Signaling lipids such as diacylglycerol (DAG) and the phosphatidylinositol polyphosphates (PIPns) play crucial roles in numerous cellular pathways. However, characterization of their activities is hindered by the complexity of associated signaling pathways and of the membrane environment. To address this issue, we have developed lipid probes that are effective for characterizing biological events using different applications, including activity-based probing (PIPns and DAG) and microarray analysis (PIPns). The activity-based probes have been applied to label receptor targets in multiple cancer cell proteomes through photocrosslinking followed by click reactions. The probes were found to label several proteins, as judged by on-gel fluorescence, and labeling was abrogated through various controls, such as heat denaturation and competition. Proteomic studies have been successfully performed to identify protein targets through biotin enrichment followed by mass spectrometric analysis. For microarray analysis, functionalized PIPn probes were synthesized and applied to develop a high throughput microarray analysis to measure protein-lipid binding affinity. These approaches will be invaluable for characterizing PIPn/DAG-regulated events and their involvement in disease. The design, synthesis and application of these lipid probes are included in this dissertation. In addition, the design and synthesis of other lipid probes are discussed, such as bis(monoacylglycero)phosphate (BMP), and lysophophatidylcholine (LPC) analogs.

Heparin binding (HB) proteins mediates a wide range of important cellular processes, which makes this class of proteins biopharmaceutically important. Engineering HB proteins could bring many advantages, but it necessitates cost effective and efficient purification methodologies compared to the currently available methods. One of the most important classes of heparin binding protein is the fibroblast growth factors (FGFs) and its receptors (FGFRs). In this study, we report an efficient off-column purification of FGF-1 from soluble fractions and purification of the D2 domain of FGFR from insoluble inclusion bodies, using a weak amberlite cation (IRC) exchanger. This approach is an alternative to conventional affinity column chromatography, which exhibit several disadvantages, including time-consuming experimental procedures and regeneration and results in high cost for production of recombinant proteins. Authenticity of the purified proteins was verified by SDS-PAGE and MALDI mass spectrum analysis. Results of the heparin binding chromatography and steady state fluorescence experiments showed that the FGF-1 and the D2 are in a native biologically active conformation. The findings of this study will not only aid an in-depth investigation of this class of proteins but will also provide avenues for inexpensive and efficient purification of other important biological macromolecules.

Despite over a century of advancement, tuberculosis remains a grave threat to world health. In particular, third world countries continue to struggle with the crushing weight of the disease. Furthermore, the emergence of drug resistance in TB strains poses a significant threat to the first world where incidence and mortality is low. The dwindling efficacy of current drug regimens necessitates research into new small molecules capable of arresting the growth and spread of TB. The capuramycin family of nucleoside antibiotics shows strong potential to become part of this new generation of anti-TB small molecules. Indeed, their ability to inhibit Translocase I, a key enzyme in the biosynthesis of bacterial cell walls, makes them exciting targets for medicinal chemistry efforts. The synthesis of the family focused on dividing the molecules into three congruent, synthetically separate parts: the variable amide linked tail, the hexauronic acid linker, and the uridine "head". Construction of the ubiquitous core structure comprised of the hexauronic acid and uridine would allow rapid diversification while the variable tail would allow SAR studies and development of novel new members of the family.

Glycosaminoglycans (GAGs) are complex linear chain carbohydrate molecules found on virtually all animal cell surfaces. Owing to their negatively charged nature, GAGs interact with a number of different proteins. Thus, although they have great potential as therapeutic agents, their apparent promiscuous interactions increase their side effect risk. GAG mimetics, including GAG oligosaccharides and non-saccharide GAG mimetics (NSGMs) are viable approaches to address this. This work discusses sulfated benzofuran thrombin inhibitors with submaximal protease inhibition, sulfated diflavonoid inhibitors of plasmin and GAG oligosaccharides with selectivity for human neutrophil elastase (HNE). Anticoagulants are very important for the treatment of thrombotic diseases. The adverse effects associated with current clinically used anticoagulants warrant the continuous search for new agents. Thrombin, being the central player in the coagulation cascade, remains a very important target for anticoagulant therapy, however drugs inhibiting its activity carry the risk of prolonged bleeding. Based on a previously identified sulfated benzofuran thrombin inhibitor, we have developed analogs with submaximal inhibition of the protease. These agents inhibit thrombin with efficacies approaching 50%, for both chromogenic and macromolecular substrates, ensuring a basal level of thrombin activity even at saturating inhibitor concentrations. The most potent of these compounds had a potency of 1.8 µM, 2-3 fold better than the lead. Additionally, these compounds utilize an allosteric mechanism for thrombin inhibition. Further, studies have revealed structural features responsible for submaximal thrombin inhibition. Fibrinolysis is an important part of hemostasis and plasmin is the most important fibrinolytic enzyme. Anti-plasmin agents are thus important for conditions such as hemophilia; however, there are no clinically used direct plasmin inhibitors. By structural modifications of a previously identified sulfated diflavonoid plasmin inhibitor, we have achieved a compound with 12-fold better potency (IC50 = 6.3 ± 0.4 µM), and a selectivity index of at least 22 over closely related serine proteases. We have shown that this compound inhibits plasmin mediated clot lysis, and further demonstrated that its activity is reversible using protamine sulfate, indicating its potential as a lead for the development of clinical anti-plasmin agents. HNE, a serine protease associated with inflammatory diseases is known to be inhibited by GAGs. However, the interactions at the molecular level have remained elusive. Using biochemical methods, and by studying the inhibitory potency of different GAGs and GAG oligosaccharides, we have shown that an octasaccharide may be the ideal GAG length for the achievement of potent HNE inhibition. Under our assay conditions, the inhibition of HNE by an octasaccharide species was only 5-fold less than that of unfractionated heparin, whereas the hexasaccharide species was 30-fold less active. The data also suggests that the inhibition of HNE by GAGs is via an allosteric mechanism and using molecular modeling, we have identified putative GAG binding sites on HNE and further identified GAG species with potential selectivity for anti-HNE activity

“Bath salts” and “plant food”, which were legally marketed synthetic cathinones, have a high potential for abuse. Several recent studies indicate that 3,4-methylenedioxypyrovalerone (MDPV) and 3,4-methylenedioxymethcathinone (methylone), two common drugs of this type, have similar pharmacology to controlled psychostimulants such as cocaine, methamphetamine, and methylphenidate. MDPV acts as a norepinephrine (NE) and dopamine (DA) reuptake inhibitor via blockade of their transporters (DAT and NET), whereas methylone is a substrate for the NE, DA, and serotonin (5-HT) transporters, increasing the non-vesicular release of these monoamines. Both drugs cause significant increases in the levels of these neurotransmitters in the cleft. Increases in DA are associated with euphoric effects and thus promote drug abuse and addiction, hence the high addiction potential of MDPV and methylone. Indeed, MDPV is 50 times more potent at the DAT and 10 times more potent at the NET than cocaine. Here, we examined the pharmacokinetics of MDPV and methylone in the brain and plasma, following intraperitoneal injection in mice. These types of injections have similar pharmacokinetics to insufflation (snorting), which is the manner in which MDPV and methylone are commonly abused. Briefly, adolescent male Swiss-Webster mice were injected intraperitoneally with either 10 mg/kg MDPV or 10 mg/kg methylone, and brains and plasma were collected at the following time points: 1, 10, 15, 30, 60, and 120 minutes. Samples were then flash-frozen and stored at -70°C until analysis. Samples were spiked with deuterium-labeled MDPV or methylone (internal standards), and the drugs were extracted from tissue using a previously published solid phase extraction method. Chromatographic separation of the compounds was achieved using a HILIC column with a gradient elution of acetonitrile and 5 mM ammonium formate at a flow rate of 0.2 mL/min. Mass spectrometric detection utilized a Shimadzu IT-TOF system with the electrospray source running in positive mode. Data acquisition utilized a direct MS-MS method using a precursor ion of 276.3 m/z for MDPV and methylone. The calibration curve ranged from 100 ng/ml to 0.1 ng/ml. These conditions allowed for a lower limit of detection (LLOD) of less than or equal to 1 ng/mL and a lower limit of quantification (LLOQ) of less than or equal to 5 ng/mL for MDPV and methylone. MDPV and methylone peak concentrations in plasma were seen immediately at 1 min, while brain concentrations peaked at 15 min; however, MDPV reached higher concentrations in the brain the methylone. This is consistent with MDPV’s higher lipophilicity (logP value). In conclusion, the pharmacokinetic profile of these drugs reflects a quick uptake and distribution of the drugs to the brain, followed by the quick distribution out of the brain, which likely contributes to the binge use of these drugs.

The hydrophobicity of many chemotherapeutic agents usually results in their nonselective passive distribution into healthy cells and organs causing collateral toxicity. Ligand-targeted drugs (LTDs) are a promising class of targeted anticancer agents. The hydrophilicity of the targeting ligands in LTDs limits its nonselective passive tissue distribution and toxicity to healthy cells. In addition, the small size of LTDs allows for better tumor penetration, especially in the case of solid tumors. However, the short circulation half-life of LTDs, due to their hydrophilicity and small size, remains a significant challenge for achieving their full therapeutic potential. Therefore, extending the circulation half-life of targeted chemotherapeutic agents while maintaining their hydrophilicity and small size will represent a significant advance towards effective and safe cancer treatment. Here, we present a new approach for enhancing the safety and efficacy of targeted chemotherapeutic agents. By endowing hydrophobic chemotherapeutic agents with a targeting moiety and a hydrophilic small molecule that binds reversibly to the serum protein transthyretin, we generated small hydrophilic drug conjugates that displayed enhanced circulation half-life in rodents and selectivity to cancer cells. To the best of our knowledge, this is the first demonstration of a successful approach that maintains the small size and hydrophilicity of targeted anticancer agents containing hydrophobic payloads, while at the same time extending their circulation half-life. This was demonstrated by the superior in vivo efficacy and lower toxicity of our conjugates in xenograft mouse models of metastatic prostate cancer.

Acid-sensitive liposome has drawn much interest as drug and gene carriers that release payloads specifically at the low-pH target sites, such as in solid tumors, tissues with inflammation, and ischemia sites. Also, it helps drug/gene to escape endosome trapping and followed lysosome degradation. The goal of this thesis research is to develop novel trans-2-aminocyclohexanols based lipids and their liposome that can be switched by mildly acidic pH. NMR study · show that in certain acidic medium, the amine group on cyclohexane will attract proton and form hydrogen bond with the neighboring -OH. This change will force the bonds switch to from equatorial conformation to axial conformation. This conformational change is transmitted by the structure of the molecular, and induces consequently dramatic conformational change of the two long lipid tails. Fluorescence leakage assay was conducted on liposomes that encapsulated with ANTs/DPX fluorescence dyes. For certain special designed cyclohexane compounds, the pH triggered lipid conformation change will rupture liposome membrane, release the encapsulated content, and thus help them escape lysosome degradation. This would in tum improve the efficiency of liposome drug delivery and gene transfection. Luciferase gene transfection was conducted on B16F10 cultured cells. The lipoplex comprising trans-2-aminocyclohexanollipid 1 significantly enhanced the Luciferase gene expression. The gene transfection efficiency correlated well with the pH-triggered membrane-rupture in the trans-aminocyclohexanol-based lipoplexes.

No description available.

The long-term goal of this project is to develop novel methods for the detection of nucleotides, oligonucleotides, and modified nucleotides such as DNA adducts by mass spectrometry. DNA adducts are important because they are formed during chemical carcinogenesis as well as during anti-cancer chemotherapy. However, DNA adducts are not routinely monitored due to difficulties associated with their detection. Mass spectrometry is a promising method for the detection of DNA adducts because it can detect almost any type of adduct, and in addition mass spectrometers can provide structural information. The work presented here shows successful detection of nucleotides and oligonucleotides of various sizes. Specific sizes detected include mononucleotides, 6-mer, 8-mer, 1 O-rner, and 16-mer oligonucleotides, and enzyme digests of genomic DNA and oligonucleotides. Through researchinvolving several separation methods (HPLC, TLC, and PAGE) and alternative detection methods (32P postlabeling and mass spectrometry), a novel method for the separation and detection of DNA adducts has been developed. The present research has shown promising results for tracking nucleotides in TLC using biomimetic dyes in order to eliminate the need for radioactive isotopes. In addition, progress has been made involving elution of nucleotides from a TLC plate and subsequent detection of these nucleotides by mass spectrometry. Together, these results will facilitate future studies that involve testing samples that contain altered DNA by different mass spectrometers, which are expected to be particularly useful for the detection and identification of mixed or novel DNA ' modifications.

Many potential therapeutic agents face challenges for their clinical development due to short circulation half-life. As a result, prolonging the half-life of therapeutic drugs in circulation while preserving their hydrophilicity and small size will be a key step toward more effective and safe pharmacological molecules. Our lab developed a new approach for enhancing the safety and efficacy of therapeutic agents. By endowing therapeutic agents with a hydrophilic small molecule (a derivative of the clinical candidate, AG10) which reversibly binds to the serum protein transthyretin (TTR), the half-life of the therapeutic agent should be extended by binding to the TTR in serum. We termed this technology TTR Ligand for half-life extension (TLHEs). The approach involved using TLHE, which binds with TTR by high specificity and affinity. Our group has already shown that this technology extends the half-life of peptides, small molecules, and proteins without seriously affecting their binding activity towards their receptor and efficacy. As we are expanding the applicability of TLHE to extend the half-life of hydrophobic moieties, increasing the polarity of the TLHE linker could be beneficial to maintain overall hydrophilicity. Our main objective here is to see the effect of TTR binding affinity and selectivity of TLHE in serum when we attach a hydrophilic glutamic acid in the TLHE linker.