Developing peptide based capture agents for diagnostics and therapeutics

Iterative in situ click chemistry (IISCC) is a robust general technology for development of high throughput, inexpensive protein detection agents. In IISCC, the target protein acts as a template and catalyst, and assembles its own ligand from modular blocks of peptides. This process of ligand discovery is iterated to add peptide arms to develop a multivalent ligand with increased affinity and selectivity. The peptide based protein capture agents (PCC) should ideally have the same degree of selectivity and specificity as a monoclonal antibody, along with improved chemical stability. We had previously reported developing a PCC agent against bovine carbonic anhydrase II (bCAII) that could replace a polyclonal antibody. To further enhance the affinity or specificity of the PCC agent, I explore branching the peptide arms to develop branched PCC agents against bCAII. The developed branched capture agents have two to three fold higher affinities for the target protein. In the second part of my thesis, I describe the epitope targeting strategy, a strategy for directing the development of a peptide ligand against specific region or fragment of the protein. The strategy is successfully demonstrated by developing PCC agents with low nanomolar binding affinities that target the C-terminal hydrophobic motif of Akt2 kinase. One of the developed triligands inhibits the kinase activity of Akt. This suggests that, if targeted against the right epitope, the PCC agents can also influence the functional properties of the protein. The exquisite control of the epitope targeting strategy is further demonstrated by developing a cyclic ligand against Akt2. The cyclic ligand acts as an inhibitor by itself, without any iteration of the ligand discovery process. The epitope targeting strategy is a cornerstone of the IISCC technology and opens up new opportunities, leading to the development of protein detection agents and of modulators of protein functions.

Biotechnologies for cancer diagnostics : cell sorting, protein analysis and imaging of cellular metabolism

This thesis presents the development of chip-based technology for informative in vitro cancer diagnostics. In the first part of this thesis, I will present my contribution in the development of a technology called “Nucleic Acid Cell Sorting (NACS)”, based on microarrays composed of nucleic acid encoded peptide major histocompatibility complexes (p/MHC), and the experimental and theoretical methods to detect and analyze secreted proteins from single or few cells.

Secondly, a novel portable platform for imaging of cellular metabolism with radio probes is presented. A microfluidic chip, so called “Radiopharmaceutical Imaging Chip” (RIMChip), combined with a beta-particle imaging camera, is developed to visualize the uptake of radio probes in a small number of cells. Due to its sophisticated design, RIMChip allows robust and user-friendly execution of sensitive and quantitative radio assays. The performance of this platform is validated with adherent and suspension cancer cell lines. This platform is then applied to study the metabolic response of cancer cells under the treatment of drugs. Both cases of mouse lymphoma and human glioblastoma cell lines, the metabolic responses to the drug exposures are observed within a short time (~ 1 hour), and are correlated with the arrest of cell-cycle, or with changes in receptor tyrosine kinase signaling.

The last parts of this thesis present summaries of ongoing projects: development of a new agent as an in vivo imaging probe for c-MET, and quantitative monitoring of glycolytic metabolism of primary glioblastoma cells. To develop a new agent for c-MET imaging, the one-bead-one-compound combinatorial library method is used, coupled with iterative screening. The performance of the agent is quantitatively validated with cell-based fluorescent assays. In the case of monitoring the metabolism of primary glioblastoma cell, by RIMChip, cells were sorting according to their expression levels of oncoprotein, or were treated with different kinds of drugs to study the metabolic heterogeneity of cancer cells or metabolic response of glioblastoma cells to drug treatments, respectively.

Succinate:ubiquinone oxidoreductase from Paracoccus denitrificans and particulate methane monooxygenase from Methylococcus capsulatus (Bath): experimental and theoretical EPR studies of the metal cofactors

This thesis summarizes the application of conventional and modern electron paramagnetic resonance (EPR) techniques to establish proximity relationships between paramagnetic metal centers in metalloproteins and between metal centers and magnetic ligand nuclei in two important and timely membrane proteins: succinate:ubiquinone oxidoreductase (SQR) from Paracoccus denitrificans and particulate methane monooxygenase (pMMO) from Methylococcus capsulatus. Such proximity relationships are thought to be critical to the biological function and the associated biochemistry mediated by the metal centers in these proteins. A mechanistic understanding of biological function relies heavily on structure-function relationships and the knowledge of how molecular structure and electronic properties of the metal centers influence the reactivity in metalloenzymes. EPR spectroscopy has proven to be one of the most powerful techniques towards obtaining information about interactions between metal centers as well as defining ligand structures. SQR is an electron transport enzyme wherein the substrates, organic and metallic cofactors are held relatively far apart. Here, the proximity relationships of the metallic cofactors were studied through their weak spin-spin interactions by means of EPR power saturation and electron spin-lattice (T_1) measurements, when the enzyme was poised at designated reduction levels. Analysis of the electron T_1 measurements for the S-3 center when the b-heme is paramagnetic led to a detailed analysis of the dipolar interactions and distance determination between two interacting metal centers. Studies of ligand environment of the metal centers by electron spin echo envelope modulation (ESEEM) spectroscopy resulted in the identication of peptide nitrogens as coupled nuclei in the environment of the S-1 and S-3 centers.

Finally, an EPR model was developed to describe the ferromagnetically coupled trinuclear copper clusters in pMMO when the enzyme is oxidized. The Cu(II) ions in these clusters appear to be strongly exchange coupled, and the EPR is consistent with equilateral triangular arrangements of type 2 copper ions. These results offer the first glimpse of the magneto-structural correlations for a trinuclear copper cluster of this type, which, until the work on pMMO, has had no precedent in the metalloprotein literature. Such trinuclear copper clusters are even rare in synthetic models.

Nuclear Energy Levels of ^31S and ^33Cl

The reaction ³²S(³He, α) ³¹S has been used to locate 42 levels in ³¹S. For 11 of the first 17 levels ℓ_n-values have been determined. The first 6 excited states of ³¹S have been studied by applying the particle-gamma correlation method of Litherland and Ferguson (their Method II) to the reaction ³²S(³He, αγ) ³¹S. The resulting spins and parities are: E_X, J^π = 1.25 MeV, 3/2⁺; 2.23 MeV, 5/2⁺; 3.08 MeV, 1/2⁺; 3.29 MeV, 5/2⁺, 3/2⁺; 3.35 MeV, 7/2, 3/2; 3.44 MeV, 3/2⁺. Mixing and branching ratios have also been determined. The ground state Q-value for the reaction ³²S(³He, α)³¹S has been measured to be 5.538 ± 0.006 MeV. Analysis of the spectra of the reaction ³²S(³He, α)³³Cl which were obtained as a by-product of the spectra of the reaction ³²S(³He, α) ³¹S located levels in ³³Cl at the following excitation energies: 0, 810 ± 9, (1978 ± 14), 2351 ± 9, 2686 ± 8, 2848 ± 9 (a known doublet), 2980 ± 9, and 4119 ± 10 keV. The 2.0 MeV level was only weakly populated, and to confirm its existence the reaction ³⁶Ar(p, α)³³Cl has been studied. In this reaction the 2.0 MeV level was strongly populated and the measured excitation energy was 1999 ± 20 keV. The experimental results for ³¹S and ³³Cl are compared with their analogs and with nuclear model predictions.

The structure specificity of alpha-chymotrypsin. I. Polypeptides as substrates. II. N-acylated peptide esters as substrates. III. Some reactive esters of N-acylated amino acids as substrates

The structural specificity of α-chymotrypsin for polypeptides and denatured proteins has been examined. The primary specificity of the enzyme for these natural substrates is shown to closely correspond to that observed for model substrates. A pattern of secondary specificity is proposed.

A series of N-acetylated peptide esters of varying length have been evaluated as substrates of α-chymotrypsin. The results are interpreted in terms of proposed specificity theories.

The α-chymotrypsin-catalyzed hydrolyses of a number of N-acetylated dipeptide methyl esters were studied. The results are interpreted in terms of the available specificity theories and are compared with results obtained in the study of polypeptide substrates. The importance of non-productive binding in determining the kinetic parameters of these substrates is discussed. A partial model of the locus of the active site which interacts with the R’₁CONH- group of a substrate of the form R’₁CONHCHR₂COR’₃ is proposed.

Finally, some reactive esters of N-acetylated amino acids have been evaluated as substrates of α-chymotrypsin. Their reactivity and stereo-chemical behavior are discussed in terms of the specificity theories available. The importance of a binding interaction between the carboxyl function of the substrate and the enzyme is suggested by the results obtained.

Nuclear reactions leading to energy levels of Ar37 and K37

In view of recent interest in the Cl³⁷ (ʋ solar’^e-)Ar³⁷ reaction cross section, information on some aspects of mass 37 nuclei has been obtained using the K³⁹ (d, ∝) Ar³⁷ and Cl³⁵ (He³, p) Ar³⁷ reactions. Ar³⁷ levels have been found at 0, 1.41, 1.62, 2.22, 2.50, 2.80, 3.17, 3.27, 3.53, 3.61, 3.71, (3.75), (3.90), 3.94, 4.02, (4.21), 4.28, 4.32, 4.40, 4.45, 4.58, 4.63, 4.74, 4.89, 4.98, 5.05, 5.10, 5.13, 5.21, 5.35, 5.41, 5.44, 5.54, 5.58, 5.67, 5.77, and 5.85 MeV (the underlined values correspond to previously tabulated levels). The nuclear temperature calculated from the Ar³⁷ level density is 1.4 MeV. Angular distributions of the lowest six levels with the K³⁹ (d, ∝) Ar³⁷ reaction at E_d = 10 MeV indicate a dominant direct interaction mechanism and the inapplicability of the 2I + 1 rule of the statistical model. Comparison of the spectra obtained with the K³⁹ (d, ∝) Ar³⁷ and Cl³⁵ (He³, p) Ar³⁷ reactions leads to the suggestion that the 5.13-MeV level is the T = 3/2 Cl³⁷ ground state analog. The ground state Q-value of the Ca⁴⁰ (p, ∝) K³⁷ reaction has been measured: -5179 ± 9 keV. This value implies a K³⁷ mass excess of -24804 ± 10 keV. Description of a NMR magnetometer and a sixteen-detector array used in conjunction with a 61-cm double-focusing magnetic spectrometer are included in appendices.

Electromagnetic decay of the 1.7- and 2.43-MeV levels in ^9Be

The 1.7- and 2.43-MeV levels in ⁹Be were populated with the reaction ¹¹B(d, α)⁹Be* by bombarding thin boron on carbon foils with 1.7-MeV deuterons. The alpha particles were analyzed in energy with a surface-barrier counter set at the unique kinematically determined angle and the recoiling ⁹Be nuclei at 90^o were analyzed in rigidity with a magnetic spectrometer, in energy by a surface-barrier counter at the spectrometer focus, and in velocity by the time delay between an alpha and a ⁹Be count. When a pulse from the spectrometer counter was in the appropriate delayed coincidence with a pulse from the alpha counter, the two pulses were recorded in a two-dimensional pulse height analyzer. Most of the ⁹Be* decay by particle breakup. Only those that gamma decay are detected by the spectrometer counter. Thus the experiment provides a direct measurement of Γ_rad/Γ. Analysis of 384 observed events gives Γ_rad/Γ = (1.16 ± 0.14) X 10^-4 for the 2.43-MeV level. Combining this ratio with the value of Γ_rad = 0.122 ± 0.015 eV found from inelastic electron scattering gives Γ = (1.05 ± 0.18) keV. For the 1.7-MeV level, an upper limit, Γ_rad/Γ ≤ 2.4 = 10^-5, was determined.

Determination of electronic energy levels of molecules by 90° low energy electron scattering

A review of the theory of electron scattering indicates that low incident beam energies and large scattering angles are the favorable conditions for the observation of optically forbidden transitions in atoms and molecules.

An apparatus capable of yielding electron impact spectra at 90° with incident electron beam energies between 30 and 50 electron volts is described. The resolution of the instrument is about 1 electron volt.

Impact spectra of thirteen molecules have been obtained. Known forbidden transitions to the helium 2³S, the hydrogen b³Ʃ⁺_u, the nitrogen A³Ʃ⁺_u, B³π_g, a’π_g, and C³π_u, the carbon monoxide a³π, the ethylene ᾶ³B_1u, and the benzene ᾶ³B_1u states from the corresponding ground states have been observed.

In addition, singlet-triplet vertical transitions in acetylene, propyne, propadiene, norbornadiene and quadricyclene, peaking at 5.9, 5.9, 4.5, 3.8, and 4.0 ev (±0.2 ev), respectively, have been observed and assigned for the first time.