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Meet the Expert: Structural Biology Services

2018-10-26

Cayman’s Structural Biology Division has proven professional experience in structural biology including construct design, protein production, characterization, crystallization, X-ray structure determination, and in silico docking and homology modeling. We offer a full suite of customizable services that can help you achieve particular milestones throughout the life of your project. We sat down with one of those experts, Zahra Assar, Ph.D., to talk about Cayman’s Structural Biology Services capabilities.

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What is your background and how long have you worked in the field of structural biology?

I received my bachelor’s degree in chemistry from Sharif University of Technology in Tehran, Iran. I continued my education at École Polytechnique Fédérale de Lausanne (EPFL) in Lausanne where I worked on improving the therapeutic properties of bicyclic peptides under the mentorship of Dr. Christian Heinis. Phase display of these peptides was pioneered by Dr. Heinis and Sir Gregory Winter, who was awarded the Nobel Prize in Chemistry in 2018.

I earned my doctoral degree in biophysical chemistry in 2017 from Michigan State University under the mentorship of Dr. Jim Geiger. During my graduate studies, I worked on the structural analysis of multiple families of proteins to understand their structures and reengineer them to adopt different chemical and biological properties.

I became very interested in understanding the molecular interactions between proteins and macromolecules during my doctoral research. In my research, I discovered a novel fold for the human cellular retinol binding protein (hCRBP-II), which was evidence for a highly ordered folding intermediate in the intercellular Lipid Binding Protein (iLBP) family. I also discovered that hCRBPII readily and irreversibly folds into domain-swapped (DS) dimers where identical structural elements swap places in two monomers to form a dimeric structure.

What brought you to Cayman?

I joined Cayman Chemical as a structural biologist in 2017, working with the Structural Biology group established by Dr. Adam Stein, Cayman’s Vice President of Biochemistry. I was drawn to Cayman because of its commitment to its mission of “helping make research possible,” and because Cayman’s Structural Biology group has all the expertise and tools to complete a “gene-to-structure” program. I brought my expertise in the field of structural biology to join the team and help pharmaceutical companies or academic institutions progress and accelerate their drug discovery programs.

I have been privileged to be able to utilize my training and research to advance medical research and enable new potential therapies for cancer, infectious diseases, and rare diseases.

Your laboratory can support a gene-to-structure program. What are the methods/considerations you use to preserve protein quality during the process?

Having a pure folded and monodispersed protein in our work is key. Therefore, we assess the quality of purified proteins through thermal shift assays (TSAs). This analysis can also be used to test formulations and cryoprotectants to optimize storage conditions for purified proteins.

Protein crystallization is inherently difficult. You recently captured a perfect star-shaped crystal of a protein. What are the challenges you must overcome to properly crystallize proteins?

In protein crystallography, the challenging step is “crystallization.” There are many variables that influence protein crystal formation: protein purity, protein concentration, precipitant, pH, age of protein, and even presence of ligands. All these variables require extensive screening, and Cayman has the resources (including automation) to perform these screens.

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Star-shaped crystals of a chaperone protein co-crystallized with its pharmacological chaperone.

We also have developed our in-house sparse matrix screenings that are the result of gained experience from working on more than 35 protein targets with more than 200 solved structures.

To date, what is the most difficult or interesting protein you have analyzed?

Due to client confidentiality, I am unable to mention the specific protein by name. However, one of our projects involved a protein that folds as a DS dimer. This is very similar to my doctoral thesis and was very exciting work for me. This type of folding is rare for proteins and so far, DS dimers have been observed in only 40 proteins.

How does the instrumentation available in your lab impact structure determination and ligand docking studies?

For protein production we have all cell culture and fermentation capabilities for protein expression work, along with multiple chromatography systems for protein purification.

We have a CFX96 Touch™ Real-Time PCR for TSA studies. In addition, automation allows many crystallization trials to run under multiple conditions simultaneously for optimal crystal growth.

For data collection after crystallization, we are a member of the Advanced Photon Source (APS) at Argonne National Labs and can utilize rapid beamline access monthly.

For in silico modeling studies, we perform ligand docking analysis using Schrödinger Maestro 11 software, which is an inclusive suite of programs to accelerate lead discovery and lead optimization.

Tell us about your most recent publication.

In October of 2018, we had a manuscript published in the ACS Biochemistry journal. The project was a collaboration between Cayman’s Structural Biology group, Dr. Costas Lyssiotis at the University of Michigan, and Dr. Luke Lairson at the Scripps Research Institute. The structure-based analysis studies resulted in the design of a novel inhibitor scaffold for glutamic-oxaloacetic transaminase (GOT1), which may provide a useful starting point to develop drugs that target redox balance in pancreatic cancer. Pancreatic ductal adenocarcinoma (PDA) cells are characterized by dysregulated metabolic programs that facilitate growth and resistance to oxidative stress. Among these programs, the metabolic pathway through GOT1 is utilized by PDA to support cellular redox homeostasis. In this work, we identified a lead compound (CBR-101) by in vitro screens that had metabolic and growth inhibitory activity in pancreatic cancer cells. The in silico docking analysis was performed to study inhibitor-GOT1 interactions with a CBR-101 analog optimized for solubility, L79015. Together, in silico docking, X-ray crystallography, and thermal shift assays using wild-type and mutant enzymes provided insights into the binding mode and mechanism of action of L79015.

To review early reports on this work, download our science poster: Study of Novel Aspartate Aminotransferase Inhibitor Binding Mechanism Through Structure-Based Mutational Analysis

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How do you provide data reports and consultation to the customer?

As with all Cayman Contract Services, the science and communication are most important. Therefore, we provide regular updates to our clients via scheduled teleconferences, email, and/or presentations to report on the progress of projects. We are also always available to address any questions or concerns our clients may have.

All experimental procedures and data are securely documented in Cayman Services laboratory notebooks and a final report is generated and delivered at the completion of the project.

What makes Cayman stand out as a service provider in the field of drug discovery?

Cayman’s Medicinal Chemistry and Structural Biology Services offer a fully integrated multidisciplinary approach from design and synthesis to screening and optimization with experienced scientists and state-of-the-art equipment for lead generation or optimization, route and methods development, screening, and scale-up.

We provide the resources to accelerate drug discovery programs in a collaborative, phase-based, flexible approach that is driven by our clients to develop their lead compounds and potential future medicines.

For more information, download our Cayman’s Structural Biology Services brochure.

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Learn more about our service capabilities at www.caymanchem.com/services.

Cayman Chemical

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Ann Arbor, Michigan 48108 USA

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