Creating 3D physical models to probe student understanding of macromolecular structure

Mothana R, M. Noman O, Eto B, Chigr F, Chigr M. Synthesis and In Silico Analysis of New Polyheterocyclic Molecules Derived from [1,4]-Benzoxazin-3-one and Their Inhibitory Effect against Pancreatic α-Amylase and Intestinal α-Glucosidase

This study focuses on synthesizing a new series of isoxazolinyl-1,2,3-triazolyl-[1,4]-benzoxazin-3-one derivatives 5a-5o. The synthesis method involves a double 1,3-dipolar cycloaddition reaction following a "click chemistry" approach, starting from the respective [1,4]-benzoxazin-3-ones. Additionally, the study aims to evaluate the antidiabetic potential of these newly synthesized compounds through in silico methods. This synthesis approach allows for the combination of three heterocyclic components: [1,4]-benzoxazin-3-one, 1,2,3-triazole, and isoxazoline, known for their diverse biological activities. The synthesis procedure involved a two-step process. Firstly, a 1,3-dipolar cycloaddition reaction was performed involving the propargylic moiety linked to the [1,4]-benzoxazin-3-one and the allylic azide. Secondly, a second cycloaddition reaction was conducted using the product from the first step, containing the allylic part and an oxime. The synthesized compounds were thoroughly characterized using spectroscopic methods, including 1H NMR, 13C NMR, DEPT-135, and IR. This molecular docking method revealed a promising antidiabetic potential of the synthesized compounds, particularly against two key diabetes-related enzymes: pancreatic α-amylase, with the two synthetic molecules 5a and 5o showing the highest affinity values of 9.2 and 9.1 kcal/mol, respectively, and intestinal α-glucosidase, with the two synthetic molecules 5n and 5e showing the highest affinity values of -9.9 and -9.6 kcal/mol, respectively. Indeed, the synthesized compounds have shown significant potential as antidiabetic agents, as indicated by molecular docking studies against the enzymes α-amylase and α-glucosidase. Additionally, ADME analyses have revealed that all the synthetic compounds examined in our study demonstrate high intestinal absorption, meet Lipinski's criteria, and fall within the required range for oral bioavailability, indicating their potential suitability for oral drug development.

An idea to explore: Augmented reality and LEGO® brick modeling in the biochemistry and cell biology classroom-two tactile ways to teach biomolecular structure-Function

We present here two accessible ways for enhanced understanding of complex biological structures and their function in undergraduate Biology and Biochemistry classrooms. These methods can be applied for in-class instruction as well as for remote lessons, as they are cheap, easily available and easy to implement. LEGO® bricks and MERGE CUBE based augmented reality can be applied to make three-dimensional representation for any structure available on PDB. We envisage these techniques to be useful for students when visualizing simple stereochemical problems or complex pathway interactions.

A gut microbiome tactile teaching tool and guided-inquiry activity promotes student learning

The gut microbiome and its physiological impacts on human and animal health is an area of research emphasis. Microbes themselves are invisible and may therefore be abstract and challenging to understand. It is therefore important to infuse this topic into undergraduate curricula, including Anatomy and Physiology courses, ideally through an active learning approach. To accomplish this, we developed a novel tactile teaching tool with guided-inquiry (TTT-GI) activity where students explored how the gut microbiome ferments carbohydrates to produce short chain fatty acids (SCFAs). This activity was implemented in two sections of a large-enrollment Human Anatomy and Physiology course at a research intensive (R1) university in the Spring of 2022 that was taught using a hyflex format. Students who attended class in person used commonly available building toys to assemble representative carbohydrates of varying structural complexity, whereas students who attended class virtually made these carbohydrate structures using a digital learning tool. Students then predicted how microbes within the gut would ferment different carbohydrates into SCFAs, as well as the physiological implications of the SCFAs. We assessed this activity to address three research questions, with 182 students comprising our sample. First, we evaluated if the activity learning objectives were achieved through implementation of a pre-and post-assessment schema. Our results revealed that all three learning objectives of this activity were attained. Next, we evaluated if the format in which this TTT-GI activity was implemented impacted student learning. While we found minimal and nonsignificant differences in student learning between those who attended in-person and those who attended remotely, we did find significant differences between the two course sections, which differed in length and spacing of the activity. Finally, we evaluated if this TTT-GI approach was impactful for diverse students. We observed modest and nonsignificant positive learning gains for some populations of students traditionally underrepresented in STEM (first-generation students and students with one or more disabilities). That said, we found that the greatest learning gains associated with this TTT-GI activity were observed in students who had taken previous upper-level biology coursework.

Teaching meiosis with the DNA triangle framework: A classroom activity that changes how students think about chromosomes

Many biology students struggle to learn about the process of meiosis and have particular difficulty understanding the molecular basis of crossing over and the importance of homologous pairing for proper segregation. To help students overcome these challenges, we designed an activity that uses a newly developed Chromosome Connections Kit® from 3-D Molecular Designs to allow learners to explore meiosis at the molecular level. We took a backwards design approach in constructing an effective classroom activity. We developed evidence-based learning objectives and designed a crossing over activity that targets students' misconceptions and key concepts about meiosis. Assessment questions were designed based on the learning objectives and common student misconceptions. The activity consists of three parts: an interactive introductory video, a model-based activity, and reflection questions. The activity was first beta-tested with a small number of students and revised based on feedback. The revised activity was deployed in a mid-level Cell and Molecular Biology course. Analysis of pre-/post-assessment data from students who completed the activity (n = 83) showed strong learning gains on concepts related to ploidy, homology, segregation, and the mechanism and purpose of crossing over. Additionally, students who participated in the activity outperformed nonparticipants on a Genetics assessment about meiosis the following semester.

Conceptualizing learning about proteins with a molecular viewer in high school based on the integration of two theoretical frameworks

The use of a molecular viewer to visualize proteins has become more prevalent in high schools in recent years. We relied on the foundations of two theoretical frameworks to analyze questions in two learning tasks designed for 10th- to 12th-grade biotechnology majors that make use of Jmol. The two theoretical frameworks were: (i) classification of scientific knowledge into content, procedural, and epistemic knowledge; and (ii) evaluation of the cognitive skills central to visual literacy in biochemistry. During the analysis, two sub-elements of procedural knowledge emerged from the data: (i) the visualization of molecular models, and (ii) the use of Jmol software features. Based on the theoretical frameworks and data analysis, we suggest a conceptualization of learning about proteins using a molecular viewer, where the scientific knowledge elements are integrated with the eight cognitive skills central to visual literacy in biochemistry. In addition, a model presenting a hierarchy for the knowledge elements and sub-elements is suggested. In this model, content knowledge is a basic requirement; without it, the other knowledge elements cannot be used. Moreover, the use of epistemic knowledge or Jmol software features is not possible without visualization of the molecular models, which requires content knowledge. This conceptualization is expected to facilitate the development of learning tasks, decrease the complexity of knowledge acquisition for students; it may also assist the teacher during the teaching process.

Aiming for the Bullseye: Targeted activities decrease misconceptions related to enzyme function for undergraduate biochemistry students

Biochemistry curricula present a particular challenge to undergraduate students with abstract concepts which can lead to misconceptions that impede learning. In particular, these students have difficulty understanding enzyme structure and function concepts. Targeted learning activities and three-dimensional (3D) physical models are proposed to help students challenge these misconceptions and increase conceptual understanding. Here we assessed such pedagogical tools using the Enzyme-Substrate Interactions Concept Inventory (ESICI) to measure (mis)conceptual changes from Pre- to Post- time points in a single semester undergraduate biochemistry course. A Control group of students engaged with the active learning activities without the 3D physical models and students in the Intervention group utilized these activities with the 3D physical models. At the Post- time point both groups had higher, yet similar ESICI scores of the same magnitude as the highest scoring group from the national sample. Concomitantly, many misconception markers decreased compared to the national sample, although some of these differed between the Control and Intervention groups. Based on this assessment, both pedagogical approaches successfully increased conceptual understanding and targeted many of the misconceptions measured by the ESICI, however, several misconceptions persisted. Surprisingly, the students who used the 3D physical models did not demonstrate a further decrease in the misconception markers. Additionally, psychometric evaluation of the ESICI with our sample recommends the revision of several questions to improve the validity of this assessment. We also offer suggestions to improve instruction and pedagogical tools with further avenues for research on learning.

Interactive Metabolism, a simple and robust active learning tool that improves the biochemistry knowledge of undergraduate students

Advances in physiology and other fields are strongly associated with a solid base knowledge of biochemistry and cell metabolism. On the other hand, the complex and abstract nature of metabolic pathways, the traditional lecture method, and other factors made the teaching-learning process of biochemistry a challenging endeavor. To overcome this, we developed and tested a novel active learning tool called Interactive Metabolism (iM-tool). The iM-tool was developed with simple and low-cost materials. We used it for interactive teaching of several metabolic pathways and physiological mechanisms for students enrolled in the Biochemistry subject belonging to different undergraduate courses. The results of evaluation tests showed that the iM-tool significantly (ANOVA, P < 0.01) and consistently improved the biochemistry knowledge of students in classrooms with up to 50 students for 7 different and consecutive academic semesters. A survey intended to mine students' opinions on the tools showed significant satisfaction with the teaching using the iM-tool over traditional lecture-based teaching, and the iM-tool contributed to collaborative learning among students. Therefore, our results showed that the iM-tool improves the biochemistry and cell metabolism teaching-learning process in a more attractive and interactive manner.

Design and implementation of active learning strategies to enhance student understanding of foundational concepts in biochemistry

For many students biochemistry is a demanding course because they are expected to apply previously learned foundational concepts to new biological contexts. These foundational concepts serve as a scaffold onto which to build threshold concepts such as the physical basis of interactions. Unfortunately, many students possess misconceptions or gaps in knowledge of these foundational concepts which hinder their understanding of new information. This paper describes the implementation of an iterative process to improve student foundational concept learning in an introductory biochemistry course. The process includes pre-assessment of foundational concept knowledge, introduction of interventions targeting low performing concepts and re-assessment of student learning gains. Diverse active learning strategies such as problem-based worksheets, tactile learning activities, review activities and learning cycle activities were introduced to target concepts including hydrogen bonding, pH/pKa, bond energy and chemical equilibrium. While all active learning strategies resulted in improved posttest scores compared to pretest scores, no one strategy appears to be more beneficial than another. Survey results suggest students recognized the value of utilizing the various active learning strategies in the classroom to enhance critical thinking skills, engagement during class time, and collaboration skills. The process allows instructors the breadth and flexibility to introduce diverse active learning strategies tailored to their specific student needs in an effort to improve student foundational concept learning.

Teaching Metabolism in Upper-Division Undergraduate Biochemistry Courses using Online Computational Systems and Dynamical Models Improves Student Performance

Understanding metabolic function requires knowledge of the dynamics, interdependence, and regulation of metabolic networks. However, multiple professional societies have recognized that most undergraduate biochemistry students acquire only a surface-level understanding of metabolism. We hypothesized that guiding students through interactive computer simulations of metabolic systems would increase their ability to recognize how individual interactions between components affect the behavior of a system under different conditions. The computer simulations were designed with an interactive activity (i.e., module) that used the predict-observe-explain model of instruction to guide students through a process in which they iteratively predict outcomes, test their predictions, modify the interactions of the system, and then retest the outcomes. We found that biochemistry students using modules performed better on metabolism questions compared with students who did not use the modules. The average learning gain was 8% with modules and 0% without modules, a small to medium effect size. We also confirmed that the modules did not create or reinforce a gender bias. Our modules provide instructors with a dynamic, systems-driven approach to help students learn about metabolic regulation and equip students with important cognitive skills, such as interpreting and analyzing simulation results, and technical skills, such as building and simulating computer-based models.

Game-based activities targeting visual literacy skills to increase understanding of biomolecule structure and function concepts in undergraduate biochemistry

Introductory biochemistry courses are often challenging for students because they require the integration of chemistry, biology, physics, math, and physiology knowledge and frameworks to understand and apply a large body of knowledge. This can be complicated by students' persistent misconceptions of fundamental concepts and lack of fluency with the extensive visual and symbolic literacy used in biochemistry. Card sorting tasks and game-based activities have been used to reveal insights into how students are assimilating, organizing, and structuring disciplinary knowledge, and how they are progressing along a continuum from disciplinary novice to expert. In this study, game-based activities and card sorting tasks were used to promote and evaluate students' understanding of fundamental structure-function relationships in biochemistry. Our results suggest that while many markers of expertise increased for both the control and intervention groups over the course of the semester, students involved in the intervention activities tended to move further towards expert-like sorting. This indicates that intentional visual literacy game-based activities have the ability to build underdeveloped skills in undergraduate students.

Combining 3D-Printed Models and Open Source Molecular Modeling of p53 To Engage Students with Concepts in Cell Biology

While understanding macromolecular structural elements and their roles in dictating cellular function is critical to grasp basic concepts in biology, it can be challenging for students to master this content—these elements naturally exist at the nanoscale and are not observable with the naked eye. Oftentimes this understanding is catalyzed by impactful illustrations and animations found online and in textbooks. In recent years, 3D printing technology has become readily accessible as an additional way to generate models and visualize entities of interest. In this report, we describe and discuss the efficacy of an approach using 3D-printed models in combination with online open-source molecular modeling analyses of the macromolecular structure of p53 to engage students with molecular concepts in cancer cell biology and human health. This pedagogy strategy has been successfully integrated into an upper-level undergraduate course at a primarily undergraduate institution and a graduate biology course at a public research university. We describe the potential benefits while providing tools for others to integrate this strategy into their teaching.

Interactive learning modules with 3D printed models improve student understanding of protein structure-function relationships

Ensuring undergraduate students become proficient in relating protein structure to biological function has important implications. With current two-dimensional (2D) methods of teaching, students frequently develop misconceptions, including that proteins contain a lot of empty space, that bond angles for different amino acids can rotate equally, and that product inhibition is equivalent to allostery. To help students translate 2D images to 3D molecules and assign biochemical meaning to physical structures, we designed three 3D learning modules consisting of interactive activities with 3D printed models for amino acids, proteins, and allosteric regulation with coordinating pre- and post-assessments. Module implementation resulted in normalized learning gains on module-based assessments of 30% compared to 17% in a no-module course and normalized learning gains on a comprehensive assessment of 19% compared to 3% in a no-module course. This suggests that interacting with these modules helps students develop an improved ability to visualize and retain molecular structure and function.

STEM BUILD: An Online Community To Decrease Barriers to Implementation of Inclusive Tactile Teaching Tools

Access to 3D printing and other "maker" technologies has opened new doors for the creation of classroom activities using physical models. Multiple strategies for implementing 3D-printed models exist, and work to define best practices is ongoing. We outline the strengths and weaknesses of common strategies for employing physical models in undergraduate biology courses and describe a novel strategy that we have developed to pair 3D-printed models with guided inquiry learning to create inclusive and interactive learning experiences. We further introduce the STEM BUILD website, a resource that we have developed to facilitate collaboration among instructors, makers, researchers, and Universal Design for Learning experts and reduce barriers to broad implementation of inclusive kinesthetic learning activities.

Flexible and modular 3D-printed peptide models

A flexible and modular peptide modeling set was designed using freely available software tools. The set consists of space-filling models of all 20 naturally occurring amino acid side chains and a modular kit for constructing peptides employing C-alpha carbons and amide bond groups. Connectors that allow free rotation about phi and psi angles on the peptide, together with explicit representation of peptide backbone hydrogen bond donor and acceptors allows for the construction of a wide range of protein secondary structure motifs. The space-filling side chain models highlight the steric, acid-base, and polarity of these groups. These models were printed using relatively affordable commercially available fused filament fabrication printers with minimal postprinting processing. Use of these models in student group activities focused on amino acids and protein secondary structural features is described. © 2019 International Union of Biochemistry and Molecular Biology, 47(4):432-437, 2019.

Student Understanding of DNA Structure-Function Relationships Improves from Using 3D Learning Modules with Dynamic 3D Printed Models

Understanding the relationship between molecular structure and function represents an important goal of undergraduate life sciences. Although evidence suggests that handling physical models supports gains in student understanding of structure-function relationships, such models have not been widely implemented in biochemistry classrooms. Three-dimensional (3D) printing represents an emerging cost-effective means of producing molecular models to help students investigate structure-function concepts. We developed three interactive learning modules with dynamic 3D printed models to help biochemistry students visualize biomolecular structures and address particular misconceptions. These modules targeted specific learning objectives related to DNA and RNA structure, transcription factor-DNA interactions, and DNA supercoiling dynamics. We also designed accompanying assessments to gauge student learning. Students responded favorably to the modules and showed normalized learning gains of 49% with respect to their ability to understand and relate molecular structures to biochemical functions. By incorporating accurate 3D printed structures, these modules represent a novel advance in instructional design for biomolecular visualization. We provide instructors with the materials necessary to incorporate each module in the classroom, including instructions for acquiring and distributing the models, activities, and assessments. © 2019 International Union of Biochemistry and Molecular Biology, 47(3):303-317, 2019.

Computational strategy for visualizing structures and teaching biochemistry

Computational techniques have great potential to improve the teaching-learning. In this work, we used a computational strategy to visualize three-dimensional (3D) structures of proteins and DNA and help the student to comprehend biochemistry concepts such as protein structure and function, substrate, and inhibitors as well as DNA structural features. The practical classes included tutorials to be done in the computer using structures from Protein Data Bank and a free 3D structure visualization software, Swiss PDB Viewer. The activity was done with 76 students from biology and pharmacy undergraduate courses. Questionnaires were administered to evaluate the knowledge regarding specific biochemistry contents before and after the activity and the opinion of the students. An overall increased percentage of correct answers post-classes (75.91%) were observed in comparison to pre-classes (35.53%). All the students indicated that it could contribute to the learning of DNA and protein structure contents; approximately 90% stated that it enables structures visualization or makes the learning and understanding easier. Therefore, the strategy has shown to be effective, allowing the contextualization of biochemistry themes and may complement theoretical classes. © 2018 International Union of Biochemistry and Molecular Biology, 47(1):76-84, 2018.

Assemble-And-Match: A Novel Hybrid Tool for Enhancing Education and Research in Rational Structure Based Drug Design

Rational drug design is the process of finding new medication that can activate or inhibit the biofunction of a target molecule by binding to it and forming a molecular complex. Here, shape and charge complementarities between drug and target are key. To help find effective drug molecules out of a huge pool of possibilities, physical and computer aided tools have been developed. Former offers a tangible experience of the molecular interactions yet lacks measurement and evaluation capabilities. Latter enables accurate and fast evaluations, but does not deliver the interactive tangible experience of physical models. We introduce a novel hybrid model called "Assemble-And-Match" where, we enhance and combine the unique features of the two categories. Assemble-And-Match works based on fabrication of customized molecular fragments using our developed software and a 3D printer. Fragments are hinged to each other in different combinations and form flexible peptide chains, conformable to tertiary structures, to fit in the binding pocket of a (3D printed) target molecule. Through embedded measurement marks, the molecular model is reconstructed in silico and its properties are evaluated. We expect Assemble-And-Match tool can enable combination of visuospatial perception with in silico computational power to aid research and education in drug design.