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 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.

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.

Structural Analysis of alpha-Fetoprotein (AFP)-like Peptides with Anti-Breast-Cancer Properties

The abundance of alpha-fetoprotein (AFP), a natural protein produced by the fetal yolk sac during pregnancy, correlates with lower incidence of estrogen receptor positive (ER+) breast cancer. The pharmacophore region of AFP has been narrowed down to a four amino acid (AA) region in the third domain of the 591 AA peptide. Our computational study focuses on a 4-mer segment consisting of the amino acids threonine-proline-valine-asparagine (TPVN). We have run replica exchange molecular dynamics (REMD) simulations and used 120 configurational snapshots from the total trajectory as starting configurations for quantum chemical calculations. We optimized structures using semiempirical (PM3, PM6, PM6-D2, PM6-H2, PM6-DH+, PM6-DH2) and density functional methods (TPSS, PBE0, M06-2X). By comparing the accuracy of these methods against RI-MP2 benchmarks, we devised a protocol for calculating the lowest energy conformers of these peptides accurately and efficiently. This protocol screens out high-energy conformers using lower levels of theory and outlines a general method for predicting small peptide structures.

The Effect of Chronic Estrogen Administration on Same-Sex Social Behavior and Central Oxytocin Levels in Prairie Voles (Microtus ochrogaster)

The purpose of our study is to investigate the effects of chronic estrogen administration on same-sex interactions during exposure to a social stressor and on oxytocin (OT) levels in prairie voles (Microtus orchrogaster). Estrogen and OT are two hormones known to be involved with social behavior and stress. Estogen is involved in the transcription of OT and its receptor. Because of this, it is generally thought that estrogen upregulates OT, but evidence to support this assumption is weak. While estrogen has been shown to either increase or decrease stress, OT has been shown to have stress-dampening properties. The goal of our experiment is to determine how estrogen affects OT levels as well as behavior in a social stressor in the voles. In addition, estrogen is required for many opposite-sex interactions, but little is known about its influence on same-sex interactions. We hypothesized that prairie voles receiving chronic estrogen injections would show an increase in OT levels in the brain and alter behavior in response to a social stressor called the resident-intruder test. To test this hypothesis, 73 female prairie voles were ovariectomized and then administered daily injections of estrogen (0.05 ¿g in peanut oil, s.c.) or vehicle for 8 days. On the final day of injections, half of the voles were given the resident-intruder test, a stressful 5 min interaction with a same-sex stranger. Their behavior was video-recorded. These animals were then sacrificed either 10 minutes or 60 minutes after the conclusion of the test. Half of the animals (no stress group) were not given the resident-intruder test. After sacrifice, trunk blood and brains were collected from the animals. Videos of the resident-intruder tests were analyzed for pro-social and aggressive behavior. Density of OT-activated neurons in the brain was measured via pixel count using immunohistochemistry. No differences were found in pro-social behavior (focal sniffing, p = 0.242; focal initiated sniffing p = 0.142; focal initiated sniffing/focal sniffing, p = 0.884) or aggressive behavior (total time fighting, p= 0.763; number of fights, p= 0.148; number of strikes, p = 0.714). No differences were found in activation of OT neurons in the brain, neither in the anterior paraventricular nucleus (PVN) (pixel count p= 0.358; % area that contains pixelated neurons p = 0.443) nor in the medial PVN (pixel count p= 0.999; % area that contains pixelated neurons p = 0.916). These results suggest that estrogen most likely does not directly upregulate OT and that estrogen does not alter behavior in stressful social interactions with a same-sex stranger. Estrogen may prepare the animal to respond to OT, instead of increasing the production of the peptide itself, suggesting that we need to shift the framework in which we consider estrogen and OT interactions.