Computer-Aided Drug Design for Undergraduates

Tantillo, Dean J.; Siegel, Justin B.; Saunders, Carla M; Palazzo, Teresa A.; Painter, Phillip P.; O’Brien, Terrence E.; Nuñez, Nicole N.; Nouri, Dustin H.; Lodewyk, Michael W.; Hudson, Brandi M.; Hare, Stephanie R.; Davis, Rebecca L.

doi:10.1021/acs.jchemed.8b00712

Cited by 24 publications

(32 citation statements)

References 35 publications

(33 reference statements)

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“…The incorporation of laboratory experiments that aimed at teaching students the basic techniques of drug design has been found to increase the students' awareness of the roles of pharmacists in the drug design process. (Szarecka & Dobson, 2019;Tantillo et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

The Effectiveness of Using Three-Dimensional Visualization Tools to Improve Students’ Understanding of Medicinal Chemistry and Advanced Drug Design Concepts

ِAbdel-Halim

2020

IJLTER

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Computer technology is an integral part of modern research. Most undergraduate pharmacy students are not aware of the use of these techniques in the drug design process. Understanding drug-target interactions plays a vital role in the drug design process, however, teaching the molecular basis of drug action is one of the major challenges we face in medicinal chemistry courses. The increase in the availability of three-dimensional macromolecule crystal structures and computer visualization software have provided better tools to study the drugs effect at the molecular level. This study evaluates the effectiveness of using three-dimensional macromolecule visualization tools in medicinal chemistry lectures on the students understanding of the molecular basis of drug action and drug design concepts. The different examples presented in this work are part of the teaching material that were developed to suite the learning objectives of the course. In addition, the "macromolecular drug targets assignment" was introduced to the course in order to allow the students to have practical experience using the new in silico techniques. Two hundred seventy students were surveyed over the past five years, the result showed that the new teaching tools have increased students' interest in medicinal chemistry and allowed them to develop better understanding of the effect of structural modification on compounds' activity and structure activity relationship. In addition, it gave them an insight into the advanced methods used in drug design.

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Section: Discussionmentioning

confidence: 99%

The Effectiveness of Using Three-Dimensional Visualization Tools to Improve Students’ Understanding of Medicinal Chemistry and Advanced Drug Design Concepts

ِAbdel-Halim

2020

IJLTER

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“…Visualization is also stressed by Tantillo et al, [31] who developed a modular course on computer-aided drug design that addresses students with various backgrounds and experiences. Their first exercise focused on the visualization of protein structure, following the first step suggested by Ban et al as a general strategy for drug design research: "Study your target to gain deep knowledge of its biology and corresponding experimental assays."…”

Section: Computational Chemistry Literacymentioning

confidence: 99%

“…From literature, three such models emerge, which are summarized in Figure 3. The first model is to devote a full course to CC, as discussed above regarding the courses developed by Grushow, [23] Tribe [24] and Tantillo et al [31] I term this approach the specialized course model. Such a course is probably the best way to provide students with a thorough theoretical discussion along with computational practice that considers all aspects of CC literacy.…”

Section: Integrating Computational Chemistry In the Undergraduate Pro...mentioning

confidence: 99%

Computational Chemistry in the Undergraduate Classroom – Pedagogical Considerations and Teaching Challenges

Tuvi-Arad

2021

Israel Journal of Chemistry

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The interdisciplinary field of computational chemistry links many facets of chemistry and provides unique insights into structure, mechanisms, dynamics, and the interplay between them. Various approaches were proposed for integrating computational chemistry in the undergraduate classroom, all highlight the benefits of including it in the chemistry curriculum. This study focuses on the desirable learning outcomes, and defines a structural framework of computational chemistry literacy. Based on this approach analysis of the pedagogical approach of selected studies that implemented computational chemistry in undergraduate chemistry classrooms is presented. Three models for including computational chemistry in the undergraduate program were uncovered in this analysis: the specialized course model, the augmented course model, and the islands of computations model. These models are discussed along with teaching and learning challenges as well as routes to bypass them.

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“…Providing students with a fuller understanding of computer-aided drug design (CADD) by the hands-on application of its methods is the goal of several educational programs that have recently been described. 28 Of course, these programs do vary somewhat in their emphases among the large variety of CADD methods that are currently practiced. All start with the nature of the problem: the primality of 3-dimensional shape and flexibility; the multiple properties that an effective drug molecule must have the many repetitive make-and-test cycles.…”

Section: Introductionmentioning

confidence: 99%

“…Tantillo et al agree with us in the motivational value of utilizing the exposures to these concepts and tools to complete a DD project. 28 The Computational Structural Biology group at Molecular Modeling Group of the SIB in Lausanne describes an elegant web-based GUI’s intended to introduce DD and CADD to a very different audience, the general public, including high school teachers and students. 29 Johnson et al 30 incorporated pharmacokinetic considerations in their use of lighter computational tools to strengthen a conventional medicinal chemistry course.…”

Section: Introductionmentioning

confidence: 99%

Teaching and Learning Computational Drug Design: Student Investigations of 3D Quantitative Structure–Activity Relationships through Web Applications

et al. 2020

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The increasing use of information technology in the discovery of new molecular entities encourages the use of modern molecular-modeling tools to help teach important concepts of drug design to chemistry and pharmacy undergraduate students. In particular, statistical models such as quantitative structure–activity relationships (QSAR)—often as its 3D QSAR variant—are commonly used in the development and optimization of a leading compound. We describe how these drug discovery methods can be taught and learned by means of free and open-source web applications, specifically the online platform . This new suite of web applications has been integrated into a drug design teaching course, one that provides both theoretical and practical perspectives. We include the teaching protocol by which pharmaceutical biotechnology master students at Pharmacy Faculty of Sapienza Rome University are introduced to drug design. Starting with a choice among recent articles describing the potencies of a series of molecules tested against a biological target, each student is expected to build a 3D QSAR ligand-based model from their chosen publication, proceeding as follows: creating the initial data set (Py-MolEdit); generating the global minimum conformations (Py-ConfSearch); proposing a promising mutual alignment (Py-Align); and finally, building, and optimizing a robust 3D QSAR models (Py-CoMFA). These student activities also help validate these new molecular modeling tools, especially for their usability by inexperienced hands. To more fully demonstrate the effectiveness of this protocol and its tools, we include the work performed by four of these students (four of the coauthors), detailing the satisfactory 3D QSAR models they obtained. Such scientifically complete experiences by undergraduates, made possible by the efficiency of the 3D QSAR methodology, provide exposure to computational tools in the same spirit as traditional laboratory exercises. With the obsolescence of the classic Comparative Molecular Field Analysis Sybyl host, the 3dqsar web portal offers one of the few available means of performing this well-established 3D QSAR method.

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Computer-Aided Drug Design for Undergraduates

Cited by 24 publications

References 35 publications

The Effectiveness of Using Three-Dimensional Visualization Tools to Improve Students’ Understanding of Medicinal Chemistry and Advanced Drug Design Concepts

The Effectiveness of Using Three-Dimensional Visualization Tools to Improve Students’ Understanding of Medicinal Chemistry and Advanced Drug Design Concepts

Computational Chemistry in the Undergraduate Classroom – Pedagogical Considerations and Teaching Challenges

Teaching and Learning Computational Drug Design: Student Investigations of 3D Quantitative Structure–Activity Relationships through Web Applications

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