Medical Biochemistry Commons^™

Development Of A Chemical Biology Approach To Uncover The Influence Of Sequence Variations On Ces1 Activity In Live Cells, Samuel James Knebel

Masters Theses

Drug metabolism is the biochemical process of modifying drugs to detoxify and remove them through enzymatic transformations. These biotransformation’s occur primarily in the liver and are critical to understanding how pharmaceutical compounds are chemically altered inside the human body. Human carboxylesterases (CESs) catalyze the hydrolysis of esters, amides, thioesters, and carbamates. CES-mediated hydrolysis plays an important role in the metabolism of many drugs including the first FDA approved antiviral treatment for COVID-19, remdesivir (Veklury), the seizure control medication rufinamide (Banzel), and the flu antiviral drug oseltamivir (Tamiflu). CES activity is known to be influenced by a variety of factors including …

Autodocking Studies Of Oxygenated Fullerenes As Inhibitors Of The Hiv Protease, Michael Kaminski

All Student Theses and Dissertations

In a previous study, several oxygenated fullerene compounds were produced by ozonation of C60 (Buckminsterfullerene) and were identified by elemental analysis and by SALI (surface analysis by laser ionization). Some of these compounds, especially a batch, SK-5, a mixture of C60O1-8, were shown to inhibit activities of HIV-Protease with IC50 (concentration for 50% inhibition) of 1 mg/mol in the in-vitro studies. The oxygenated fullerenes were shown to have epoxide, ketones, and hydroxyl functionalities. As expected, C60 interacted with ozone with alkene functionality and not as an aromatic compound. It was postulated that C60O had epoxide functionality, as a product of …

Development Of Raman Spectroscopy-Integrated Calcium Oxalate Crystallization Index (Rcoci) Test And Its Clinical Validation For Diagnosing Calcium Oxalate Urolithiasis, Kamonchat Boonkam

Chulalongkorn University Theses and Dissertations (Chula ETD)

Urinary stone disease is mostly formed in the kidney and is highly recurrent. The most common type of urinary stones is calcium oxalate (CaOx). The development of urinary screening tests for estimating risk of CaOx stone formation is still challenging. Recently, we developed a urinary test, called indole-reacted calcium oxalate crystallization index (iCOCI) test, that provided a high diagnostic accuracy for CaOx urolithiasis. However, the iCOCI test is time-consuming and highly acidic chemicals are required for quantifying amount of CaOx. In this study, we proposed to develop a new method, called Raman spectroscopy-integrated calcium oxalate crystallization index (rCOCI) test, that …

Crispr-Cas12a-Based Detection And Differentiation Of Mycobacterium Spp., Peeraphan Compiro

Chulalongkorn University Theses and Dissertations (Chula ETD)

Mycobacterium species cause several vital human diseases, including tuberculosis (TB) and non-tuberculous mycobacterial (NTM) infections. TB is a chronic infectious disease caused by the Mycobacterium tuberculosis complex (MTBC). Additionally, non-tuberculous mycobacteria infections are caused by major NTM species, including Mycobacterium abscessus, Mycobacterium avium, Mycobacterium fortuitum, Mycobacterium kansasii, Mycobacterium gordonae, and Mycobacterium intracelulare, are medically necessary. Both groups of infections can lead to outbreaks in immunocompromised individuals and AIDS patients. It is crucial to differentiate between these two groups of mycobacterial infections, as they require distinct treatment approaches. However, initial diagnosis poses limitations in terms of time and diagnostic tools. Therefore, …

การแสดงออกและระดับการเติมหมู่เมทิลของยีนตัวรับวิตามินดีในโรคกระดูกสันหลังส่วนเอวเสื่อม, ลดาวัลย์ วัชรินทรางกูร

Chulalongkorn University Theses and Dissertations (Chula ETD)

โรคกระดูกสันหลังส่วนเอวเสื่อม (lumbar degenerative disease, LDD) เป็นสาเหตุสำคัญที่ทำให้ผู้สูงอายุไม่สามารถทำกิจกรรมต่าง ๆ ได้ตามปกติจึงส่งผลต่อการดำเนินชีวิตประจำวัน ในปัจจุบันการวินิจฉัย ตรวจติดตามและรักษาโรค อาศัยภาพถ่ายคลื่นแม่เหล็กไฟฟ้า (magnetic resonance imaging, MRI) เพื่อช่วยตรวจหมอนรองกระดูกสันหลังเสื่อม การรักษาประกอบด้วยการให้ยาไปจนถึงการผ่าตัด ซึ่งทำให้เกิดบาดแผลและใช้เวลาในการฟื้นฟู โรคกระดูกสันหลังเสื่อมมีส่วนเกี่ยวข้องกับวิตามินดีที่มีบทบาทเสริมสร้างความแข็งแรงให้กับกระดูก ดังนั้นในงานวิจัยนี้จึงมีความสนใจศึกษาความสัมพันธ์ของระดับวิตามินดี การแสดงออกยีนและโปรตีนตัวรับวิตามินดี (vitamin D receptor, VDR) และระดับการเติมหมู่เมทิลของ VDR (VDR promoter methylation) ในเซลล์เม็ดเลือดขาวและเนื้อเยื่อ nucleus pulposus (NP) จากในผู้ป่วย LDD จำนวน 35 ราย เทียบกับกลุ่มควบคุม จำนวน 15 ราย จากการวิจัยพบว่ากลุ่ม LDD มีภาวะการทำกิจกรรมถูกจำกัด (40.00 %) จากการประเมิน Oswestry disability index (ODI) มากกว่ากลุ่มควบคุม (13.33 %) อย่างมีนัยสำคัญ (P < 0.001) และกลุ่ม LDD มีระดับ serum vitamin D เท่ากับ 24.30 ng/mL สูงกว่ากลุ่มควบคุม (16.20 ng/mL) อย่างมีนัยสำคัญ (P = 0.039) ส่วนระดับการแสดงออกของยีน VDR ทั้งในเซลล์เม็ดเลือดขาวและเนื้อเยื่อ NP ของทั้งสองกลุ่มไม่แตกต่างกัน แต่ระดับของโปรตีน VDR ในเลือดนั้น พบว่ากลุ่มควบคุมมีโปรตีน VDR เท่ากับ 53.28 ng/mg protein ต่ำกว่ากลุ่ม LDD ที่มีระดับการแสดงออกเท่ากับ 64.60 ng/mg protein อย่างมีนัยสำคัญ (P = 0.02) นอกจากนี้กลุ่ม LDD มีระดับ VDR promoter methylation เท่ากับ 22.02 % ในขณะที่กลุ่มควบคุมมีเพียง 14.18 % ซึ่งกลุ่ม LDD มีการเติมหมู่เมทิลสูงกว่ากลุ่มควบคุมอย่างมีนัยสำคัญ (P < 0.001) นอกจากนี้เมื่อศึกษาความสัมพันธ์ของระดับความรุนแรงของโรคที่แบ่งตาม Pfirrmann grade พบว่ามีความสัมพันธ์กันแปรผันกับระดับวิตามินดี (r = 0.588, P < 0.001) และมีความสัมพันธ์แปรผันกับ VDR promoter methylation (r = 0.377, P = 0.026) อีกทั้งพบความสัมพันธ์แปรผันของ VDR mRNA ในเซลล์เม็ดเลือดขาวกับระดับโปรตีน VDR ใน serum (r = 0.420, P = 0.012) นอกจากนี้ได้พบความสัมพันธ์แปรผกผันของระดับวิตามินดีกับ ODI ของผู้ป่วย LDD (r = -0.359, P = 0.034) และความสัมพันธ์แปรผันของ VDR promoter methylation กับดัชนีมวลกาย (r = 0.348, P = 0.041) ดังนั้นสรุปได้ว่าระดับ VDR promoter methylation อาจนำมาประยุกต์และพัฒนาเพื่อนำไปใช้เป็นตัวบ่งชี้ทางชีวภาพในการพยากรณ์ระดับความรุนแรงของโรคได้ในอนาคต

Effects Of Atrazine Exposure On Human Bone Marrow-Derived Mesenchymal Stromal Cells Assessed By Combinatorial Assay Matrix, Crystal C Uwazie, Bonnie M Pirlot, Tyler U Faircloth, Mihir Patel, Rhett N Parr, Halie M Zastre, Peiman Hematti, Guido Moll, Devi Rajan, Raghavan Chinnadurai

Faculty, Staff and Student Publications

INTRODUCTION: Mesenchymal Stromal/Stem cells (MSCs) are an essential component of the regenerative and immunoregulatory stem cell compartment of the human body and thus of major importance in human physiology. The MSCs elicit their beneficial properties through a multitude of complementary mechanisms, which makes it challenging to assess their phenotype and function in environmental toxicity screening. We here employed the novel combinatorial assays matrix approach/technology to profile the MSC response to the herbicide Atrazine, which is a common environmental xenobiotic, that is in widespread agricultural use in the US and other countries, but banned in the EU. Our here presented approach …

Structural Basis Of Ferroportin Inhibition By Minihepcidin Pr73, Azaan Saalim Wilbon, Jiemin Shen, Piotr Ruchala, Ming Zhou, Yaping Pan

Faculty, Staff and Students Publications

Ferroportin (Fpn) is the only known iron exporter in humans and is essential for maintaining iron homeostasis. Fpn activity is suppressed by hepcidin, an endogenous peptide hormone, which inhibits iron export and promotes endocytosis of Fpn. Hepcidin deficiency leads to hemochromatosis and iron-loading anemia. Previous studies have shown that small peptides that mimic the first few residues of hepcidin, i.e., minihepcidins, are more potent than hepcidin. However, the mechanism of enhanced inhibition by minihepcidins remains unclear. Here, we report the structure of human ferroportin in complex with a minihepcidin, PR73 that mimics the first 9 residues of hepcidin, at 2.7 …

Quantitative Measurement Of Protac Intracellular Accumulation, Xin Yu, Jin Wang

Faculty, Staff and Students Publications

In recent years, Proteolysis Targeting Chimera (PROTAC) technology has emerged as one of the most promising approaches to remove disease-associated proteins by utilizing cells' own destruction machinery. To achieve successful degradation of a protein of interest (POI), the heterobifunctional PROTAC molecules must penetrate into the cells first, followed by target engagement and formation of the POI-PROTAC-E3 ligase complex. Based on this understanding, the assessment of cell permeability and in cell target engagement are of great importance to evaluate the efficacy of PROTAC candidates. PROTAC molecules can be classified as non-covalent and covalent, and covalent PROTACs can be further divided into …

Association Of Smoking With Total Oxidant And Antioxidant Levels In Breast Milk, Nesibe Yildiz, Adnan Yilmaz

Makara Journal of Health Research

Background: Breast milk is a natural food that contains all the fluids, energy, and nutrients necessary for the optimum growth and development of newborns. Smoking is a public health problem that has harmful effects on the mother and baby. This study aimed to examine the association of exposure to smoking with total oxidant status (TOS) and total antioxidant status (TAS) in breast milk.

Methods: Healthy mothers without any health problems during their pregnancy and lactation periods were selected as subjects. Eighty-eight milk samples (44 in the smoking group and 44 in the nonsmoking group) were examined. TOS and …

Kras Inhibitor That Simultaneously Inhibits Nucleotide Exchange Activity And Effector Engagement, Cynthia V Pagba, Amit K Gupta, Ali K Naji, Dharini Van Der Hoeven, Kelly Churion, Xiaowen Liang, Jacob Jakubec, Magnus Hook, Yan Zuo, Marisela Martinez De Kraatz, Jeffrey A Frost, Alemayehu A Gorfe

Faculty, Staff and Student Publications

We describe a small molecule ligand ACA-14 (2-hydroxy-5-{[(2-phenylcyclopropyl) carbonyl] amino} benzoic acid) as an initial lead for the development of direct inhibitors of KRAS, a notoriously difficult anticancer drug target. We show that the compound binds to KRAS near the switch regions with affinities in the low micromolar range and exerts different effects on KRAS interactions with binding partners. Specifically, ACA-14 impedes the interaction of KRAS with its effector Raf and reduces both intrinsic and SOS-mediated nucleotide exchange rates. Likely as a result of these effects, ACA-14 inhibits signal transduction through the MAPK pathway in cells expressing mutant KRAS and …

In Silico Identification Of A Β2-Adrenoceptor Allosteric Site That Selectively Augments Canonical Β2ar-Gs Signaling And Function, Sushrut D Shah, Christoffer Lind, Francesco De Pascali, Raymond B Penn, Alexander D Mackerell, Deepak A Deshpande

Department of Biochemistry and Molecular Biology Faculty Papers

Activation of β2-adrenoceptors (β2ARs) causes airway smooth muscle (ASM) relaxation and bronchodilation, and β2AR agonists (β-agonists) are front-line treatments for asthma and other obstructive lung diseases. However, the therapeutic efficacy of β-agonists is limited by agonist-induced β2AR desensitization and noncanonical β2AR signaling involving β-arrestin that is shown to promote asthma pathophysiology. Accordingly, we undertook the identification of an allosteric site on β2AR that could modulate the activity of β-agonists to overcome these limitations. We employed the site identification by ligand competitive saturation (SILCS) computational method to comprehensively map the entire 3D structure of in silico-generated β2AR intermediate conformations and identified …

The Role Of Lipocalin 2 In Type 1 Diabetic Osteopathy, Rawan Mahmoud Bdair

Theses

Lipocalin 2 (LCN2), also known as neutrophil gelatinase-associated lipocalin (NGAL), plays an important role in the innate immune response and functions as a growth factor. The role of LCN2 as an anti-inflammatory protein and its function in bone metabolism is poorly understood. It is hypothesized that the administration of Lipocalin-2 in diabetic and non-diabetic rats will positively improve the bone microstructure. This study investigated the effect of lipocalin2 on bone metabolism in type 1 diabetic osteopathy (T1DO). Three-month-old male Wistar rats (n=24) were obtained from the animal house facility at United Arab Emirates University (UAEU) for this study. All animal …

Computer-Aided Drug Discovery For Helicobacter Pylori, Nicole Ann Vita

Theses and Dissertations (ETD)

Helicobacter pylori is a high-priority drug-resistant pathogen and is currently the only bacteria considered to be a class I carcinogen and there is a critical need to identify novel chemical matter to treat H. pylori infections. Hp is responsible for greater than 60% of gastric cancer related deaths and 89% of all gastric cancer morbidities. In a previous study, our lab identified novel Hp thienopyrmidine inhibitors that target respiratory complex I, an essential enzyme in respiration. Respiratory complex I is a large asymmetric multidomain and membrane bound enzyme and due to these innate features, it is not practical for biophysical …

Unilateral ‘Crazy-Paving’ Pattern: An Exceptional Presentation Of Squamous Cell Carcinoma Of The Lung, Sumeera Banday, Shamim U Khan, Sabina Khan, Surinderpal S Anand, Ashok Shah

Faculty, Staff and Student Publications

The 'crazy-paving' pattern on high resolution computed tomography (HRCT) is a distinct imaging appearance that is still considered to be a radiological hallmark of pulmonary alveolar proteinosis. However, since its first description about three decades ago, more than 40 different clinical entities presenting as 'crazy-paving' patterns have been documented. This rather remarkable but uncommon imaging appearance is now considered to be a non-specific manifestation. A 62-year-old male referred for evaluation of productive cough, breathlessness and fever presented with 'crazy-paving' pattern on HRCT. Endobronchial biopsy done on presentation was consistent with the diagnosis of squamous cell carcinoma. This report highlights this …

Right Ventricular Energetic Biomarkers From 4d Flow Cmr Are Associated With Exertional Capacity In Pulmonary Arterial Hypertension, Xiaodan Zhao, Shuang Leng, Ru-San Tan, Ping Chai, Tee Joo Yeo, Jennifer Ann Bryant, Lynette L S Teo, Marielle V Fortier, Wen Ruan, Ting Ting Low, Ching Ching Ong, Shuo Zhang, Rob J Van Der Geest, John C Allen, Marina Hughes, Pankaj Garg, Teng Hong Tan, James W Yip, Ju Le Tan, Liang Zhong

Faculty, Staff and Student Publications

BACKGROUND: Cardiovascular magnetic resonance (CMR) offers comprehensive right ventricular (RV) evaluation in pulmonary arterial hypertension (PAH). Emerging four-dimensional (4D) flow CMR allows visualization and quantification of intracardiac flow components and calculation of phasic blood kinetic energy (KE) parameters but it is unknown whether these parameters are associated with cardiopulmonary exercise test (CPET)-assessed exercise capacity, which is a surrogate measure of survival in PAH. We compared 4D flow CMR parameters in PAH with healthy controls, and investigated the association of these parameters with RV remodelling, RV functional and CPET outcomes.

METHODS: PAH patients and healthy controls from two centers were prospectively …

Clinicopathological And Prognostic Significance Of Cxcr4 Expression In Osteosarcoma: A Meta-Analysis, I Gusti Ngurah Ananda Wira Kusuma, Grace Yulia Alphani Yapson, John Nolan, I Gede Eka Wiratnaya, I Gede Putu Supadmanaba

BioMedicine

Background: The C-X-C Motif Chemokine Receptor (CXCR4) is an oncogene that has been widely studied and associated with worse clinicopathological features and prognosis outcomes in many types of cancer. Besides that, significance of CXCR4 expression on clinicopathological features and prognostic factors in osteosarcoma (OS) requires further validation.

Aim: We conducted a meta-analysis to evaluate the association between positive CXCR4 expression with clinicopathological features and prognosis in OS.

Methods: Literature searches on Pubmed, Cochrane Library, and Web of Science were conducted systematically up to December 2021 to find relevant references. The effects of CXCR4 expression on clinicopathological characteristics and prognostic were …

Applications Of Covalent Chemistry In Targeted Protein Degradation, Dong Lu, Xin Yu, Hanfeng Lin, Ran Cheng, Erika Y Monroy, Xiaoli Qi, Meng C Wang, Jin Wang

Faculty, Staff and Students Publications

Proteolysis-targeting chimeras (PROTACs) and targeted covalent inhibitors (TCIs) are currently two exciting strategies in the fields of chemical biology and drug discovery. Extensive research in these two fields has been conducted, and significant progress in these fields has resulted in many clinical candidates, some of which have been approved by FDA. Recently, a novel concept termed covalent PROTACs that combine these two strategies has emerged and gained an increasing interest in the past several years. Herein, we briefly review and highlight the mechanism and advantages of TCIs and PROTACs, respectively, and the recent development of covalent PROTACs using irreversible and …

Terminase Subunits From The Pseudomonas-Phage E217, Ravi K Lokareddy, Chun-Feng David Hou, Steven G Doll, Fenglin Li, Richard E Gillilan, Francesca Forti, David S Horner, Federica Briani, Gino Cingolani

Department of Biochemistry and Molecular Biology Faculty Papers

Pseudomonas phages are increasingly important biomedicines for phage therapy, but little is known about how these viruses package DNA. This paper explores the terminase subunits from the Myoviridae E217, a Pseudomonas-phage used in an experimental cocktail to eradicate P. aeruginosa in vitro and in animal models. We identified the large (TerL) and small (TerS) terminase subunits in two genes ∼58 kbs away from each other in the E217 genome. TerL presents a classical two-domain architecture, consisting of an N-terminal ATPase and C-terminal nuclease domain arranged into a bean-shaped tertiary structure. A 2.05 Å crystal structure of the C-terminal domain revealed …

The Detection Of Periodic Reemergence Events Of Sars-Cov-2 Delta Strain In Communities Dominated By Omicron., Claire E. Westcott, Kevin J. Sokoloski, Eric C. Rouchka, Julia H. Chariker, Rochelle H. Holm, Ray A. Yeager, Joseph B. Moore Iv, Erin M. Elliott, Daymond Talley, Aruni Bhatnagar

Faculty and Staff Scholarship

Despite entering an endemic phase, SARS-CoV-2 remains a significant burden to public health across the global community. Wastewater sampling has consistently proven utility to understanding SARS-CoV-2 prevalence trends and genetic variation as it represents a less biased assessment of the corresponding communities. Here, we report that ongoing monitoring of SARS-CoV-2 genetic variation in samples obtained from the wastewatersheds of the city of Louisville in Jefferson county Kentucky has revealed the periodic reemergence of the Delta strain in the presence of the presumed dominant Omicron strain. Unlike previous SARS-CoV-2 waves/emergence events, the Delta reemergence events were geographically restricted in the community …

Integrating Genomic Information With Tumor-Immune Microenvironment In Triple-Negative Breast Cancer, David Otohinoyi, Aditi Kuchi, Jiande Wu, Chindo Hicks

School of Graduate Studies Faculty Publications

Background: the development and progression of triple-negative breast cancer (TNBC) is driven by somatic driver mutations and the tumor-immune microenvironment. To date, data on somatic mutations has not been leveraged and integrated with information on the immune microenvironment to elucidate the possible oncogenic interactions and their potential effects on clinical outcomes. Here, we investigated possible oncogenic interactions between somatic mutations and the tumor-immune microenvironment, and their correlation with patient survival in TNBC. Methods: We performed analysis combining data on 7,875 somatic mutated genes with information on 1,751 immune-modulated genes, using gene-expression data as the intermediate phenotype, and correlated the resulting …