Dynamics of protein-drug interactions inferred from structural ensembles and physics-based models

The conformational flexibility of target proteins is a major challenge in understanding and modeling protein-drug interactions. A fundamental issue, yet to be clarified, is whether the observed conformational changes are controlled by the protein, or induced by the inhibitor. While the concept of induced fit has been widely adopted for describing the structural changes that accompany ligand binding, there is growing evidence in support of the dominance of proteins' intrinsic dynamics, which has been evolutionarily optimized to accommodate its functional interactions. The wealth of structural data for target proteins in the presence of different ligands now permits us to make a critical assessment of the balance between these two effects in selecting the bound forms. We focused on three widely studied drug targets, HIV-1 reverse transcriptase, p38 MAP kinase, and cyclin-dependent kinase 2. A total of 292 structures determined for these enzymes in the presence of different inhibitors as well as unbound form permitted us to perform an extensive comparative analysis of the conformational space accessed upon ligand binding, and its relation to the intrinsic dynamics prior to ligand binding as predicted by elastic network model analysis. Further, we analyzed NMR ensembles of ubiquitin and calmodulin representing their microseconds range solution dynamics. Our results show that the ligand selects the conformer that best matches its structural and dynamic properties amongst the conformers intrinsically accessible to the protein in the unliganded form. The results suggest that simple but robust rules encoded in the protein structure play a dominant role in pre-defining the mechanisms of ligand binding, which may be advantageously exploited in designing inhibitors. We apply these lessons to the study of MAP kinase phosphatases (MKPs), which are therapeutically relevant but challenging signaling enzymes. Our study provides insights into the interactions and selectivity of MKP inhibitors and shows how an allosteric inhibition mechanism holds for a recently discovered inhibitor of MKP-3. We also provide evidence for the functional significance of the structure-encoded dynamics of rhodopsin and nicotinic acetylcholine receptor, members of two membrane proteins classes serving as targets for more than 40% of all current FDA approved drugs

Razvoj 10 kW trofaznog izmjenjivača spojenoga na mrežu

In this paper, modeling, simulation and experimental study of a 10 kW three-phase grid connected inverter are presented. The mathematical model of the system is derived, and characteristic curves of the system are obtained in MATLAB with m-file for various switching frequencies, dc-link voltages and filter inductance values. The curves are used for parameter selection of three-phase grid connected inverter design. The parameters of the system are selected from these curves, and the system is simulated in Simulink. Modeling and simulation results are verified with experimental results at 10 kW for steady state response, at 5 kW for dynamic response and at -3.6 kVAr for reactive power. The inverter is controlled with Space Vector Pulse Width Modulation technique in d-q reference frame, and dSPACE DS1103 controller board is used in the experimental study. Grid current total harmonic distortion value and efficiency are measured 3.59% and 97.6%, respectively.U ovom radu prikazano je modeliranje, simuliranje i eksperimentalno istraživanje 10 kW trofaznog izmjenjivača spojenoga na mrežu. Izveden je matematički model te su u MATLAB-u uz korištenje m-skripti dobivene karakteristične krivulje sustava za različite preklopne frekvencije, napone dc-linka i vrijednosti induktiviteta filtra. Krivulje su korištene za odabir parametara dizajna trofaznog izmjenjivača spojenoga na mrežu. Parametri sustava su odabrani iz krivulja, a sustav je simuliran u Simulinku. Rezultati modeliranja i simuliranja eksperimentalno su verificirani na 10 kW odziva u stacionarnom stanju, 5 kW donamičkog odziva i -3.6 kVAr reaktivne snage. U eksperimentalnom istraživanju izmjenjivač je upravljan tehnikom prostorno vektorske širinsko-impulsne modulacije u d-q referentnom sustavu te je korištena dSPACE DS1103 upravljačka pločica. Ukupna harmonička distorzija mrežne struje i efikasnost su 3.59% i 97.6%

Myositic Type of Idiopathic Orbital Pseudotumor in a 4-Year-Old Child: A Case Report

Idiopathic orbital pseudotumor is a benign, noninfectious, and nonneoplastic disease with unknown cause. It is the third most common orbital disease after thyroid orbitopathy and lymphoproliferative disorder. Idiopathic orbital pseudotumor is extremely rare in pediatric age group and may cause real diagnostic problems. This paper describes a 4-year-old girl who presented with sudden ptosis in the right eye and swollen eyelid. She recovered completely with high-dose steroid therapy. We report clinical and magnetic resonance imaging findings of orbital myositis, which is a rare subtype of idiopathic orbital pseudotumor in children and needs to be differentiated from other orbital disease especially malignancy

The effects of post-deposition annealing conditions on structure and created defects in Zn0.90Co0.10O thin films deposited on Si(100) substrate

We analyze the effect of post-deposition annealing conditions on both the structure and the created defects in Zn0.90Co0.10O thin films deposited on the Si (100) substrates by RF magnetron sputtering technique using home-made targets. We concentrated on understanding the homogeneity of substituted Co+2 ions and the annealing effects on the amount of defects in the ZnO lattice. Orientations of thin films are found to be in the [0002] direction with a surface roughness changing from 67±2 nm to 25.8±0.6 nm by annealing. The Co+2 ion substitutions, changing from 7.5±0.3 % to 8.8±0.3 %, cause to form Zn–O–Co bonds instead of Zn–O–Zn and split the Co2p energy level to Co2p1/2 and Co2p3/2 with 15.67±0.06 eV energy difference. In addition, the defects in the lattice were revealed from the correlations between Zn–O–Co bonds and intensity of Raman peak at around 691 cm-1. Furthermore, the asymmetry changes of O1s peak positions in X-ray Photoelectron Spectra (XPS) were also found to be in accordance with the Raman results

Effect of mirtazapine on gastric oxidative stress and DNA injury created with methotrexate in rats

In this study, effect of mirtazapine on gastric oxidative stress and DNA injury created with methotrexate was investigated. Experimental results showed that GSH (nmol/g protein), MDA (?mol/g protein) and MPO (?/g protein) in the gastric tissue of the control group rats receiving methotrexate are 4.97 ± 0.37, 2.78 ± 0.30 and 3.12 ± 0.18, respectively. GSH, MDA and MPO measurements in the gastric tissue of rats receiving mirtazapine + methotrexate were detected to be 9.23 ± 0.51(p < 0.0001), 1.80 ± 0.31(p < 0.0001) and 1.63 ± 0.25 (p < 0.0001), respectively. GSH, MDA and MPO values in the intact rat group were found 8 ± 0.38 (p < 0,0001), 1.63 ± 0.28 (p < 0.0001) and 1.37 ± 0.21 (p < 0.0001), respectively. In addition, while 8-ohdG/dG quantity that DNA injury product in the control group administered methotrexate was 2.4 ± 0.11 pmol/L, this quantity was 1.3 ± 0.14 pmol/L (p < 0.001), 1.1 ± 0.10 pmol/L (p < 0.001) in mirtazapine and intact group, respectively. As a result, it was seen that mirtazapine prevents increase of oxidative stress and DNA injury created with methotreaxete in the gastric tissue of rat

Toward a Molecular Understanding of the Interaction of Dual Specificity Phosphatases with Substrates: Insights from Structure-Based Modeling and High Throughput Screening

Dual-specificity phosphatases (DSPs) are important, but poorly understood, cell signaling enzymes that remove phosphate groups from tyrosine and serine/threonine residues on their substrate. Deregulation of DSPs has been implicated in cancer, obesity, diabetes, inflammation, and Alzheimer’s disease. Due to their biological and biomedical significance, DSPs have increasingly become the subject of drug discovery high-throughput screening (HTS) and focused compound library development efforts. Progress in identifying selective and potent DSP inhibitors has, however, been restricted by the lack of sufficient structural data on inhibitor-bound DSPs. The shallow, almost flat, substrate binding sites in DSPs have been a major factor in hampering the rational design and the experimental development of active site inhibitors. Recent experimental and virtual HTS studies, as well as advances in molecular modeling, provide new insights into the potential mechanisms for substrate recognition and binding by this important class of enzymes. We present herein an overview of the progress, along with a brief description of applications to two types of DSPs: Cdc25 and MAP kinase phosphatase (MKP) family members. In particular, we focus on combined computational and experimental efforts for designing Cdc25B and MKP-1 inhibitors and understanding their mechanisms of interactions with their target proteins. These studies emphasize the utility of developing computational models and methods that meet the two major challenges currently faced in structure-based in silico design of lead compounds: the conformational flexibility of the target protein and the entropic contribution to the selection and stabilization of particular bound conformers

Coupling between Catalytic Loop Motions and Enzyme Global Dynamics

Catalytic loop motions facilitate substrate recognition and binding in many enzymes. While these motions appear to be highly flexible, their functional significance suggests that structure-encoded preferences may play a role in selecting particular mechanisms of motions. We performed an extensive study on a set of enzymes to assess whether the collective/global dynamics, as predicted by elastic network models (ENMs), facilitates or even defines the local motions undergone by functional loops. Our dataset includes a total of 117 crystal structures for ten enzymes of different sizes and oligomerization states. Each enzyme contains a specific functional/catalytic loop (10-21 residues long) that closes over the active site during catalysis. Principal component analysis (PCA) of the available crystal structures (including apo and ligand-bound forms) for each enzyme revealed the dominant conformational changes taking place in these loops upon substrate binding. These experimentally observed loop reconfigurations are shown to be predominantly driven by energetically favored modes of motion intrinsically accessible to the enzyme in the absence of its substrate. The analysis suggests that robust global modes cooperatively defined by the overall enzyme architecture also entail local components that assist in suitable opening/closure of the catalytic loop over the active site. © 2012 Kurkcuoglu et al

Performansa Göre Ücretlendirme’nin Doktorlar Tarafından Algılanan Negatif Yönleri

Gelişen teknoloji, sosyal ve politik yapı, yasalar ve bireylerin beklentileri kısaca kamu kurumlarının içerisinde bulunduğu ve ilişkide olduğu tüm çevre her geçen gün hızlıbir biçimde değişmektedir. Kamu kurumlarının hizmet kalitesini arttırmak, çalışan memnuniyetini yükseltmek ve bireylerin beklentilerini karşılayabilmek amacıyla farklıyöntemler uygulanmaktadır. Bu yöntemlerden birisi olan performansa göre ücretlendirme diğer yöntemlere göre daha fazla önem kazanmaktadır. Kamu kesiminde de son zamanlarda yoğun ilgi duyulan performansa göre ücretleme, Türkiye’de özellikle sağlık sektöründe yaygın olarak kullanılmaya başlanılmıştır. Bu sebeple etkin bir rekabet ortamıoluşturup, kaliteli hizmet sunumu ile müşteri memnuniyetini gerçekleştirmede büyük bir payıolan bu sistemin olumlu yönlerini görüp, üzerinde ayrıntılıbir biçimde durulmasıgerekmektedir. Performansa göre ücret uygulamasında birçok sorunla karşılaşılmaktadır. Sağlık politikasıbelirlemede PGÜ’nün öncelik kazanması, hasta aleyhine gelişmelere yol açabilmektedir. Bu sorunlar karşısında sisteme yöneltilen eleştiriler de artmaktadır. Bu eleştirilerden birisi, özellikle de bireysel performansa göre ücret sistemi başta olmak üzere, PGÜ sistemlerinin dayandığıteorik temellerin tümden geçersiz olduğu yönündedir. Dolayısıyla, bu görüşe göre, bu sistemlerin başarılıolmasımümkün görülmemektedir. Diğer yandan literatürde, sistemin kendisi değil, uygulama hatalarının olumsuzluklara yol açtığıgörüşü ağır basmaktadır. Buna göre uygulama sırasında yapılan hataların giderilmesi sistemin başarısıaçısından belirleyici olmaktadır. Bu araştırma KAHRAMANMARAŞDevlet Hastanesi, Kadın Doğum ve Çocuk Hastanesi’nde çalışan doktorların, performansa göre ücretlendirme uygulamalarının negatif yönlerini tespit etmek amacıyla yapılmıştır. Araştırmada veri toplama aracıolarak anket kullanılmıştır. Anketle toplanan sayısal verilerin çözümlenmesinde yüzde analizi, Oluşturulan hipotezleri test etmek amacıyla ANOVA analizi kullanılmıştır. Doktorların PGÜ sistemine ilişkin ankette yer alan önermelere verdikleri yanıtlara bağlıolarak oluşturulan katılımcıgruplarıarasında anlamlıfarklılıklar olup olmadığına ilişkin dört tane araştırma hipotezi kurgulanmışve araştırma için elde edilen veriler ile analiz edilmişlerdir. Araştırma hipotezlerinin tümünün yapılan incelemeler sonucunda doğrulandığıgörülmüştür. Doktorlar işyüklerine, PGÜ sistemini güvenilir bulmalarına, PGÜ sisteminden memnuniyet düzeylerine ve PGÜ sisteminin performans ve motivasyonlarınıne düzeyde etkilediğine ilişkin algılamalarına göre, PGÜ sistemini farklıölçülerde değerlendirmektedirler

Comparative review of biochemistry and cell anatomy of the hepatic tissue in rats administered some anti hypertensive drug for a long time

The adverse biochemical and structural effects of antihypertensive drugs over a long period (clonidine, methyldopa, rilmenidine, amlodipine, ramipril) on hepatic tissue has been examined in this study. The results are considered to be beneficial for the identification of indications and contraindications in hypertensive patients. Severe bile duct proliferation, portal inflammation, interface hepatitis, focal necrosis and hepatocyte degeneration were demonstrated in the clonidine and amlodipine groups, which had higher oxidant parameters, aspartate aminotransferase, alanine amino transferase and lactate dehydrogenase activity and a higher amount of 8-OH Gua. In the group receiving rilmenidine, all the histopathological findings were the same as those in the clonidine and amlodipine groups, except for bile duct proliferation and interface hepatitis. On histopathological examination of the cell anatomy, it was shown that methyldopa and ramipril caused mild liver damage. While clonidine and amlodipine gave rise to severe liver damage, rilmenidine caused moderate damage, and methyldopa and ramipril led to mild loss of liver function.Colegio de Farmacéuticos de la Provincia de Buenos Aire

Towards a three-dimensional microfluidic liver platform for predicting drug efficacy and toxicity in humans

Although the process of drug development requires efficacy and toxicity testing in animals prior to human testing, animal models have limited ability to accurately predict human responses to xenobiotics and other insults. Societal pressures are also focusing on reduction of and, ultimately, replacement of animal testing. However, a variety of in vitro models, explored over the last decade, have not been powerful enough to replace animal models. New initiatives sponsored by several US federal agencies seek to address this problem by funding the development of physiologically relevant human organ models on microscopic chips. The eventual goal is to simulate a human-on-a-chip, by interconnecting the organ models, thereby replacing animal testing in drug discovery and development. As part of this initiative, we aim to build a three-dimensional human liver chip that mimics the acinus, the smallest functional unit of the liver, including its oxygen gradient. Our liver-on-a-chip platform will deliver a microfluidic three-dimensional co-culture environment with stable synthetic and enzymatic function for at least 4 weeks. Sentinel cells that contain fluorescent biosensors will be integrated into the chip to provide multiplexed, real-time readouts of key liver functions and pathology. We are also developing a database to manage experimental data and harness external information to interpret the multimodal data and create a predictive platform