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Students participating in this Biotechnology Training Program are required to satisfy their home department's course requirements for a Ph.D. degree as well as those of the training program. Course requirements of the Biotechnology Training Program include required and elective courses as described below.

REQUIRED COURSES

All trainees are required to successfully complete the following core courses: Advanced Pharmaceutical Biotechnology (PHCH 870); Principles and Practice of Chemical Biology (PHCH 860) or equivalent; Issues in Scientific Integrity (PHCH 801); Careers in Biomedical Sciences (PHCH 816); and Roadmap to Discovery, Development and Regulatory Approval of New Drugs (PHCH 712).

Pharmaceutical Chemistry 870 (PHCH 870): Advanced Pharmaceutical Biotechnology. The objective of this course is to introduce the students to the discovery, development, and production of pharmaceutical macromolecules, vaccines, and cell-based therapeutics. In the discovery section, the role of structure in governing activity, specificity, and stability, particularly for pharmaceutically important proteins, is covered. Physical and spectroscopic methods for the qualitative and quantitative analysis of macromolecular structures are described. Degradation processes, both chemical and physical, that are peculiar to proteins, other macromolecules and stability of cell based systems will be presented, as well as strategies designed to prevent them. Introduction to recombinant DNA technology, large-scale production, and purification and isolation procedures used for recombinant proteins in the pharmaceutical industry will be covered. Basic immunology principles of vaccines and methods and challenges in vaccine development will also be described. Procedures for handling regulatory guidelines (filing of NDAs and INDs) will also be addressed. Instructors: T.J. Siahaan (Coordinator, KU), M.J. Hageman (KU), C.R. Middaugh (KU), T. Tolbert (KU), S. Gehrke (KU), D. Volkin (KU), Z. Shahrokh (Biotechnology Consultant), A. Wakankar (Stem CentRx Inc.), M. Federici (Biotechnology, Consultant), and Bruce Kerwin (Process & Product Development, Consultant).

Pharmaceutical Chemistry 860 (PHCH 860): Principles and Practice of Chemical Biology. This course will provide trainees with the basic background molecular biology, structural biology, cell biology and chemical biology. The overall emphasis is to understand how chemistry can be used to interrogate and control biology in the context of the topics listed in the course schedule. The course specifically discusses the following topics (a) macromolecular structures, (b) kinetics and thermodynamics, (c) various biochemical pathways, (d) transcription and translation, (e) cell signaling, (f) genetics and genomics, (g) peptide and carbohydrate synthesis, (h) natural product and nucleic acid biosynthesis, (i) bioconjugation, and (j) bio-orthogonal chemistry. Instructors: P. Hanson (Chemistry), A. Lamb (Mol. Biosciences), and T. Prisinzano (Medicinal Chemistry).

Pharmaceutical Chemistry 801 (PHCH 801): Issues in Scientific Integrity. The course consists of discussion sessions led by members of the Departments of Pharmaceutical Chemistry and Medicinal Chemistry and the Office of Research and Graduate Studies. The course utilizes a textbook entitled, “On Being a Scientist: A Guide to Responsible Conduct in Research,” 3rd Edition, The National Academies Press, Washington, DC. The topics discussed include the nature of ethics, the scientist in the laboratory, and the scientist as author, grantee, reviewer, employer/employee or student/teacher, and citizen. The discussions focus on case histories with emphasis on student participation and feature topics on (a) the origin of ideas and the allocation of credit, (b) the personal and professional complexities of the research environment, (c) the treatment of data, (d) scientific misconduct through the researcher’s and the institution’s perspectives, (e) scientific misconduct through the author’s, reviewer’s and editor’s perspectives, (f) intellectual property and entrepreneurship, and (g) the researcher in society. Instructors: W. Picking (Coordinator, KU), K.L. Audus (KU), T. Siahaan (KU), C. Berkland (KU), D. Volkin (KU), T. Prisinzano (KU), W. Picking (KU), J. Stobaugh (KU), and C.R. Middaugh (KU).

Pharmaceutical Chemistry 816 (PHCH 816): Careers in Biomedical Sciences. The objective of this course is to provide trainees with a roadmap for pursuing their career goals. The course uses “Next Gen PhD: A Guide to Career Paths in Science” by Melanie V. Sinche. The course gives an opportunity for trainees to discuss possible career paths for PhD scientists. The formation of individual development plans (IDP) in conjunction with their mentors will be introduced. The course covers (a) practical training in career development (i.e., preparation of CV; application letter; letters of reference; networking; and communication skills), (b) refresher of scientific ethics, (c) training in avoiding bias, (d) training in rigor and reproducibility, and (e) improving quantitative skills (e.g., statistical analysis of data). The trainees have the opportunity to (a) invite and host seminar speakers, (b) discuss the papers published by each seminar speaker in a journal club, and (c) organize the joint BTP-CBTP Biomedical Sciences Symposium. Instructors: A. Lamb (KU), P. Hanson (KU), T. Prisinzano (KU), and M.J. Hageman (KU).

Pharmaceutical Chemistry 712 (PHCH 712): Roadmap to Discovery, Development and Regulatory Approval of New Drugs. The course covers developing and progressing a new drug through pharmaceutical development, regulatory approval and into commercial use. Development of both traditional small-molecule drugs, biotechnology-based protein drugs, vaccines and cell-based therapies will be discussed. The specific topics covered in the course  include (a) process in moving a drug candidate from laboratory discovery to human clinical trials, (b) common hurdles in developing a new drug candidate up to large scale production in manufacturing facility and drug distribution via the supply chain, (c) requirements and process of approval of a new drug candidate by FDA, (d) protecting the intellectual properties, (e) financing research for the discovery and development of a new drug candidate, and (f) explorations for making drugs and vaccines more accessible in developing countries. The instructors are scientists from industries, venture capitals, government, and private institutions. Instructors: D. Volkin (KU), T.J. Siahaan (KU), M. Hageman (KU), T. Martin (Adjuvance Technologies), T. Lubiniecki (Janssen R&D, J&J; retired). V. Zia (Gilead Sciences), M. Powell (Sofinnova Ventures), R. Krawczyk (Blue Fin Group; retired), V. Hsu (Bill and Melinda Gates Foundation), and D. Mudra (Eli Lilly).

ELECTIVE COURSE REQUIREMENTS FOR AREAS OF SPECIALIZATION

In addition to the core course requirements, trainees are required to select an area of specialization and to take two elective courses in his or her specific area of specialization. The elective courses are required in each area of specialization to provide the trainees with exposure to both practical problems and theoretical background associated with their particular area of interest. The elective courses are categorized according to the area of research specialty of the trainee:

               Formulation and Process Design:
Physical Chemistry of Solutions, Solids and Surfaces (PHCH 862) and Mechanisms of Drug Degradation and Stabilization (PHCH 972)
              
               Drug Delivery and Targeting:
               Drug Delivery (PHCH 715) and Pharmacokinetics (PHCH 976)
 
               Drug Analysis:
Pharmaceutical Analysis I (PHCH 864) and Mass Spectrometry (CHEM 826)
 
Protein Structure:
Modern Biochemical and Biophysical Methods (BIOL 918) and Spectrochemical Methods of Analysis (CHEM 908)
 
Bioinformatics:
Bioinformatics I (BINF 701) and Bioinformatics II (BINF 702).
 
Vaccine Design and Formulation:
Drug Delivery (PHCH 715) and Physical Chemistry of Solutions, Solids and Surfaces (PHCH 862)

Some flexibility can be provided in selecting the two elective courses, depending on the research demands of the trainee. The descriptions of each course are provided below.

Pharmaceutical Chemistry 862 (PHCH 862): Physical Chemistry of Solutions, Solids and Surfaces. The objective of this course is to discuss topics on equilibria and physical chemistry of aqueous and non-aqueous systems, solids and surfaces with emphasis on systems of interest to pharmaceutical and biotechnology scientists, including (a) association-dissociation equilibria, (b) complexation and protein binding,  (c) estimation of solubility and ionization constants, (d) thermodynamics and dynamics of amorphous and crystalline solids, and (e) interactions of molecules with surfaces. Physical properties of ideal and nonideal solutions are discussed in the presence and absence of solids and surfaces, including methods for determining and predicting solubility and ionization phenomena. The thermodynamics of ligand-binding and surface-binding interactions coupled with macromolecular conformational equilibria are developed, with special attention to small-molecule protein binding equilibria. Instructors: M.J. Hageman (Coordinator, KU), L. Forrest (KU), and C.R. Middaugh (KU).

Pharmaceutical Chemistry 972 (PHCH 972): Mechanisms of Drug Degradation and Stabilization. The objective of the course is to prepare students to recognize drug molecules, based on their chemical structures, that are likely to present stability problems under a variety of conditions in both solution and solid states. The course provides students with the principles necessary to conduct stability evaluations of drugs and the associated quantitative interpretation of data from a thorough study. Examples of compounds (small molecule and macromolecule) and formulations that may be susceptible to chemical decomposition will discussed. Particular emphasis is placed on how these degradation processes can be prevented or reduced, allowing formulation of these drugs for therapeutic use. Instructors: C. Schöneich (Coordinator, KU), T.J. Siahaan (KU), and J. Stobaugh (KU).

Pharmaceutical Chemistry 715 (PHCH 715): Drug Delivery. The objective of this course is to provide students with a knowledge of the current trends in drug delivery systems utilizing conventional routes of administration. Factors that influence the delivery of drugs, such as drug physicochemical properties, excipients, mechanisms of drug release, and methods of evaluation, will be discussed. The performance of calculations related to the physical and chemical properties of drugs and common dosage forms (solubility, stability, release, dissolution, diffusion, partitioning, dose, absorption, and disposition) will also be taught. Finally, the presence of biological barriers and the mechanisms of sub-cellular trafficking of drugs will be described. The performance of calculations based on a fundamental understanding of mass transport concepts governing the disposition of a drug during administration and upon contact with biological barriers will be covered. Instructor: C. Berkland (KU).

Pharmaceutical Chemistry 976 (PHCH 976): Pharmacokinetics. This course provides trainees with exposure to the quantitative treatment of the processes involved in drug absorption, distribution, metabolism, and excretion in living systems. Topics covered in this course include classical pharmacokinetics, non-linear pharmacokinetics, advanced concepts in pharmacokinetic modeling, biological barriers to efficient drug delivery, and pharmacokinetics in dosage form development. The students will be able to appreciate and use quantitative information to increase drug effectiveness through individualized dosing. The areas of biopharmaceutics, pharmacokinetics, and clinical pharmacokinetics will be presented. Instructors: J. Stobaugh (Coordinator, KU) and J. Krise (KU).

Pharmaceutical Chemistry 864 (PHCH 864): Pharmaceutical Analysis. The course focuses on the principles of liquid phase separations accomplished by pressure-driven chromatography, a limited discussion of gas chromatography, electrically driven separations via capillary electrophoresis, mass spectrometry and sample preparation techniques useful for biological samples. Further aspects include assay validation and statistics, principles of the detectors used in LC and CE, immunoassays technologies and an introduction to DNA sequencing. Instructors: J. Stobaugh (Coordinator, KU), S. Lunte (KU), Z. Wang (KU), and L. Van Haandel (KU).

Chemistry 826 (CHEM 826): Mass Spectrometry. This course is focused on introducing students to mass spectrometry methods. The various ionization techniques and mass analyzers will be discussed, and many examples of different mass spectrometric applications will be introduced. Instructor: H. Desaire (KU).

Biology 918 (BIOL 918): Modern Biochemical and Biophysical Methods. A course emphasizing the use of techniques for solving problems of structure and function of biological macromolecules. Students complete several modules that consist of lectures relating to theory and practical aspects of each methodological approach and applying these techniques to solving a specific problem. Instructor: K. Kuczera (KU).

Bioinformatics 701 and 702 (BINF 701 and 702): Bioinformatics I and II. BINF 701/702 is the bioinformatics core course developed at the KU Center for Bioinformatics. The objective is to help the students to use bioinformatics tools to solve problems in their own research. The course is designed to introduce the most important and basic concepts, methods, and tools used in Bioinformatics. Topics include (but are not limited to) bioinformatics databases, sequence and structure alignment, protein structure prediction, protein folding, protein-protein interaction, Monte Carlo simulation, and molecular dynamics. Emphasis will be on the understanding and utilization of these concepts and algorithms. Second semester (BINF 702) covers topics including protein quaternary structure modeling (protein-protein/DNA/small ligand docking, binding, computer-aided drug design), protein structure-function relationships, biological membranes (structure and function of integral membrane proteins, protein-membrane and protein-protein interactions in membranes), phylogenetic trees, modeling of genome-wide protein interaction networks based on structure, sequence, experiment and data-mining. Instructors: I. Vakser (Coordinator, KU), E. Deeds, C. Ray and J. Slusky.


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