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Parthenolide, a natural product from the feverfew plant and member of the large family of sesquiterpene lactones, exerts multiple biological and therapeutic activities including anti-inflammatory and anti-cancer effects. Herein, we further study parthenolide mechanism of action using activity-based protein profiling (ABPP)-based chemoproteomic platforms to map additional covalent targets engaged by parthenolide in human breast cancer cells. We find that parthenolide, as well as other related exocyclic methylene lactone-containing sesquiterpenes, covalently modify cysteine 427 (C427) of focal adhesion kinase 1 (FAK1) leading to impairment of FAK1-dependent signaling pathways and breast cancer cell proliferation, survival, and motility. These studies reveal a novel functional target exploited by members of a large family of anticancer natural products.

Targeted protein degradation has arisen as a powerful strategy for drug discovery allowing the targeting of undruggable proteins for proteasomal degradation. This approach most often employs heterobifunctional degraders consisting of a protein-targeting ligand linked to an E3 ligase recruiter to ubiquitinate and mark proteins of interest for proteasomal degradation. One challenge with this approach, however, is that only a few E3 ligase recruiters currently exist for targeted protein degradation applications, despite the hundreds of known E3 ligases in the human genome. Here, we utilized activity-based protein profiling (ABPP)-based covalent ligand screening approaches to identify cysteine-reactive small-molecules that react with the E3 ubiquitin ligase RNF4 and provide chemical starting points for the design of RNF4-based degraders. The hit covalent ligand from this screen reacted with either of two zinc-coordinating cysteines in the RING domain, C132 and C135, with no effect on RNF4 activity. We further optimized the potency of this hit and incorporated this potential RNF4 recruiter into a bifunctional degrader linked to JQ1, an inhibitor of the BET family of bromodomain proteins. We demonstrate that the resulting compound CCW 28-3 is capable of degrading BRD4 in a proteasome- and RNF4-dependent manner. In this study, we have shown the feasibility of using chemoproteomics-enabled covalent ligand screening platforms to expand the scope of E3 ligase recruiters that can be exploited for targeted protein degradation applications.

Targeted protein degradation has arisen as a powerful strategy for drug discovery allowing the targeting of undruggable proteins for proteasomal degradation. This approach most often employs heterobifunctional degraders consisting of a protein-targeting ligand linked to an E3 ligase recruiter to ubiquitinate and mark proteins of interest for proteasomal degradation. One challenge with this approach, however, is that only few E3 ligase recruiters currently exist for targeted protein degradation applications, despite the hundreds of known E3 ligases in the human genome. Here, we utilized activity-based protein profiling (ABPP)-based covalent ligand screening approaches to identify cysteine-reactive small-molecules that react with the E3 ubiquitin ligase RNF4 and provide chemical starting points for the design of RNF4-based degraders. The hit covalent ligand from this screen reacted with either of two zinc-coordinating cysteines in the RING domain, C132 and C135, with no effect on RNF4 activity. We further optimized the potency of this hit and incorporated this potential RNF4 recruiter into a bifunctional degrader linked to JQ1, an inhibitor of the BET family of bromodomain proteins. We demonstrate that the resulting compound CCW 28-3 is capable of degrading BRD4 in a proteasome- and RNF4-dependent manner. In this study, we have shown the feasibility of using chemoproteomics-enabled covalent ligand screening platforms to expand the scope of E3 ligase recruiters that can be exploited for targeted protein degradation applications.

Chemical genetics has arisen as a powerful approach for identifying novel anti-cancer agents. However, a major bottleneck of this approach is identifying the targets of lead compounds that arise from screens. Here, we coupled the synthesis and screening of fragment-based cysteine-reactive covalent ligands with activity-based protein profiling (ABPP) chemoproteomic approaches to identify compounds that impair colorectal cancer pathogenicity and map the druggable hotspots targeted by these hits. Through this coupled approach, we discovered a cysteine-reactive acrylamide DKM 3-30 that significantly impaired colorectal cancer cell pathogenicity through targeting C1101 on reticulon 4 (RTN4). While little is known about the role of RTN4 in colorectal cancer, this protein has been established as a critical mediator of endoplasmic reticulum tubular network formation. We show here that covalent modification of C1101 on RTN4 by DKM 3-30 or genetic knockdown of RTN4 impairs endoplasmic reticulum and nuclear envelope morphology as well as colorectal cancer pathogenicity. We thus put forth RTN4 as a potential novel colorectal cancer therapeutic target and reveal a unique druggable hotspot within RTN4 that can be targeted by covalent ligands to impair colorectal cancer pathogenicity. Our results underscore the utility of coupling the screening of fragment-based covalent ligands with isoTOP-ABPP platforms for mining the proteome for novel druggable nodes that can be targeted for cancer therapy.

NEUROTRANSMITTER IMAGING AND PLANT NANOBIONICS Interview with Professor Markita Landry BY CATRIN BAILEY, ISABEL CRAIG, NIKHIL CHARI, YANA PETRI, ELENA SLOBODYANYUK Dr. Markita Landry is an Assistant Professor of Chem- ical and Biomedical Engineering at the University of California, Berkeley. Professor Landry’s laboratory focuses on understanding and exploiting optical nanomaterials to access information about biological systems. In this interview, we discuss semiconducting single-walled carbon nanotubes (SWNTs) and their applications in the detection of dopamine in the brain and biological cargo delivery to plant systems. Professor Markita Landry [Source: UC Berkeley College of Chemis- ing biophysics tools in engineering space. That's how I ended up here as well. BSJ Chemical and Biomedical Engineering? : What has made you so interested in optical I trained in Physics for my undergraduate BSJ nanomaterials and nano-sensor design? ML degree and Ph.D. The focus of my Ph.D. work was to study molecular interactions. To do so, There is a lot of opportunity in developing our lab developed high spatial and temporal reso- ML nanosensors, especially for molecules that : How did you first get involved in the field of lution instruments, which were well-suited for the systems that we were studying. When I graduated, I felt that these instruments were more broadly appli- cable and wanted to translate their use into nano- technology. For my postdoc, I planned to come back to physics and then apply nanotechnology tools, but biophysics tools ended up being really useful for nanotechnology. That's how I was introduced to Chemical and Biomolecular Engineering: by build- Berkeley Scientific Journal | SPRING 2017 are otherwise very difficult to access information from. For example, when we diagnose something like cancer, we use quantitative methods: typically, a blood screen for biomarkers and then an assay that shows how many cytokines are in the blood. For behavioral disorders like psychosis and depression, we have only very qualitative methods. That's where my interests are: in the more challenging areas to develop sensors for. I'm trying to make diagnosis

Author(s): Liu, Jiarui; Luo, Yu; Petri, Yana; Sangteerasintop, Sasinan; Wong, Jordan; Woo, Soohan; Zhu, Laura

THE ROLE OF ADENO-ASSOCIATED VIRUSES Interview with Professor David Schaffer BY CATRIN BAILEY, YANA PETRI, ELENA SLOBODYANYUK, JORDAN WONG, TIANSHU ZHAO, DANIEL YOON Dr. David Schaffer is a Professor of Chemical and Biomolecular Engineering, Bioengineering, and Neu- roscience at the University of California, Berkeley. Professor Schaffer is interested in stem cell bioengi- neering, gene delivery systems, molecular virology, and their applications to biomedical problems. In this interview, we talk about the role of adeno-associated viruses in gene therapy and discuss its molecular basis and directed evolution approaches. Professor David Schaffer [Source: The Schaffer Lab] BSJ in Chemical and Biomolecular Engineering? BSJ in gene therapy? : How did you first get involved in research DS background both on the basic sciences side : Well, I come from a family with a medical and the clinical side. I was always interested in problems related to human health. I like molecules and I like thinking about problems quantitatively. So, if you put that all together - math, molecules, application towards healthcare - at the time, it was Chemical and Biomolecular Engineering. These days I think that this research takes place in both the CBE department as well as the Bioengineering depart- ment and reflecting that I have an appointment in both. Berkeley Scientific Journal | FALL 2016 : What has inspired your interest specifically DS graduate school (that was a number of years : Well, I began to work in gene therapy during ago, I probably shouldn’t tell you as it is going to date me), so I have been working in the field for over 20 years. At that time, there was a lot of excitement: people were talking about sequencing the human genome, the Human Genome Project was getting underway. The genes that cause haemophilia B, haemophilia A, cystic fibrosis, muscular dystrophy, and Huntington’s disease were getting cloned and se- quenced and it brought up the idea that DNA could be used as a medicine to be able to treat diseases. I thought that this would be revolutionary and got really excited because up until that point many of

Climate change is expected to decrease heating demand and increase cooling demand for buildings and affect outdoor thermal comfort. Here, we project changes in residential heating degree-days (HDD) and cooling degree-days (CDD) for the historical (1981–2010) and future (2080–2099) periods in the United States using median results from the Climate Model Intercomparison Project phase 5 (CMIP5) simulations under the Representation Concentration Pathway 8.5 (RCP8.5) scenario. We project future HDD and CDD values by adding CMIP5 projected changes to values based on historical observations of US climate. The sum HDD + CDD is an indicator of locations that are thermally comfortable, with low heating and cooling demand. By the end of the century, station median HDD + CDD will be reduced in the contiguous US, decreasing in the North and increasing in the South. Under the unmitigated RCP8.5 scenario, by the end of this century, in terms of HDD and CDD values considered separately, future New York, NY, is anticipated to become more like present Oklahoma City, OK; Denver, CO, becomes more like Raleigh, NC and Seattle, WA, becomes more like San Jose, CA. These results serve as an indicator of projected climate change and can help inform decision-making.

I nterview with P rofessor H itoshi M urayama : S upersymmetry By: Sabrina Berger, Juwon Kim, Yana Petri, Kevin Nuckolls Professor Hitoshi Murayama is the MacAdams Professor of Physics at the University of California, Berkeley. He is also the director of the Kavli Institute for the Physics and Mathematics of the Universe at the University of Tokyo. His research interests include the investigation of dark matter, grand unification, neutrino physics, and physics beyond the standard model, including Supersymmetry. How did you get into theoretical particle physics? Professor Murayama: Well, I was born in Japan, lived in Germany for four years during my childhood, went back to Japan, and eventually got a degree from the University of Tokyo. I found my way to Berkeley as a post-doc up here at the lab, and then acquired a faculty position here. I don’t know exactly the story about getting interested in science. But I was a very curious child, for sure. I was the kind of child who kept asking questions to my parents and so on. My dad was a researcher who worked for Hitachi. He was doing research on semiconductors for the company. He didn’t have a PhD, but he had a Masters degree. My memory is, of course, hazy from those days, but I do remember that he answered many of those naive questions I had at that time, so that’s probably how I got interested. That’s also how I learned that many questions have answers, which is actually not an obvious thing for many children, I’m afraid. If they’re not inquisitive enough, or if their parents or teachers aren’t resourceful enough, then many of their questions just go answered. That doesn’t nurture curiosity. I was lucky enough to be in that kind of position, I guess. I was also a very sick child. I had a very bad case of asthma as a child, so I missed many school days. I stayed home quite a bit, so I had to find something to do while I was at home. So, I turned the TV on, the soap operas were not interesting for kids, so I ended up turning my TV to educational channels. Back in those days, in Japan, the educational programs were actually pretty good. Some of them were really sort of story-based. There was one story I particularly remember talking about how infinite series can converge. The story was about a guy in ancient Edo in “I do remember that he answered many of those naive questions I had at that time, so that’s probably how I got interested. That’s also how I learned that many questions have answers, which is actually not an obvious thing for many children, I’m afraid.” the 17th century who was trying to buy tofu. So, he brings his bowl, and gets one piece of tofu, but wanted some extra. So, he gives many compliments to the tofu shop owner to please him. He keeps praising until, eventually, he got another half piece of tofu. So he continues to praise until the tofu owner gives him half of the rest, and half of the rest, and so on. This guy in the story thought, “Eventually, I’ll have a huge amount of tofu, enough tofu for the rest of my life.” But, in the end, he only gets two pieces of tofu. So, that was the story, and it intrigued me. Another program I remember was a physics program about a little booth, where some man is making some food, and there was a nice aroma. Then comes this strange looking guy who comes close to the booth, smells it, and goes home. He does this everyday, so the owner got fed up with this guy, and eventually gives him an invoice saying, “You’ve been smelling my food everyday without paying. You owe me 100 dollars.” The rest of the show is spent checking the legitimacy of this request. They first try to figure out what exactly it is that we are smelling. So B erkeley S cientific J ournal • S ymmetry • F all 2015 • V olume 20 • I ssue 1 • 21 B S J BSJ: Can you start off by describing your background?

A n I nterview with P rofessor K enneth R aymond on S upramolecular C hemistry : S ymmetry B ased C luster F ormation B S J Manraj Gill, Yana Petri, Tiffany Nguyen, Sabrina Berger Dr. Kenneth Raymond is a Chancellor’s Professor in the Department of Chemistry at University of California, Berkeley. Professor Raymond has been interested in a variety of topics in bioinorganic chemistry and coordination chemistry. In this interview, we focus on one of his specialties, the assembly of highly symmetric supramolecular clusters. We discuss not only the role of symmetry in the Figure #1. Dr. Kenneth formation of such molecular Raymond, Chancellor’s Professor of Chemistry structures but also the application of these clusters in catalytic chemistry. Berkeley Scientific Journal: How did you get involved in research in chemistry? Kenneth Raymond: I liked chemistry since I was 12 years old. I was 12 years old when I got my first chemistry set. My mother thought I was too young when I wanted it two years earlier. In those days, real chemicals came in those chemistry sets! In high school, I had a really good chemistry teacher who also taught physics. He let me have free run of the lab for making standard solutions. Aside from almost killing myself a couple of times, that was a really good experience! Also, it got me into Reed College, which turned my life around. In my first two years of high school, I had a math teacher that was sort of egg shaped and wore these purple dresses. She would be up next to the chalkboard and would get this perfect white ring around her. And she looked just like an Easter egg. She thought I was rude and I’m sure that’s true. She gave me bad grades for behavior but all of the people I was tutoring in the class were getting A’s. So, by my reckoning at the time, I thought I was winning this battle. In my junior year, I decided I didn’t want to be a juvenile delinquent; I wanted to be an intellectual. And that turned out to be more productive. BSJ: And was it at Reed that you began focusing on chemistry? KR: I started doing undergraduate research at Reed after my freshman year. And Reed had this undergraduate thesis. It’s up there on the shelf but I won’t show it to you, it’s too embarrassing. An undergraduate research thesis was great preparation for the PhD. The PhD was almost easy by comparison. My best friend at Northwestern Graduate School and I were probably the two best-prepared students. He was from Harvard; I was from Reed. So I was in a hurry; I went straight from graduate school to my job here. I have never applied for a job in my life! BSJ: Really? KR: It was a different world. My PhD supervisor was a very well known inorganic chemist at Northwestern. He pulled me into his office at the end of my second year and said, “Well Ken, things are going fast for you this year. What do you want to do in the future? Not industry right?” I said, “I don’t think so.” “Not the national labs?” “No.” “So you want to be an academic?” “Yeah, what do I do?” “Don’t worry I’ll take care of it.” Next thing you know, I get a phone call from Caltech, Berkeley, and Riverside. So I went off to give talks. Harry Gray, who just turned 80, introduced me at my interview at Caltech and I was so nervous—I had just turned 25. I got up and said, “It is very nice to be here at MIT.” True story! He thought it was a joke and everybody laughed. Things got easier after that and I got the job of my dreams and I kept it. Very dull job history; I’ve been here my whole career! Figure #2. The molecular structure of ferritin 35 • B erkeley S cientific J ournal • S ymmetry • F all 2015 • V olume 20 • I ssue 1