MAY 29, 2024

Virtual Biotechs – A Student Group Learning Project Enhanced Through Application of Schrödinger Maestro in a Medicinal Chemistry Course

The Department of Chemistry at Saint Louis University offers an introductory medicinal chemistry course for juniors, seniors, and graduate students every spring. In 2019, an active learning group project was developed over the course of the semester wherein student teams of “virtual biotech” companies were formed to work through the drug discovery process on a virtual project. This was introduced as an experiment to help break up a 2.5 hour night course while applying what the students were learning in a more “real world” application that mimics working on diverse teams that occurs naturally in the pharmaceutical industry workforce. Student groups work to identify a disease with unmet medical need, target candidate profile, suitable biological targets for drug discovery, processes for hit identification, and propose an optimization strategy. The group project continues to evolve each year based on student feedback. Incorporation of structure-based drug design utilizing Schrödinger Maestro molecular modeling software was introduced in 2022 and is now integrated throughout the semester in individual weekly assignments to learn the software and the group project to utilize the software to apply what the students were learning in class to their project. The project teams conduct a virtual screen for their target using commercial screening libraries, evaluate hits, and use Ligand Designer to propose new analogs. At the end of the semester, the project teams present their work as a 10-minute project pitch to “virtual investors” (their classmates) to select a project for “virtual investment”.

MAY 30, 2024

Leveraging high-impact practices in the chemistry curriculum with molecular modeling

Undergraduate research (including course-based experiences, or CURE), capstone projects, and community-based learning (CBL) are integral components of the chemistry curriculum at Saint Joseph’s College of Maine. To leverage gains from these existing high-impact practices, students at SJC use molecular modeling tools throughout their learning in Organic Chemistry I & II. As a regular part of both classroom and laboratory activities, students build technical competency and diversify their media for learning critical concepts and applications of organic chemistry. This year, organic chemistry students have also designed a CBL project focused on sharing molecular modeling tools with local high school chemistry students, as part of a larger on-going curriculum at SJC. For those students who take Medicinal Chemistry in their junior or senior year, their familiarity and competency with computational molecular modeling serve as a critical foundation for designing and carrying out a drug discovery project in this CURE-based class.

This talk will share how molecular modeling is weaved through multiple chemistry courses at SJC, best practices that we have learned from our pilot years, and our current plans to expand student access and competency in this area. Importantly, it will discuss why tools such as Teaching with Schrödinger has been so instrumental in supporting high-impact practices in chemistry, modernizing the organic chemistry classroom, and ultimately, better equipping STEM students with the skills and resilience needed to tackle new challenges and questions in the future.

JUN 13, 2023

Using computer aided drug design and Teaching with Schrödinger in a medicinal chemistry CURE course

Course-based Undergraduate Research Experiences (CUREs) are an impactful and inclusive way for undergraduate students to be exposed to research experiences. Students in CURE Medicinal Chemistry at Weber State University learn foundational medicinal chemistry concepts and explore computer aided drug design (CADD) applications. Students apply these concepts and applications in a self-selected project where they formulate and explore a new idea/hypothesis related to medicinal chemistry. Students research their selected topic, propose specific drug modifications based on medicinal chemistry concepts, and test those structures in silico for improved drug characteristics. Molecular modeling is crucial for the research project hypotheses and molecular docking is essential for the data analysis component. Teaching with Schrödinger (TwS) has allowed for better and easier modeling and docking while also providing more equitable access to students because TwS just requires internet connection. Students in CURE Medicinal Chemistry disseminate their work as poster presentations at the WSU undergraduate research symposium.

JUN 14, 2023

Exploring Schrödinger Modeling Software: Enhancing Teaching and Learning in an Undergraduate Drug Hunter for Beginner Class

This talk highlights the integration of Schrödinger modeling software in pharmaceutical science education for senior-level students in the course “Drug Hunting for Beginners.” This project-based class focuses on students pursuing PharmD or PhD degrees, where teams pitch a drug discovery project integrating knowledge from medicinal chemistry, biochemistry, and pharmacology. By incorporating the software, we bridge the gap between theory and practice, providing a platform for experiential learning and collaborative problem-solving. Through case studies and capstone projects, students gain a deeper understanding of the drug discovery process, including evaluating therapeutic targets, hit identification, structure-based drug design, and improving drug-like properties through in silico prediction. Our experience offers insights for educators seeking to enhance medicinal chemistry teaching methods and empower students to integrate knowledge in drug discovery.

JUN 13, 2023

Finding a CURE for the Common Classroom: Reimagining Undergraduate Research

Course-based research experiences (CUREs) are an innovative and effective way to introduce undergraduate students to scientific research. These experiences provide students with the opportunity to engage in research within the context of a course, allowing them to gain practical experience in scientific inquiry while still fulfilling course requirements. CUREs have numerous benefits for students, including improving critical thinking, problem-solving, and communication skills, as well as providing valuable hands-on experience with scientific methods and techniques. Additionally, CUREs have been shown to increase retention and graduation rates for students in science, technology, engineering, and mathematics (STEM) fields, particularly among underrepresented minority groups. Furthermore, CUREs can provide meaningful research experiences to students who may not have the opportunity to participate in traditional research internships or programs.

In this lecture, I will talk about a course I created called Structural Bioinformatics of Proteins. This course is divided into two parts. The first half of the semester, students learn how to use the visualization software PyMOL and other cutting-edge bioinformatics tools and methods to analyze protein structures. In the second half of the semester, students are given recently determined, high-quality, three-dimensional coordinates provided by the Seattle Structural Genomics Center for Infectious Disease and must write a final paper based on the analysis of their datasets using the skills learned in the first half of the course. At the end of the semester, students give an oral or a poster presentation at our university-wide Undergraduate Research Symposium. Students who produce outstanding work have the opportunity to publish it in a peer-review scientific journal. Course evaluations from students consistently report that this class provided them with valuable skills, experiences, and opportunities needed to succeed in scientific research and STEM fields.

JUN 14, 2023

Curriculum redesign through design: A PyMOL poster project to assess program learning outcomes

Teaching biomolecular visualization skills can improve students’ comprehension of foundational concepts in life science education. Molecular modeling is a gateway to understanding molecular interactions, structure-function relationships, and the use of appropriate renderings to convey specific information about a protein structure. Accordingly, a major goal of the curriculum redesign effort at the University of Texas at Austin is to incorporate modeling throughout the biochemistry degree plan. Scaffolded PyMOL activities have been developed to advance students’ modeling skills from beginner level to comfortably displaying molecular interactions and producing high-quality images. In Foundations of Biochemistry, the first upper division course in the degree plan, these skills are integrated in a culminating Signature Assignment: a task that best encompasses the knowledge and skills essential to the course objectives. Students explore enzyme inhibition in the context of small molecule disease treatment, and, throughout the latter half of the semester, craft a scientific poster. Presentations incorporate students’ original PyMOL images and connect the enzyme–inhibitor interaction to the biochemistry of the disease. Importantly, this project is one of several being developed to track students’ achievement of programmatic learning outcomes for the biochemistry degree plan and will ultimately be used as one measure to assess student success and the overall curriculum redesign effort.

JUN 15, 2023

Computational drug design and chemo-informatics: a hands-on course at the University of Antwerp

The University of Antwerp is the third-largest university in the Dutch-speaking region of Belgium, with over 20,000 students annually. Within the Biochemistry and Biotechnology curriculum, students have the option to take a three-ECTS course on computational drug design and chemo-informatics. The course is organized in a modular fashion and covers both theoretical and practical sessions.

During the theoretical sessions, students learn about chemo-informatics and virtual screening, which includes concepts such as chemical fingerprints, molecular similarity, clustering, machine learning models, and virtual screening performance metrics. The course also covers molecular docking and pharmacophore searching. The concepts covered in the theoretical sessions are then put into practice in a series of hands-on sessions.

For the chemo-informatics tasks, the students use Google Colab with RDKit as a chemo-informatics toolkit, while for the pharmacophore and docking-related aspects, they use Maestro, Phase, and Glide. These tools are made available through the “”Teaching with Schrödinger”” web-based virtual workstations, which allows students to access them from anywhere at any time. Finally, using an internally-developed virtual reality system, the students can graphically study the non-bonded interactions between ligand and protein.

At the start of the course, a drug design project is defined based on ongoing research programs in the Faculty. The goal of the project is to identify a limited number of commercially-available compounds (5-10) that are subsequently purchased and biochemically characterized for their inhibitory properties. The students complete the program with a written report, which serves as the basis for the oral examination at the end.

JUN 15, 2023

Teaching computer-aided drug design techniques to graduate students specializing in medicinal chemistry

Medicinal chemists are scientists who specialize in the design, synthesis, and optimization of molecules with therapeutic properties. They work in the pharmaceutical industry, government research institutions, or academia, and collaborate with other scientists, such as biologists, pharmacologists, and clinicians, to develop new drugs. Teaching computational chemistry is important for medicinal chemists because it can help to streamline the drug discovery process, improve the potency and selectivity of drug candidates, and provide insights into drug-target interactions. It also provides medicinal chemists with a valuable skillset that can be applied to a variety of research problems. During my presentation, I will elaborate on our utilization of Schrödinger educational resources to improve the instruction of computer-based drug design approaches to students pursuing a master’s degree in Medicinal Chemistry. Additionally, I will outline the practical application of these concepts by students through computer-based drug design assignments.

JUN 15, 2023

Teach computer-aided drug design (CADD) in the upper-level bioinformatics/biochemistry /molecular modeling courses using schrodinger package

Computer-aided drug design (CADD) has become an integral part of modern drug discovery and development processes. To equip students with essential skills in CADD, it is imperative to incorporate relevant tools and software packages into the curriculum of bioinformatics, biochemistry, and molecular modeling courses. This talk presents the effective integration of the Schrödinger Small-Molecule Drug Discovery Suite, a widely used suite of computational chemistry tools, in teaching CADD concepts to students at the upper-level courses. The Schrödinger package offers a comprehensive range of modules and functionalities for homology modeling, molecular docking, virtual screening, and molecular dynamics simulations. By introducing students to this powerful software package, they can gain hands-on experience in utilizing computational techniques for rational drug design. The talk discusses the potential benefits, challenges, and strategies for integrating the Schrödinger package into the curriculum, focusing on enhancing students’ understanding of CADD principles, fostering critical thinking skills, and providing practical training for future research and industry applications. Furthermore, it highlights the importance of incorporating real-world case studies and collaborative projects to reinforce the learning experience and encourage interdisciplinary approaches. Through the incorporation of the Schrödinger package in upper-level courses, students can develop valuable computational skills and be better prepared to contribute to the rapidly evolving field of drug discovery and design.

JUL 28, 2021

A Recipe for a Short Course in Molecular Simulations as Part of Special Topics in Biological Chemistry

The Biological Chemistry II course at University of Connecticut is a team taught course covering special topics in the field biological chemistry. This talk will cover a first attempt to introduce students, pursuing a biological chemistry track within their PhD program, with the essentials of biomolecular simulations. The course covers the basic theory underlying current molecular simulation methods and provides a hands-on experience on the use of software for computational chemistry applications, from small molecules to proteins. This has been made possible only recently by the ability to stream specialized software via virtual machine platforms, without the need of special hardware requirements and software installation.

JUL 28, 2021

Making Lemonade, Giving Students a Choice, and NOT Reinventing the Wheel in Introduction to Bioinformatics Course

Student choice, POGIL, and flipped classroom approaches are successfully used to engage students in Introduction to Bioinformatics (BIMM 143) during the Winter and Spring quarters of 2021 at UC San Diego. The majority of the students enrolled in the course are fourth year biology students with a range of majors, from Human Biology to Molecular Biology. The majority of students have no coding experience prior to this course. Students are paired at the beginning of the quarter into groups & given access to DataCamp, an online education platform for learning how to code in python and R (students choose which coding track they would prefer at the beginning of the quarter as well). These groups were affectionately renamed PODs (for People of DataCamp) and each PODmate was given a role similar to the structure of POGIL activities (process oriented guided inquiry based learning). Students choose whether they want to participate in weekly trivia based on that week’s DataCamp activities or do a challenge problem that is loosely based on DataCamp activities. Students also participate in Code-Together Meetings and share notes from DataCamp for participation credit in the course. DataCamp and PODs formed the foundation for supporting students in their learning so that they could accomplish two major projects throughout the quarter. For one of the projects in the course, students can choose to either formulate their own unique scientific question and hypothesis that can be answered through a bioinformatics method OR they can opt to participate in Schrodinger’s Molecular Modeling course. Students that choose the molecular modeling course then present on the course findings and learnings to the rest of the students as an extra credit opportunity for BIMM 143 students not enrolled in the Molecular Modeling course. Student’s response to this course format is very positive. The biggest take-home has been that students really appreciate having choice, whereas having PODmates and using a flipped classroom has gotten mixed reviews.

JUL 28, 2021

Embedding Computation within the Chemistry Syllabus in an Applied Manner

With advancing technology, the importance of computational chemistry continues to grow. This topic should not remain for postgraduate education or higher, but holistically included in undergraduate curriculum at every stage to provide students modern transferable skills and prepare them for their future workplace. There are two branches of computational chemistry that we have focused on teaching our students; molecular modelling and programming. Both require students to be proficient in data analysis – an important skill to nurture. Our fundamental approach is based on understanding why certain methodologies are chosen to answer a particular chemistry question by knowing each method’s limitations and then vitally linking results back to real chemistry scenarios.