Modern Approaches To Treating Hospital Acquired Infections: An Overview Of Current Treatments Using Antibiotics And New Therapies Centered Around Photo-Activated Porphyrins, Meghan Johns

Senior Honors Theses

Annually, hospital-acquired infections (HAIs) affect hundreds of thousands of people in the U.S. and impose a great economic burden. The current problem is further exacerbated due to the failure of traditional treatment strategies considering the rise in antimicrobial resistance rates. Besides the fact that antimicrobial resistances complicates clinical treatment strategies, patients are also more vulnerable to secondary infections and complications from prolonged antibiotic use. As a result, research investigating novel treatment strategies for bacterial infections has recently increased. A strategy using porphyrin-based compounds is showing promise. Porphyrins and their derivatives have exhibited bactericidal effects against Gram-positive bacteria by the destruction …

Antibiotic Susceptibility Of Proteus Mirabillis That Isolates Of Diabetic Foot Ulcers In Al- Diwaniyah Hospital, Aseel Hussein Jaber, Suaad A. Fazaa Almiyah

Al-Qadisiyah Journal of Pure Science

The current study have been included 250 samples diabetic foot ulcer patients attending in Al-Diwaniyah Teaching Hospital and private clinics at a period of study from beginning October 2021 to February 2022, Isolates were identified by morphological form on blood agar and macConkey agar, traditional biochemical tests and then confirmed by Vitek 2 system. The result of bacterial culture have been recorded that only 80 samples had positive result to P. mirabilis formed (32%) of this result. Prevalence of P. mirabilis isolates in male more than female (34.78%) and (28.57%) respectively, after then were determination of antibiotics susceptibility pattern of …

Expanding Our Grasp Of Two-Component Signaling In Clostridioides Difficile, Orlando Berumen Alvarez, Erin B. Purcell

Chemistry & Biochemistry Faculty Publications

The intestinal pathogen Clostridioides difficile encodes roughly 50 TCS, but very few have been characterized in terms of their activating signals or their regulatory roles. A. G. Pannullo, B. R. Zbylicki, and C. D. Ellermeier (J Bacteriol 205:e00164-23, 2023, https://doi.org/10.1128/jb.00164-23) have identified both for the novel C. difficile TCD DraRS. DraRS responds to antibiotics that target lipid-II molecules in the bacterial cell envelope, and regulates the production of a novel glycolipid necessary for bacitracin and daptomycin resistance in C. difficile.

Synthesis Of Bioactive Heterocycles, Shaila Akter Shetu

Theses and Dissertations

The Discovery of a variety of heterocyclic drugs for the treatment of cancer and other diseases (e.g, neglected tropical diseases) is a medical breakthrough and inspiring for the research community as a whole. A wide range of natural, semi-synthetic, and synthetic anticancer drugs are synthesized using various methods. Among them, β -lactams stand out as a novel class of antibiotics that has different types of biological as well as anti-cancer properties. β -lactam has become a premier and active research subject towards the development of revolutionary anti-cancer drugs. In recent years, a large amount of investigations have been done to …

Extraction And Partial Purification Of An Antibiotic-Like Compound From The Soil Bacterium Rhodococcus Strain Kchxc3, Elizabeth Bond

Undergraduate Honors Theses

Rhodococcus bacteria have many secondary metabolic pathways that may produce novel natural products. The bacterium Rhodococcus strain KCHXC3 was isolated from a soil sample collected near Kingsport, Tennessee and was found to produce an inhibitory compound active against a broad array of bacterial species, including the Gram negative pathogen Shigella sonnei. The aim of this research is to extract and purify the compound for future structure elucidation. A mixture of compounds from 3 month old agar plates inoculated with strain KCHXC3 was extracted using ethyl acetate. The crude extract was then partially purified utilizing a Sephadex LH-20 column, followed …

Antibacterial Activity, Structure-Activity Relationships, And Scale-Up Reaction Of 1,3,4-Oxadiazoles, Olivia Marie Smith

Undergraduate Honors Thesis Projects

Oxadiazoles are compounds in the field of organic chemistry that have been gathering interest in the medicinal chemistry and microbiology communities for their biological properties, which range from anti-inflammatory agents, to chemotherapy drugs, to antibiotics. The synthesis of oxadiazoles can be difficult due to the expensive and complex nature of the techniques used as well as the volatile reagents and elevated temperatures that are often required in organic synthesis. The Grote lab has recently developed a new method for the synthesis of 1,3,4-oxadiazoles under mild conditions. The goals of this thesis were thus twofold: to develop a viable scale-up procedure …

Biotinylation As A Tool To Enhance The Uptake Of Small Molecules In Gram-Negative Bacteria, Ankit Pandeya, Ling Yang, Olaniyi Alegun, Chamikara Karunasena, Chad Risko, Zhenyu Li, Yinan Wei

Chemistry Faculty Publications

Antibiotic resistance is a major public health concern. The shrinking selection of effective antibiotics and lack of new development is making the situation worse. Gram-negative bacteria more specifically pose serious threat because of their double layered cell envelope and effective efflux systems, which is a challenge for drugs to penetrate. One promising approach to breach this barrier is the “Trojan horse strategy”. In this technique, an antibiotic molecule is conjugated with a nutrient molecule that helps the antibiotic to enter the cell through dedicated transporters for the nutrient. Here, we explored the approach using biotin conjugation with a florescent molecule …

Donnan Potential Across The Outer Membrane Of Gram-Negative Bacteria And Its Effect On The Permeability Of Antibiotics, Olaniyi Alegun, Ankit Pandeya, Jian Cui, Isoiza Ojo, Yinan Wei

Chemistry Faculty Publications

The cell envelope structure of Gram-negative bacteria is unique, composed of two lipid bilayer membranes and an aqueous periplasmic space sandwiched in between. The outer membrane constitutes an extra barrier to limit the exchange of molecules between the cells and the exterior environment. Donnan potential is a membrane potential across the outer membrane, resulted from the selective permeability of the membrane, which plays a pivotal role in the permeability of many antibiotics. In this review, we discussed factors that affect the intensity of the Donnan potential, including the osmotic strength and pH of the external media, the osmoregulated periplasmic glucans …

Development Of Small Molecule Inhibitors Of Therapeutic Target Enzymes: Paths To Discover Novel Antimicrobials, Thahani Shifna Habeeb Mohammad

Dissertations

The rising antimicrobial resistance to antibiotics is a major global problem, which has been exacerbated by the inappropriate use of antibiotics. The effectiveness of frequently prescribed penicillin derivatives and β-lactamase inhibitors are compromised by the evolution of bacterial β-lactamases and antibiotic-resistant bacteria. Consequently, design and synthesis of small-molecule inhibitors of identified novel antibiotic targets is an urgent unmet medical need. We previously demonstrated that N-functionalized α-aminocyclobutanones can act as peptidomimetic enzyme inhibitors, including inhibition of a key esterase in Francisella Tularensis. The carbonyl of a cyclobutanone is electrophilic due to ring strain, therefore cyclobutanone derivatives can serve as transition state …

Two Forms Of Tyrosyl-Trna Synthetase From Pseudomonas Aeruginosa: Characterization And Discovery Of Inhibitory Compounds, Casey Anne Hughes, Varesh Gorabi, Yaritza Escamilla, Frank B. Dean, James M. Bullard

Chemistry Faculty Publications and Presentations

Pseudomonas aeruginosa is a multidrug-resistant (MDR) pathogen and a causative agent of both nosocomial and community-acquired infections. The genes (tyrS and tyrZ) encoding both forms of P. aeruginosa tyrosyl-tRNA synthetase (TyrRS-S and TyrRS-Z) were cloned and the resulting proteins purified. TyrRS-S and TyrRS-Z were kinetically evaluated and the Km values for interaction with Tyr, ATP, and tRNATyr were 172, 204, and 1.5 μM and 29, 496, and 1.9 μM, respectively. The kcatobs values for interaction with Tyr, ATP, and tRNATyr were calculated to be 3.8, 1.0, and 0.2 s–1 and 3.1, 3.8, and 1.9 s–1, …

Glutaminyl-Trna Synthetase From Pseudomonas Aeruginosa: Characterization, Structure, And Development As A Screening Platform, Yaritza Escamilla, Casey A. Hughes, Jan Abendroth, David M. Dranow, Samantha Balboa, Frank B. Dean, James M. Bullard

Chemistry Faculty Publications and Presentations

Pseudomonas aeruginosa has a high potential for developing resistance to multiple antibiotics. The gene (glnS) encoding glutaminyl-tRNA synthetase (GlnRS) from P. aeruginosa was cloned and the resulting protein characterized. GlnRS was kinetically evaluated and the KM and kcatobs , governing interactions with tRNA, were 1.0 μM and 0.15 s-1 , respectively. The crystal structure of the α2 form of P. aeruginosa GlnRS was solved to 1.9 Å resolution. The amino acid sequence and structure of P. aeruginosa GlnRS were analyzed and compared to that of GlnRS from Escherichia coli. Amino acids that interact with ATP, glutamine, and tRNA are well …

Influence Of Conformational Restriction On The Antibacterial Activity And Ribosomal Selectivity Of Aminoglycoside Antibiotics, Michael Gabriel Pirrone

Wayne State University Dissertations

The ever-increasing threat posed by multidrug-resistant infectious bacteria necessitates

the development of novel antibiotics. Aminoglycoside antibiotics are growing in interest due to

their broad spectrum of activity, lack of known drug related allergies, low manufacturing cost,

and their well-studied mechanism of action. The simplification of rational drug design due to the

well-studied mechanism of action is the key to overcoming the issues presented by these drugs,

namely ototoxicity and nephrotoxicity.

A study of the effect of the conformation of the aminoglycoside ring I side chain is

described wherein it was discovered that an increase in a particular conformation augments the …

Lysyl-Trna Synthetase From Pseudomonas Aeruginosa: Characterization And Identification Of Inhibitory Compounds, Samantha Balboa, Yanmei Hu, Frank B. Dean, James M. Bullard

Chemistry Faculty Publications and Presentations

Pseudomonas aeruginosa is an opportunistic pathogen that causes nosocomial infections and has highly developed systems for acquiring resistance against numerous antibiotics. The gene (lysS) encoding P. aeruginosa lysyl-tRNA synthetase (LysRS) was cloned and overexpressed, and the resulting protein was purified to 98% homogeneity. LysRS was kinetically evaluated, and the Km values for the interaction with lysine, adenosine triphosphate (ATP), and tRNALys were determined to be 45.5, 627, and 3.3 µM, respectively. The kcatobs values were calculated to be 13, 22.8, and 0.35 s−1, resulting in kcatobs/KM values of 0.29, 0.036, and 0.11 s−1µM−1, …

Antifungal Defense Molecules From Bacterial Symbionts Of North American Trachymyrmex Ants, Georgia Scherer

CMC Senior Theses

Defensive symbioses, in which microbes provide molecular defenses for an animal host, hold great potential as untapped sources of therapeutically useful antibiotics. Fungus-growing ants use antifungal defenses from bacterial symbionts to suppress pathogenic fungi in their nests. Preliminary chemical investigations of symbiotic bacteria from this large family of ants have uncovered novel antifungal molecules with therapeutic potential, such as dentigerumycin and selvamicin.

In this study, the bacterial symbionts of North American Trachymyrmex fungus-growing ants are investigated for antifungal molecules. Plate-based bioassays using ecologically-relevant fungal pathogens confirmed that these bacteria have antifungal activity. In order to purify and identify the antifungal …

Synthesis Of An Ideal Inhibitor For The Lpxc Enzyme, Taejun Lee

Honors Theses

Due to the growing need of antibiotics in modern day medicine, this study attempts to apply a method of medicinal chemistry that would create a novel inhibitor for a lesser known target of gram negative bacteria, the LpxC enzyme. This study proposes that a synthetic plan which consists of combining components of different molecules would create a more effective inhibitor. These components include a binding group for the active site of the enzyme, a hydrophobic chain which has been shown to interact with an allosteric site on the LpxC enzyme, and the isoxazoline ring which interacts with the zinc ion. …

Interaction Of High Molecular Weight Compounds With A, Β-Unsaturated Carbonyl Moiety With Mammalian And Drosophila Melanogaster Thioredoxin Reductase, Anupama Tuladhar

FIU Electronic Theses and Dissertations

The thioredoxin system is the major cellular reductant system present in the cell, whose role is to maintain cellular redox homeostasis. It does this in part, by regulating the activity of many other enzymes including ribonucleotide reductase, which is essential for DNA synthesis. It also acts as an antioxidant, reducing destructive reactive oxygen species. The thioredoxin system is comprised of thioredoxin (Trx) which reduces target protein disulfide bridges by thiol-disulfide exchange and thioredoxin reductase (TrxR) which reduces Trx back to its active state. Thioredoxin reductase is a common target for many cancer drugs including cisplatin and auranofin. Recently we have …

Discovery And Characterization Of Chemical Compounds That Inhibit The Function Of Aspartyl-Trna Synthetase From Pseudomonas Aeruginosa, Araceli Corona, Stephanie O. Palmer, Regina Zamacona, Benjamin Mendez, Frank B. Dean, James M. Bullard

Chemistry Faculty Publications and Presentations

Pseudomonas aeruginosa, an opportunistic pathogen, is highly susceptible to developing resistance to multiple antibiotics. The gene encoding aspartyl-tRNA synthetase (AspRS) from P. aeruginosa was cloned and the resulting protein characterized. AspRS was kinetically evaluated, and the KM values for aspartic acid, ATP, and tRNA were 170, 495, and 0.5 μM, respectively. AspRS was developed into a screening platform using scintillation proximity assay (SPA) technology and used to screen 1690 chemical compounds, resulting in the identification of two inhibitory compounds, BT02A02 and BT02C05. The minimum inhibitory concentrations (MICs) were determined against nine clinically relevant bacterial strains, including efflux pump …

The Dimerization Domain In Dape Enzymes Is Required For Catalysis, Boguslaw Nocek, Anna Starus, Magdalena Makowska-Grzyska, Blanca Gutierrez, Stephen Sanchez, Robert Jedrzejczak, Jamey C. Mack, Kenneth W. Olsen, Andrzej Joachimiak, Richard C. Holz

Ken Olsen

The emergence of antibiotic-resistant bacterial strains underscores the importance of identifying new drug targets and developing new antimicrobial compounds. Lysine and meso-diaminopimelic acid are essential for protein production and bacterial peptidoglycan cell wall remodeling and are synthesized in bacteria by enzymes encoded within dap operon. Thereforedap enzymes may serve as excellent targets for developing a new class of antimicrobial agents. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) convertsN-succinyl-L,L-diaminopimelic acid to L,L-diaminopimelic acid and succinate. The enzyme is composed of catalytic and dimerization domains, and belongs to the M20 peptidase family. To understand the specific role …

Lysine Biosynthesis In Bacteria: A Metallodesuccinylase As A Potential Antimicrobial Target, Danuta M. Gillner, Daniel P. Becker Ph.D., Richard C. Holz

Richard C. Holz

In this review, we summarize the recent literature on dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) enzymes, with an emphasis on structure–function studies that provide insight into the catalytic mechanism. Crystallographic data have also provided insight into residues that might be involved in substrate and hence inhibitor recognition and binding. These data have led to the design and synthesis of several new DapE inhibitors, which are described along with what is known about how inhibitors interact with the active site of DapE enzymes, including the efficacy of a moderately strong DapE inhibitor.

The Dimerization Domain In Dape Enzymes Is Required For Catalysis, Boguslaw Nocek, Anna Starus, Magdalena Makowska-Grzyska, Blanca Gutierrez, Stephen Sanchez, Robert Jedrzejczak, Jamey C. Mack, Kenneth W. Olsen, Andrzej Joachimiak, Richard C. Holz

Richard C. Holz

The emergence of antibiotic-resistant bacterial strains underscores the importance of identifying new drug targets and developing new antimicrobial compounds. Lysine and meso-diaminopimelic acid are essential for protein production and bacterial peptidoglycan cell wall remodeling and are synthesized in bacteria by enzymes encoded within dap operon. Thereforedap enzymes may serve as excellent targets for developing a new class of antimicrobial agents. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) convertsN-succinyl-L,L-diaminopimelic acid to L,L-diaminopimelic acid and succinate. The enzyme is composed of catalytic and dimerization domains, and belongs to the M20 peptidase family. To understand the specific role …

Kinetic Characterization Of Listeria Monocytogenes 2-C- Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase ( Cms ) Enzymes Using High Performance Liquid Chromatography ( Hplc ), Mark Oblazny

Theses and Dissertations

Infectious diseases, with increasing prevalence of antibiotic resistant bacteria, coupled with the declining rate in discovery of antimicrobial agents, impose one of the most significant threats to human health. Here we identify 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (CMS) as a valid target for antibiotic development which is an enzyme in pathogenic organisms that leads to the biosynthesis of isoprene precursor molecules. Isoprene molecules are one of nature’s most common building blocks that are vital to many biological metabolic processes and are synthesized via the mevalonic acid dependent (MVA), or methylerythritol phosphate (MEP) pathway. Vertebrates utilize the MVA pathway, while many pathogenic bacteria …

Mobility Characteristics Of Azithromycin In Soil, Ryan Minter, Jihyun Kim, Linda Lee

The Summer Undergraduate Research Fellowship (SURF) Symposium

The presence of pharmaceutical and personal care products (PPCPs) in the environment has become a widespread problem in recent decades. Azithromycin, a macrolide antibiotic commonly prescribed for infections in humans, has been detected in waste treatment plant discharge and surface waters across the world. Data on the mobility characteristics of azithromycin in soil is scarce, and further studies must be performed to explore the potential for azithromycin leaching to groundwater or becoming available for plant uptake. In this study, azithromycin sorption isotherms were measured on eight soils varying in pH, organic carbon content, and clay content. Soil was equilibrated with …

Triarylmethyl Cation Catalysis: A Tunable Lewis Acid Organocatalyst For The Synthesis Of Bisindolylmethanes, Nicholas G. Boekell, Dana J. Cerone, Maria M. Boucher, Wilfried B. Nganyak Tentchou, Christine G. Reavis, Ifeanyi I. Okoh, Jordan O.A. Reid, Hayley E. Berg, Briana A. Chang, Cheyenne S. Brindle

Faculty Scholarship

Triarylmethyl cations serve as tunable organocatalysts for the synthesis of bisindolylmethanes. The catalyst structure can be modified to increase or decrease reactivity as needed to match the requirements of the substrate. High yields are achieved for a variety of substrates by using these green catalysts. Catalyst tuning allows for the use of less reactive electrophiles by increasing the reactivity of the catalyst. Acid-sensitive products can be isolated under these mild reaction conditions.

Identification And Characterization Of A Chemical Compound That Inhibits Methionyl-Trna Synthetase From Pseudomonas Aeruginosa, Sara Robles, Yanmei Hu, Tahyra Resto, Frank Dean, James M. Bullard

Chemistry Faculty Publications and Presentations

Background: Pseudomonas aeruginosa is an opportunistic pathogen problematic in causing nosocomial infections and is highly susceptible to development of resistance to multiple antibiotics. The gene encoding methionyl-tRNA synthetase (MetRS) from P. aeruginosa was cloned and the resulting protein characterized.

Methods: MetRS was kinetically evaluated and the KM for its three substrates, methionine, ATP and tRNAMet were determined to be 35, 515, and 29 μM, respectively. P. aeruginosaMetRS was used to screen two chemical compound libraries containing 1690 individual compounds.

Results: A natural product compound (BM01C11) was identified that inhibited the aminoacylation function. The compound inhibited P. aeruginosa MetRS with an …

Part 1: Design, Synthesis, And Evaluation Of Novel Gram-Positive Antibiotics Part 2: Synthesis Of Dihydrobenzofurans Via A New Transition Metal Catalyzed Reaction Part 3: Design, Synthesis, And Evaluation Of Bz/Gabaa Α6 Positive Allosteric Modulators, Christopher Michael Witzigmann

Theses and Dissertations

Part 1. Lead compound SK-03-92 represents a new scaffold for antibiotic drug discovery. Development of a new process for the synthesis of analogs has led to the development of a number of new ligands with even more potent activity against gram-positive bacteria, including drug-resistant strains of S. aureus. Compounds 36 and 38 represent some of the most potent analogs developed thus far, and preliminary results indicate that they are also not cytotoxic. Research into a Heck-mediated transition metal catalyzed pathway towards electron-rich stilbenoid analogs has greatly expanded the scope of future SAR studies. This development has led to 14 new …

Development Of In Vivo Systems For Detecting And Studying Ribosome Inhibition By Small Molecules, Shijie Huang

Chemistry and Chemical Biology ETDs

The ribosome is the quintessential antibacterial drug target, with many structurally and mechanistically distinct classes of antibacterial agents acting by inhibiting ribosome function. Detecting and quantifying ribosome inhibition by small molecules and investigating their binding modes and mechanisms of action are critical to antibacterial drug discovery and development efforts. To develop a ribosome inhibition assay that is operationally simple, yet provides direct information on the drug target and the mechanism of action, we have developed engineered E. coli strains harboring an orthogonal ribosome controlled green fluorescent protein reporter that produce fluorescent signal when the O-ribosome is inhibited. As a proof …

Synthesis, Structure-Activity Relationship Study, And Mode Of Action Study Of 1,4-Naphthoquinone Based Anticancer And Antimicrobial Agents, Jaya P. Shrestha

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The first three projects involve the synthesis and the mode of action study of 1,4-naphthoquinone based anticancer agents. These anticancer agents are highly potent against a wide range of cancer cell lines. These compounds showed ~8-fold selectivity towards the lung cancer cell line than the normal cell line. We also studied the mode of action and observed that generation of reactive oxygen species is the primary mode of action.

The final project involves the synthesis of multi-cationic antimicrobial agents. These compounds are active against both bacteria and fungi. These compounds are very easy to synthesize and can be scaled up …

Synthesis Of Apramycin And Paromomycin Derivatives As Potential Next Generation Aminoglycoside Antibiotics And Chemistry Of Isothiocyanato Sialyl Donors, Appi Reddy Mandhapati

Wayne State University Dissertations

AGAs are clinically important antibacterials for human therapy and have long been used as highly potent antibiotics for treating several bacterial infections. The fidelity of protein synthesis is affected by AGAs in the course of binding to specific sites of the bacterial rRNA. The clinical use of AGAs and their applications as therapeutics is restricted by toxicity (irreversible ototoxicity and reversible nephrotoxicity) and by the resistance of pathogens. The objective of this research was the development of proficient AGAs that are less toxic (i.e., more selective) and that evade resistance. The first three chapters of this thesis are aimed towards …

Adsorption Of Antibiotics By Vermiculite, Mosa J. Ferdous

Dissertations and Theses

The occurrence of residual antibiotics in the environment has been a worldwide issue and warrants the development of inexpensive yet effective methods for antibiotics removal from contaminated water. In this thesis work, the adsorption of four antibiotics, namely chlorotetracycline (CTC), oxytetracycline (OTC), ofloxacin (OFL), and enrofloxacin (ENR), onto natural vermiculite has been studied using batch (static) and column (dynamic) adsorption techniques. The Langmuir and Freundlich isotherm models were initially used to explain the adsorption processes. The separation factor (RL) values derived from the Langmuir model and the 1/n values derived from Freundlich model in the present investigation were less than …

Synthesis, Rna Binding And Antibacterial Studies Of 2-Dos Mimetics And Development Of Polymer Supported Nanoparticle Catalysts For Nitroarene And Azide Reduction, Venkata Reddy Udumula

Theses and Dissertations

Project I 2-Deoxystreptamine (2-DOS), the most conserved central scaffold of aminoglycosides, is known to specifically recognize the 5'-GU-'3 sequence step through highly conserved hydrogen bonds and electrostatic interactions within and without the context of aminoglycosides (Figure 1a). We proposed that a novel monomeric unnatural amino acid building block using 2-DOS as a template would allow us to develop RNA binding molecules with higher affinity and selectivity than those currently available. Conjugating two or more of the monomeric building blocks by an amide bond would introduce extra hydrogen bonding donors and acceptors that are absent in natural aminoglycosides and increase specificity …