-273X VL - 8 IS - 4 ER - TY - JOUR A1 - Karnati, Srikanth A1 - Guntas, Gulcan A1 - Rajendran, Ranjithkumar A1 - Shityakov, Sergey A1 - Höring, Marcus A1 - Liebisch, Gerhard A1 - Kosanovic, Djuro A1 - Ergün, Süleyman A1 - Nagai, Michiaki A1 - Förster, Carola Y. T1 - Quantitative lipidomic analysis of Takotsubo syndrome patients' serum JF - Frontiers in Cardiovascular Medicine N2 - Takotsubo syndrome (TTS), also known as the transient left ventricular apical ballooning syndrome, is in contemporary times known as novel acute cardiac syndrome. It is characterized by transient left ventricular apical akinesis and hyperkinesis of the basal left ventricular portions. Although the precise etiology of TTS is unknown, events like the sudden release of stress hormones, such as the catecholamines and the increased inflammatory status might be plausible causes leading to the cardiovascular pathologies. Recent studies have highlighted that an imbalance in lipid accumulation might promote a deviant immune response as observed in TTS. However, there is no information on comprehensive profiling of serum lipids of TTS patients. Therefore, we investigated a detailed quantitative lipid analysis of TTS patients using ES-MSI. Our results showed significant differences in the majority of lipid species composition in the TTS patients compared to the control group. Furthermore, the computational analyses presented was able to link the altered lipids to the pro-inflammatory cytokines and disseminate possible mechanistic pathways involving TNFα and IL-6. Taken together, our study provides an extensive quantitative lipidome of TTS patients, which may provide a valuable Pre-diagnostic tool. This would facilitate the elucidation of the underlying mechanisms of the disease and to prevent the development of TTS in the future. KW - TTS KW - inflammation KW - lipids KW - TNF-α KW - IL6 KW - PIK3R1 KW - NF-kappa-B KW - phosphatidylinositol Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-270832 SN - 2297-055X VL - 9 IS - 797154 ER - TY - JOUR A1 - Sarukhanyan, Edita A1 - Shityakov, Sergey A1 - Dandekar, Thomas T1 - In silico designed Axl receptor blocking drug candidates against Zika virus infection JF - ACS Omega N2 - After a large outbreak in Brazil, novel drugs against Zika virus became extremely necessary. Evaluation of virus-based pharmacological strategies concerning essential host factors brought us to the idea that targeting the Axl receptor by blocking its dimerization function could be critical for virus entry. Starting from experimentally validated compounds, such as RU-301, RU-302, warfarin, and R428, we identified a novel compound 2′ (R428 derivative) to be the most potent for this task amongst a number of alternative compounds and leads. The improved affinity of compound 2′ was confirmed by molecular docking as well as molecular dynamics simulation techniques using implicit solvation models. The current study summarizes a new possibility for inhibition of the Axl function as a potential target for future antiviral therapies. KW - free energy KW - molecular docking KW - molecular dynamics KW - simulation KW - pharmacology KW - proteins KW - structure-activity relationship KW - viruses KW - Zika virus Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-176739 VL - 3 IS - 5 ER - TY - JOUR A1 - Shityakov, Sergey A1 - Nagai, Michiaki A1 - Ergün, Süleyman A1 - Braunger, Barbara M. A1 - Förster, Carola Y. T1 - The protective effects of neurotrophins and microRNA in diabetic retinopathy, nephropathy and heart failure via regulating endothelial function JF - Biomolecules N2 - Diabetes mellitus is a common disease affecting more than 537 million adults worldwide. The microvascular complications that occur during the course of the disease are widespread and affect a variety of organ systems in the body. Diabetic retinopathy is one of the most common long-term complications, which include, amongst others, endothelial dysfunction, and thus, alterations in the blood-retinal barrier (BRB). This particularly restrictive physiological barrier is important for maintaining the neuroretina as a privileged site in the body by controlling the inflow and outflow of fluid, nutrients, metabolic end products, ions, and proteins. In addition, people with diabetic retinopathy (DR) have been shown to be at increased risk for systemic vascular complications, including subclinical and clinical stroke, coronary heart disease, heart failure, and nephropathy. DR is, therefore, considered an independent predictor of heart failure. In the present review, the effects of diabetes on the retina, heart, and kidneys are described. In addition, a putative common microRNA signature in diabetic retinopathy, nephropathy, and heart failure is discussed, which may be used in the future as a biomarker to better monitor disease progression. Finally, the use of miRNA, targeted neurotrophin delivery, and nanoparticles as novel therapeutic strategies is highlighted. KW - diabetic retinopathy KW - diabetes mellitus KW - microvascular complications KW - diabetic nephropathy KW - heart failure KW - microRNA KW - neurotrophins Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-285966 SN - 2218-273X VL - 12 IS - 8 ER - TY - JOUR A1 - Esmaeilpour, Donya A1 - Broscheit, Jens Albert A1 - Shityakov, Sergey T1 - Cyclodextrin-based polymeric materials bound to corona protein for theranostic applications JF - International Journal of Molecular Sciences N2 - Cyclodextrins (CDs) are cyclic oligosaccharide structures that could be used for theranostic applications in personalized medicine. These compounds have been widely utilized not only for enhancing drug solubility, stability, and bioavailability but also for controlled and targeted delivery of small molecules. These compounds can be complexed with various biomolecules, such as peptides or proteins, via host-guest interactions. CDs are amphiphilic compounds with water-hating holes and water-absorbing surfaces. Architectures of CDs allow the drawing and preparation of CD-based polymers (CDbPs) with optimal pharmacokinetic and pharmacodynamic properties. These polymers can be cloaked with protein corona consisting of adsorbed plasma or extracellular proteins to improve nanoparticle biodistribution and half-life. Besides, CDs have become famous in applications ranging from biomedicine to environmental sciences. In this review, we emphasize ongoing research in biomedical fields using CD-based centered, pendant, and terminated polymers and their interactions with protein corona for theranostic applications. Overall, a perusal of information concerning this novel approach in biomedicine will help to implement this methodology based on host-guest interaction to improve therapeutic and diagnostic strategies. KW - cyclodextrin KW - theranostics KW - protein corona KW - nanomedicine KW - therapy KW - polymers Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-297399 SN - 1422-0067 VL - 23 IS - 21 ER - TY - JOUR A1 - Fareed, Muhammad Mazhar A1 - Qasmi, Maryam A1 - Aziz, Shaan A1 - Völker, Elisabeth A1 - Förster, Carola Yvette A1 - Shityakov, Sergey T1 - The role of clusterin transporter in the pathogenesis of Alzheimer’s disease at the blood–brain barrier interface: a systematic review JF - Biomolecules N2 - Alzheimer’s disease (AD) is considered a chronic and debilitating neurological illness that is increasingly impacting older-age populations. Some proteins, including clusterin (CLU or apolipoprotein J) transporter, can be linked to AD, causing oxidative stress. Therefore, its activity can affect various functions involving complement system inactivation, lipid transport, chaperone activity, neuronal transmission, and cellular survival pathways. This transporter is known to bind to the amyloid beta (Aβ) peptide, which is the major pathogenic factor of AD. On the other hand, this transporter is also active at the blood–brain barrier (BBB), a barrier that prevents harmful substances from entering and exiting the brain. Therefore, in this review, we discuss and emphasize the role of the CLU transporter and CLU-linked molecular mechanisms at the BBB interface in the pathogenesis of AD. KW - clusterin transporter KW - Wnt signaling KW - Alzheimer’s disease KW - AD pathogenesis KW - blood–brain barrier KW - apolipoprotein J Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-290279 SN - 2218-273X VL - 12 IS - 10 ER - TY - JOUR A1 - Förster, Carola Y. A1 - Shityakov, Sergey A1 - Scheper, Verena A1 - Lenarz, Thomas T1 - Linking cerebrovascular dysfunction to age-related hearing loss and Alzheimer’s disease — are systemic approaches for diagnosis and therapy required? JF - Biomolecules N2 - Alzheimer’s disease (AD), the most common cause of dementia in the elderly, is a neurodegenerative disorder associated with neurovascular dysfunction, cognitive decline, and the accumulation of amyloid β peptide (Aβ) in the brain and tau-related lesions in neurons termed neurofibrillary tangles (NFTs). Aβ deposits and NFT formation are the central pathological hallmarks in AD brains, and the majority of AD cases have been shown to exhibit a complex combination of systemic comorbidities. While AD is the foremost common cause of dementia in the elderly, age-related hearing loss (ARHL) is the most predominant sensory deficit in the elderly. During aging, chronic inflammation and resulting endothelial dysfunction have been described and might be key contributors to AD; we discuss an intriguing possible link between inner ear strial microvascular pathology and blood–brain barrier pathology and present ARHL as a potentially modifiable and treatable risk factor for AD development. We present compelling evidence that ARHL might well be seen as an important risk factor in AD development: progressive hearing impairment, leading to social isolation, and its comorbidities, such as frailty, falls, and late-onset depression, link ARHL with cognitive decline and increased risk of dementia, rendering it tempting to speculate that ARHL might be a potential common molecular and pathological trigger for AD. Additionally, one could speculate that amyloid-beta might damage the blood–labyrinth barrier as it does to the blood–brain barrier, leading to ARHL pathology. Finally, there are options for the treatment of ARHL by targeted neurotrophic factor supplementation to the cochlea to improve cognitive outcomes; they can also prevent AD development and AD-related comorbidity in the future. KW - Alzheimer’s disease KW - age-related hearing loss KW - neurovasculature KW - blood–brain barrier KW - blood–labyrinth barrier KW - spiral ganglion neuron KW - pharmacotherapy KW - neurotrophic factor KW - inner ear Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-297552 SN - 2218-273X VL - 12 IS - 11 ER - TY - JOUR A1 - Wilhelms, Benedikt A1 - Broscheit, Jens A1 - Shityakov, Sergey T1 - Chemical analysis and molecular modelling of cyclodextrin-formulated propofol and its sodium salt to improve drug solubility, stability and pharmacokinetics (cytogenotoxicity) JF - Pharmaceuticals N2 - Propofol is a widely used general anesthetic in clinical practice, but its use is limited by its water-insoluble nature and associated pharmacokinetic and pharmacodynamic limitations. Therefore, researchers have been searching for alternative formulations to lipid emulsion to address the remaining side effects. In this study, novel formulations for propofol and its sodium salt Na-propofolat were designed and tested using the amphiphilic cyclodextrin (CD) derivative hydroxypropyl-β-cyclodextrin (HPβCD). The study found that spectroscopic and calorimetric measurements suggested complex formation between propofol/Na-propofolate and HPβCD, which was confirmed by the absence of an evaporation peak and different glass transition temperatures. Moreover, the formulated compounds showed no cytotoxicity and genotoxicity compared to the reference. The molecular modeling simulations based on molecular docking predicted a higher affinity for propofol/HPβCD than for Na-propofolate/HPβCD, as the former complex was more stable. This finding was further confirmed by high-performance liquid chromatography. In conclusion, the CD-based formulations of propofol and its sodium salt may be a promising option and a plausible alternative to conventional lipid emulsions. KW - propofol KW - anaesthesiology KW - HPβCD KW - \(^1\)H-NMR spectroscopy KW - calorimetry KW - molecular modelling KW - cytotoxicity KW - genotoxicity Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-313705 SN - 1424-8247 VL - 16 IS - 5 ER -