| WEEK # | TOPICS | LECTURE SUMMARIES |
|---|---|---|
| 1 | Introduction of Instructor and Students and Course Overview |
In the first meeting, we will introduce ourselves. Then we will discuss the syllabus, including expectations and goals of the class. We will also discuss how to conduct literature searches using PubMed and Scopus. Lastly, the instructor will provide an overview of antimicrobial peptides, peptide signaling and peptides as promising drugs. There are no papers assigned for this week. Watch a video about innate immune defense |
| 2 | Antimicrobial Peptides in Innate Immune Defense and Their Production |
The antimicrobial peptide human α defensin 5 (HD5) is expressed in Paneth cells, secretory epithelial cells in the small intestine. The first paper shows that antimicrobial peptide HD5 is part of the innate immune defense in mammals, and its expression is upregulated during an infection. The second paper reports the discovery of a protease that is responsible for cleaving the precursor of HD5 (prepropeptide) and regulates the production of this peptide. Watch a video about Paneth cells |
| 3 | Antimicrobial Peptides as Double Agents |
Antimicrobial peptides can also act as a signals for several other immune related events in eukaryotic systems. The first paper discussed the inhibition of protein kinase C (PKC) and phosphorylation of proteins in rats by human neutrophil peptides. PKC is believed to play an important role in mediating immune responses, regulating cell growth, and in learning and memory. Hence, PKC enzymes play important roles in several signal transduction cascades. These functions are achieved by PKC-mediated phosphorylation of other proteins. By inhibiting PKC, these neutrophil peptides may regulate various PKC activities in the cells. In the second paper, the authors demonstrated that UV radiation (UVR) can trigger the production of murine β-defensin-14 (mBD-14) in mice. UVR-inducible antimicrobial peptide mBD-14 switches mature conventional T cells into a regulatory phenotype by inducing the expression of specific proteins like Foxp3 and CTLA-4. T regulatory cells are a component of the immune system that suppress immune responses of other cells. Regulatory T cells are involved in shutting down immune responses after they have successfully eliminated invading organisms. The authors have showed that this way mBD-14 kills the bacteria in body and still avoid the hypersensitive response from the adaptive immune system. |
| 4 | Folding Matters for Antimicrobial Peptides | This week we will learn about the link between structure and activity of antimicrobial peptides. The first paper reports the importance of disulphide linkage in the bioactivity of antimicrobial peptides and how reduction of cysteines plays an important role in antimicrobial activity. The second paper discusses the various isomers of a defensin with different pairing of thiol groups in various cysteines (regioisomers) and their functional significance. |
| 5 | Techniques to Study Antimicrobial Peptides |
Methods for identification and detection of antimicrobial peptides are important to study them. Furthermore, several techniques have been developed for the identification of their interacting partners. The first paper discusses the contribution of the chemical biology tool kit for identification of receptors involved in binding vancomycin, a modified glycopeptide (a peptide with carbohydrate side chain) antibiotic. The authors used a photoaffinity reaction to enrich the binding receptor. The second paper shows the rapid and sensitive analysis of cysteine-rich peptides in complex mixtures. The authors used the powerful LC-MS approach for elucidating the presence and sequences of cysteine-rich peptides in snails. Watch a very short movie about vancomycin mode of action. |
| 6 | Peptides in Biotic Interactions |
In addition to intra-species communication, some antimicrobial peptides are involved in inter-species communication. There are fascinating examples of multiple usages of the preexisting signaling machinery in various biotic interactions. In this session, we will learn about the role of antimicrobial peptides in symbiosis. The first paper discusses the symbiosis between legumes and Sinorhizobium bacteria, showing that plant peptides can control bacterial physiology and morphology. The second paper shows that human gut commensals are resistant to cationic antimicrobial peptides present in human gut. This observation may have big impact in designing antibiotics to specifically kill pathogenic bacteria. Watch a video about a new technology, iChip, used to discover novel antibiotics. |
| 7 | Peptide Transporters in Various Organisms |
In addition to how signaling peptides affect cells, another interesting question is how peptides are transported inside cells. The first paper describes a landmark discovery about the mammalian proton-coupled oligopeptide transporter. Before the discovery of this oligopeptide transporter, PepT1, it was thought that a Na+ gradient is the primary driver of active transport of organic solutes in mammalian cells. Export of sodium from the cell provides the driving force for several membrane transport proteins, which import glucose, amino acids, and other nutrients into the cell. This paper was the first to show the role of a proton pump in active transport of organic solutes in mammals. Protons are expelled by the ATP synthase enzyme, generating the proton motive force (PMF). ATP is made indirectly using the PMF as a source of energy. This energy can be used by membrane transport proteins for active transport in the cells. The second paper reports the functional characterization of the SbmA bacterial inner membrane transporter, shown to transport antimicrobial peptide Bac7. SbmA mutants are more sensitive towards antimicrobial peptides like Bac7. In addition, SbmA has homologs in Mycobacterium tuberculosis, an important pathogenic bacterium that causes tuberculosis; this makes SbmA a major drug target. Watch a video that explains bacteria efflux pumps |
| 8 | Peptide Signals in the Brain | The discovery of neuropeptides revolutionized the field of signaling. So far, around 100 peptides have been discovered in the human brain. The first article describes the classic discovery of morphine-like peptides in the calf brain. Endogenous ligands for opiate receptors were discovered by studying the competition of binding between radiolabeled naloxone (a synthetic opiate) and candidate ligands. This paper discusses methods of peptide separation and purification. Also, it shows the interaction between opiate receptors and enkephalin neuropeptides. The second paper discusses the maturation pathways and processing of β-endorphin peptides in cells that can produce antibodies (immunocytes). These two articles show that our body uses complex pathways to generate pain relievers. |
| 9 | Molecules of Hunger and Love | Neuropeptides are known to modulate or control the behavior of all animals. One interesting example is ghrelin, the "hunger hormone," which is a peptide produced by ghrelin cells in the gastrointestinal tract and functions as a neuropeptide in the central nervous system. Beyond regulating hunger, ghrelin also plays a significant role in regulating the distribution and rate of use of energy. The first paper gives insights into the role of ghrelin and its modified form des-n-octanoyl ghrelin (des-acyl ghrelin) in inducing food intake in rats. The authors confirmed that des-acyl ghrelin increases the intracellular calcium concentrations in orexin neurons dispersed from the lateral hypothalamic area (LHA) by calcium-imaging analysis. The LHA belongs to the lateral zone of the hypothalamus, a region of the brain that functionally links the nervous system to the endocrine system. Also, the authors demonstrated that modified ghrelin increased feeding by activation of neurons in the LHA. Unmodified ghrelin binds to the ghrelin receptor for its function. Surprisingly, the authors found that modified ghrelin appears to regulate feeding independently of the known ghrelin receptor. The second article describes neuropeptides controlling the sexual behavior of rodents. Vasopressin is an important hormone in mammals. The authors showed the association between quantitative distribution of vasopressin receptor and sexual behavior of voles. The overexpression and underexpression of vasopressin receptor is correlated with polygamy and monogamy behavior of two species of voles. |
| 10 | Epidermal Growth Factors (EGFs) as Signaling Peptides | Growth factors such as platelet-derived growth factor and epidermal growth factors (EGFs) are peptides. In this session, we will learn how peptides bind to their receptors and how this binding affects downstream signaling. The first article shows that EGFs bind to and activate cell-surface receptors with intrinsic tyrosine kinase activities. The second paper reports that the dimerization and phosphorylation at tyrosine residues (activation) of an EGF receptor is required for downstream signaling. |
| 11 | Molecules in Action: Antimicrobial Peptides as Drugs | Before our visit to Merck, it will be interesting to know more about their products. In this class, we will learn about the antimicrobial peptide Daptomycin, which was approved by the FDA for the treatment of complicated skin infections, including infections either involving deeper soft tissue or requiring significant surgical intervention, such as infected ulcers, burns, and major abscesses. Most of these infections are caused by Gram-positive bacteria. Daptomycin has a distinct mechanism of action, disrupting multiple aspects of the Gram-positive bacterial cell membrane and is an attractive antibiotic for such kinds of infections. Daptomycin is commercially manufactured by Merck Pharmaceuticals. The first paper discusses Daptomycin biosynthesis and the production of this modified peptide. The second paper discusses antimicrobial activities and pharmacological properties of this molecule. |
| 12 | Field Trip to Merck Pharmaceuticals | On Week 12, we will visit Merck Pharmaceuticals in Lexington, MA. Cubist Pharmaceuticals, a subsidiary of Merck Pharmaceuticals, is a company that produces stable antimicrobial peptides for the treatment of various rare bacterial infections. This visit will introduce students to peptide research in an industrial setting. The company's main product is Daptomycin, a modified peptide that is effective against Gram-positive bacterial infections, S. aureus bacteraemia, and right-sided S. aureus endocarditis. In one of our classes prior to the visit, we will learn about Daptomycin biosynthesis, pharmacological properties, efficacy and toxicity. Daptomycin (marketed as Cubicin) accounted for over 90% of the company's total revenue in 2013. Daptomycin competes strongly with Pfizer's Zyvox (linezolid) and Astellas's Vibativ (telavancin) in treatment of methicillin-resistant S. aureus (MRSA) on the market. MRSA refers to strains of S. aureus that have developed through the process of natural selection resistance to beta-lactam antibiotics, which include the penicillins and the cephalosporins. Resistance to antibiotics makes MRSA infection more difficult to treat with standard types of antibiotics and thus more dangerous than wild-type strains. |
| 13 | Signaling Peptides as Potential Drugs for Treating Cancers |
In this class, we will discuss two different strategies for treating cancer. In addition to antimicrobial activities, various antimicrobial peptides possess antitumor activities. One example is Tachyplesin, which is isolated from the horseshoe crab. In the first article, authors discovered that Tachyplesin uses the classic complement cascade which damages the integrity of the membranes of the tumor cells resulting in their death. The second paper deals with the certain receptors of epidermal growth factors (EGFRs) that are overexpressed in cancer. EGFR2 (HER2 in humans), which promotes the growth of cancer cells is a well-known example. In about one of every five breast cancers, the cancer cells make an excess of HER2 because of a gene mutation. Designing inhibitors of this receptor or raising monoclonal antibodies against HER2 are two approaches toward new drugs for cancer. Trastuzumab (marketed as Herceptin) is an Anti-EGFR monoclonal antibody used clinically for HER2 positive breast cancer patients. The second paper discusses the use of monoclonal antibodies against EGFRs. Antibodies against EGFRs block the kinase activity of the receptor, hence slow down the growth of cancer cells. Watch the video on EGF |
| 14 | Signaling Peptides in Signal Transduction |
Transduction of a mitogenic signal from the cell membrane to the nucleus involves multiple steps. Different kinds of proteins assist in this process. We will discuss the molecular mechanisms that transduce signals from cell-surface receptors. The first paper describes the role of cross talk between G-protein-coupled receptors and epidermal growth factor receptors. The second paper discusses the discovery of growth factor receptor-bound protein 2 also known as Grb2 in rat and human. Grb2 is an adaptor protein involved in signal transduction by binding to the EGF receptor. Adaptor proteins contain a variety of protein-binding modules that link protein-binding partners together and facilitate the creation of larger signaling complexes. Watch a video on signal transduction |
| 15 | Last Day of the Class: Oral Presentations, General Discussion of the Course, and Course Evaluations | This session will be devoted to student presentations. Each student will make a 15-20 minute presentation based on a preselected paper. The students should be prepared to answer questions during the presentation, and the entire group will engage in a discussion based on the presentations. See description of oral presentations on page 2. We will generally discuss the course—what worked well and what might have been improved. Also, students will complete course evaluations forms. |