Computational Design and Experimental Discovery of an Anti-estrogenic Peptide Derived from Alpha-Fetoprotein

Breast cancer is the most common cancer among women, and tamoxifen is the preferred drug for estrogen receptor-positive breast cancer treatment. Many of these cancers are intrinsically resistant to tamoxifen or acquire resistance during treatment. Consequently, there is an ongoing need for breast cancer drugs that have different molecular targets. Previous work has shown that 8-mer and cyclic 9-mer peptides inhibit breast cancer in mouse and rat models, interacting with an unsolved receptor, while peptides smaller than eight amino acids did not. We show that the use of replica exchange molecular dynamics predicts the structure and dynamics of active peptides, leading to the discovery of smaller peptides with full biological activity. Simulations identified smaller peptide analogues with the same conserved reverse turn demonstrated in the larger peptides. These analogues were synthesized and shown to inhibit estrogen-dependent cell growth in a mouse uterine growth assay, a test showing reliable correlation with human breast cancer inhibition.

The Search for Low Energy Conformational Families of Small Peptides: Searching for Active Conformations of Small Peptides in the Absence of a Known Receptor

Breast cancer is the most common cancer among women. Tamoxifen is the preferred drug for estrogen receptor-positive breast cancer treatment, yet many of these cancers are intrinsically resistant to tamoxifen or acquire resistance during treatment. Therefore, scientists are searching for breast cancer drugs that have different molecular targets. Previous work revealed that 8-mer and cyclic 9-mer peptides inhibit breast cancer in mouse and rat model systems, interacting with an unknown receptor, while peptides smaller than eight amino acids did not inhibit breast cancer. We have shown that the use of replica exchange molecular dynamics predicts structure and dynamics of active peptides, leading to the discovery of smaller peptides with full biological activity. These simulations identified smaller peptide analogs with a conserved turn, a β-turn formed in the larger peptides. These analogs inhibit estrogen-dependent cell growth in a mouse uterine growth assay, a test showing reliable correlation with human breast cancer inhibition. We outline the computational methods that were tried and used with the experimental information that led to the successful completion of this research.

Computational approaches for the design of peptides with anti-breast cancer properties

Background: Breast cancer is the most common cancer among women. Tamoxifen is the preferred drug for estrogen receptor-positive breast cancer treatment, yet many of these cancers are intrinsically resistant to tamoxifen or acquire resistance during treatment. Therefore, scientists are searching for breast cancer drugs that have different molecular targets. Methodology: Recently, a computational approach was used to successfully design peptides that are new lead compounds against breast cancer. We used replica exchange molecular dynamics to predict the structure and dynamics of active peptides, leading to the discovery of smaller bioactive peptides. Conclusions: These analogs inhibit estrogen-dependent cell growth in a mouse uterine growth assay, a test showing reliable correlation with human breast cancer inhibition. We outline the computational methods that were tried and used along with the experimental information that led to the successful completion of this research.

The organization of memory for familiar songs

Investigated the organizing principles in memory for familiar songs in 2 experiments. It was hypothesized that individuals do not store and remember each song in isolation. Rather, there exists a rich system of relationships among tunes that can be revealed through similarity rating studies and memory tasks. One initial assumption was the division of relations among tunes into musical (e.g., tempo, rhythm) and nonmusical similarity. In Exp I, 20 undergraduates were asked to sort 60 familiar tunes into groups according to both musical and nonmusical criteria. Clustering analyses showed clear patterns of nonmusical similarity but few instances of musical similarity. Exp II, with 16 Ss, explored the psychological validity of the nonmusical relationships revealed in Exp I. A speeded verification task showed that songs similar to each other are confused more often than are distantly related songs. A free-recall task showed greater clustering for closely related songs than for distantly related ones. The relationship between these studies and studies of semantic memory is discussed. Also, the contribution of musical training and individual knowledge to the organization of the memory system is considered. (19 ref) (PsycINFO Database Record (c) 2012 APA, all rights reserved)

Shading Silhouettes of Smaller Ones

I am truly honored to have been given the amazing opportunity to create this original piece, this powerful journey through memory and emotive exploration of the loss of childhood. How do we feel about the loss of our child-self? Could we ever get them back? How long, how deep would one have to dig in the graveyards, the playgrounds of memory, to uncover what was buried there... to un-erase what waserased? shading silhouettes of smaller ones will ultimately encourage a reconnection with the Inner Child hidden inside all of us, as well as an intimate awareness of the adult version of the self by looking back to the smaller ones. The main inspiration for this piece is then of course, Inner Child Work. Most people may not be familiar with this therapeutic exploration of childhood... It wasimportant to me then, to present this concept in an imaginative, theatrical way, as a gift to you - a comprehensive and intensely moving gift. Speaking from experience, working on my Inner Child - my little Bianca - has been the most painful, frightening, yetrewarding and powerful experience within my personal life. Some people spend their entire lives trying to love themselves, to prove themselves, or be accepted. Some are too afraid to look back to where it all began. The characters within this piece will face thatfear... in a regression from the complexities of adulthood to the confusion of adolescence, all the way back to the wonder and bliss of childhood. They will reveal memories, of both joy and pain, love and abandonment, journeying backwards through time - through memory - through a playground - back to the beginning... We will enter a world where a push of a merry-go-round spins us to games of Truth or Dare after a high school dance at 16 - or the slam of a metal fence reminds us of the door Dad slammed in our face at 9 - where the sound of chain links swings us back to scrapping our knee by the sandbox at 5 This piece will attempt to connect everyone, both cast and audience, through a universal understanding and discussion of what it means to grow up, as well as a discovery of WHY we are the way we are - how experiences or relationships from our childhood have shaped our adult lives. We will attempt to challenge your honesty and nerve by inviting you to ask questions of yourselves, your past - to remember what it's like to have the innocence and hope of a child, to engage with and discover your Inner Child, to realize when or why you left them behind, and if you want to this magical part of yourself. It is my hope that you will join us in a collective journey - gather the courage to dig up the little kid you buried so long ago...* The creation, design, choreography, and direction for shading silhouettes of smaller ones mark the culminating experience of a year-long independent study in Theatre.

Enzymatic Activity of Soybean Lipoxygenase-1 on Linoleoyl-Derivatized Agarose

Soybean lipoxygenase-1 (SBLO-1) catalyzes the oxygenation of linoleic acid to form 13(S) and 9(R) hydroperoxides. The manner in which substrates bind to the lipoxygenase family of enzymes is not known. It is believed fatty acid substrates may bind either with the aliphatic end first or with the carboxylate group facing the interior of the protein. This thesis tested a potential methyl-end first substrate binding mechanism by studying the activity of SBLO-1 to oxygenate immobilized linoleoyl residues attached to an insoluble polymer. Linoleic acid was attached to aminohexyl agarose in the presence of N-(3- dimethylaminopropyl)-N’-ethylcarbodiimide hydrochloride (EDC) and Nhydroxysuccinimide (NHS). The concentration of the covalently attached residues was facilitated by enriching linoleic acid with a small amount of the radioactive 14C-isotope. Functionalization yields of 3% available primary amines on the resin were obtained. Enzymatic oxygenation of the linoleoyl-residues was verified using the ferrous oxidation in xylenol orange (FOX) assay. Approximately 30% of the attached linoleoyl moieties were converted to hydroperoxides in the presence of SBLO-1. A disulfide-containing cleavable linker, cystamine, was used as part of an improved method to isolate the product in a facile manner. Cystamine was attached to NHS-activated agarose with approximately 5% overall functionalization yield of available functional groups. 14C-linoleic acid was successfully covalently linked to the cystamine moieties in the presence of EDC and NHS. The FOX assay verified the enzymatic oxygenation of the linoleoyl residues attached to cystamine-derivatized agarose. The isolation of the peroxide product was attempted in a series of extractions in organic solvents. The product was analyzed using GC/MS which did not show a new peak indicative of product. Further work is needed to successfully analyze the stereoand regiochemistry of the oxygenated product. The presence of the peroxides in this study indicated the linoleoyl residues behave as substrates of SBLO-1. It is unknown how bulky substrates bind to the active site; however, it is difficult to rationalize a carboxylate group-first binding mode. Discovery of the 13(S)-hydroperoxide product on the linoleoyl-agarose would support the claim of a potential methyl-end first binding mechanism.