Pharmaceutical Chemistry
Pharmaceutical Chemistry
Pharmaceutical Chemistry
#Qa de Alcalá
TEACHING GUIDE
PHARMACEUTICAL
CHEMISTRY
(Reviewed on CD on 05-27-2021)
Degree in PHARMACY
University of Alcalá
TEACHING GUIDE
DEGREE IN PHARMACY
Degree in which it is taught:
Department and Area of Organic Chemistry and Inorganic Chemistry
Knowledge: (area
of Organic Chemistry)
Character: Mandatory
ECTS credits: 12 ECTS (9 Theoretical + 3 Practical)
Course and period Third Course / Annual
Faculty:
Dr. Ana Mª Cuadro Palacios Dr. Lourdes Gude
Rodríguez Dr. Mª Teresa Quirós López
Coordinator: Dr. Ana Mª Cuadro Palacios
Tutoring Schedule: Prior appointment with the subject teachers
Language in which it is Spanish
taught:
1. PRESENTATION
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Behavior is hardly predictable taking into account only its elementary functionalization.
In the Chemical Laboratory, the knowledge acquired in the theoretical part will be developed.
2. COMPETENCES
Specific competencies:
1. Acquire basic knowledge of Heterocyclic Chemistry, especially regarding its
differentiating characteristics with respect to General Organic Chemistry.
2. Know the methods and strategies used to obtain drugs.
3. Understand the interrelationship between the structure, the physical-chemical properties
and the therapeutic activity.
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4. Know and consider the structural modifications that affect the properties of drugs.
5. Be able to predict the transformations of drugs in the body.
6. Recognize and predict interactions between drugs and their biological targets.
7. Ability to find similarities between groups of drugs with the same profile.
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8. Ability to derive a pharmacophore from a set of substances.
9. Know and use spectroscopic methods for the identification and structural elucidation of
drugs and related compounds.
10. Know the main families of drugs, their mechanisms of action and their therapeutic uses.
11. Know, propose and carry out syntheses of representative drugs of the main families
studied.
12. Ability to propose chemical transformations of drugs aimed at improving their activity.
13. Know how to acquire and use information related to drugs.
3. CONTENTS
Theorists:
THEMATIC UNIT I: Heterocycles. Generalities
Topic 1
Heterocycles. Classification. Nomenclature and structure. Synthesis: most relevant strategies
and processes.
THEMATIC UNIT II: Pi-deficient aromatic heterocycles
Topic 2
Pi-deficient aromatic heterocycles I. Pyridine. Structure and reactivity. Reactions with
electrophiles. Oxidation. Reactions with nucleophiles. Reduction. Substituted pyridines: C-
derivatives and N-derivatives. Synthesis methods. Derivatives for pharmaceutical use.
Theme 3
Pi-deficient aromatic heterocycles II. Quinoline and Isoquinoline. Structure and reactivity.
Reactions with electrophiles. Oxidation. Reactions with nucleophiles. Reduction. C- and N-
derivatives. Synthesis methods. Derivatives for pharmaceutical use.
Theme 4
Pi-deficient aromatic heterocycles III. Diazines. Structure and reactivity. Reactions with
electrophiles. Oxidation. Reactions with nucleophiles. Reduction. C- and N-derivatives.
Synthesis methods. Derivatives for pharmaceutical use.
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THEMATIC UNIT III: Surplus pi aromatic heterocycles
Topic 5
Surplus pi aromatic heterocycles I. Pyrrole, Thiophene and Furan. Structure and reactivity.
Reactions with electrophiles. Oxidation. Reduction. Benzoderivatives. Synthesis methods.
Derivatives for pharmaceutical use.
Topic 6
Surplus pi aromatic heterocycles II. 1,3-Azoles and 1,2-azoles: structure, reactivity and
derivatives. Synthesis methods. Derivatives for pharmaceutical use. Other related
heterocycles.
THEMATIC UNIT IV: The drug. Introduction, physical-chemical, chemical and structural
properties
Topic 7
The drug: Introduction. Drug and medication. Drug development, phases and costs. Origin
and origin of drugs. Interaction of the drug development process with the patent cycle. Drugs
on the market and generic drugs
Topic 8
Physical-chemical, chemical and structural properties of drugs. Structurally specific and
nonspecific drugs. Pharmacophores. Drug-receptor binding forces. Most relevant physical-
chemical properties in drug-receptor binding, pKa, partition coefficient. Geometric factors.
Lipinski rules. Stereochemistry and pharmacological activity. Conformational constraint.
Optical isomerism.
THEMATIC UNIT V: The three fundamental phases of the action of a drug: Pharmaceuticals,
Pharmacokinetics and Pharmacodynamics
Topic 9
The three fundamental phases of the action of a drug: Pharmaceuticals, Pharmacokinetics
and Pharmacodynamics. Pharmaceutical phase based on chemical structure.
Pharmacokinetic phase. Absorption, distribution and excretion of drugs and their relationship
with chemical structure. Pharmacodynamic phase. The receptor, nature and forces of drug-
receptor binding. Agonists and antagonists: concept and relationship with their chemical
structure.
Topic 10
Pharmacokinetic phase II. Drug metabolism. Reactions mediated by “oxene”, through
cytochrome P-450 and its formation from atmospheric oxygen. Microsomal oxidation reactions
of alkanes in allylic and benzylic positions. Oxidation reactions in the α position to carbonyls
and imines. Oxidation reactions in ω and ω-1 position. Oxidation reactions of arenes:
formation of epoxides and displacement NIH. Oxidation reactions of alkenes. Oxidation
reactions of compounds with heteroatoms and their types: oxidation reactions of ethers.
Oxidation reactions of compounds with sulfur. Oxidation reactions of nitrogenous compounds:
reactions in tertiary and secondary, aromatic and heteroaromatic and alicyclic amines. Other
microsomal oxidation reactions. Non-microsomal oxidation reactions: Oxidation reactions of
primary amines, alcohols and aldehydes. Microsomal and non-microsomal reduction
reactions. Hydrolysis reactions. Conjugation reactions: conjugation with glucuronic acid.
Conjugation as sulfate. Conjugation
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with amino acids. Conjugation reactions with glutathione: Formation of mercapturic acids.
Methylation reactions. Generation of toxic metabolites. Metabolite prediction models.
THEMATIC UNIT VI: Drug design
Topic 11
Drug design I. Find a seed. Choice of disease, target, bioassay. Search for seed prototypes:
screening of natural products. Screening of sample libraries. Improvement of existing drugs.
Variations on the natural ligand. Combinatorial synthesis. Computer design. Serendipity. Other
ways to generate prototypes. Drug-like products.
Topic 12
Drug design II. Improved interaction with the target. Structure-activity relationships.
Identification of a pharmacophore. Strategies in drug design. Variation of substituents.
Extension of the structure. Chain and ring extension/contraction. Ring variation. Ring fusion.
Bioisostery. Simplification of the structure. Rigidification and conformational blocking. Another
resources. Siamese drugs.
Topic 13
Drug design III. Improved access to the target. Improved absorption. Drugs more resistant to
chemical or enzymatic degradation. Drugs less resistant to metabolism. Drug vectorization.
Reduction of toxicity. Prodrugs. Drug alliances. Endogenous products such as drugs.
Topic 14
IV drug design: QSAR. Introduction. Hydrophobicity of the molecule. Hydrophobicity of the
substituents. Electronic effects: Hammett constant. Electronic R & F factors. Electronic effects
on aliphatic substituents. Steric factors. Hansch equation. Craig Plot. Topliss scheme.
Bioisosteres. Free-Wilson approximation. 3D QSAR.
Topic 15
Molecular modeling. Molecular and quantum mechanics. Three-dimensional design of
structures. Real structures: X-ray diffraction. Energy minimization. Dimensions and molecular
properties. Conformational analysis. Identification of the active conformation. Pharmacophore
identification. Docking and in silico screening techniques. Protein mapping. New design.
Techniques.
THEMATIC UNIT VII: Prodrugs
Topic 16
Drug design based on metabolic processes. Prodrugs: concept and types. Carrier-bound
prodrugs: practical applications. Improvement of bioavailability, solubility and stability. Release
in specific areas. Long duration. Prodrug cascade. Examples of cascade prodrugs. Polymer-
linked prodrugs. Bioprecursors: By oxidation, reduction and mixed. Other bioprecursors. Hard
and soft drugs: concept and types.
THEMATIC UNIT VIII: FAMILIES OF PHARMACOS. The groups of drugs that are chosen to
be included in this section will be taught in the following order: Origin and
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generalities. Classification. Agonists and antagonists. Structure-activity relationships.
Synthesis.
Topic 17. Drugs that affect the Autonomous and Peripheral Nervous System.
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Topic 18. Drugs that affect the Central Nervous System.
Topic 19. Drugs that affect the Endocrine System and Metabolism.
Topic 20. Drugs that affect the cardiovascular system.
Topic 21. Antibiotics and antimicrobials
Topic 22. Anticancer drugs
Topic 23. Antiulcerants
Practical:
Practice 1 Synthesis of a dihydrobenzoxazine
Practice 2 Hantzsch synthesis.
Practice 3 Synthesis of benzotriazole
Practice 4 Synthesis of 5,10,15,20-tetraphenylporphyrin.
Practice 5 Mechanisms and reaction conditions: Stoichiometries and yield calculations
Practice 6 Structural elucidation by spectroscopic methods.
Practice 7 Separation and identification of a drug and one of its metabolites.
Practice 8 Biginelli Synthesis
Practice 9 Benzoin condensation in the presence of thiamine.
Other activities:
Seminar program
Seminar 1.- Thematic unit II seminars
1. Resolution of reactivity and synthesis problems of pyridines and derivatives.
2. Resolution of reactivity and synthesis problems of quinolines, isoquinolines and derivatives
3. Resolution of issues of reactivityand synthesis of diazines and derivatives
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Seminar 3.- Thematic unit IV seminars
7. Resolution of exercises on establishing non-bonding interactions, prediction of solubilities,
and logP, charge distribution and pKas in drugs.
8. Chiral drugs: Identification of stereogenic centers and assignment of configurations.
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Practice 5 Mechanisms and reaction conditions:
Stoichiometries and yield calculations
IV. The Drug:
Topic 7.- The Drug. Introduction 5 h T,
Introduction.
Physical- 2 hrs
chemical, Topic 8.-Physicochemical, chemical and structural
chemical and properties of drugs
structural
properties of
drugs
Topic 9.- Pharmaceutical, Pharmacokinetic and 4 h T,
V. Phases of the Pharmacodynamic Phases.
action of a drug 1 hr S
Topic 10.- Drug metabolism
VIII. Topic 17.- Drugs that affect the Autonomous and 8 a.m. T
Peripheral Nervous System.
Drug Families
Topic 18.- Drugs that affect the Central Nervous
System.
Topic 19. Drugs that affect the Endocrine System
and Metabolism.
Topic 20. Drugs that affect the cardiovascular
system.
Topic 21. Antibiotics and antimicrobials.
Topic 22. Anticancer drugs
Topic 23.- Antiulcer drugs
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IV-VIII will be taught, which consist of 4.5 theoretical ECTS and 1.5 practical ECTS (Chemical
Laboratory).
The training activities that have been planned for each topic have been divided into expository
classes and seminars or problem classes.
- The presentations (or master classes) are held in the classroom in large groups and aim to
provide new information on each topic. Pharmaceutical Chemistry I and II have been assigned
3.75 ECTS for each section.
- The seminars are used to solve questions and problems that complement the information
provided in each topic. In addition, they serve as the teacher's control over the student's level of
reception and personal work. We work in the classroom with small groups of students. 1.5
ECTS have been assigned to Pharmaceutical Chemistry Seminars.
- In relation to the laboratory practices (Chemical Laboratory), before starting, a practice script
will be made available to the students in which the objectives and foundations of the
experiments that must be carried out are indicated. It is very important that, prior to carrying out
the practice, the student reads the script. The Chemical Laboratory of Pharmaceutical
Chemistry has been assigned 3 ECTS.
- The teaching-learning process is completed with group tutorials where personal and direct
teacher-student communication will be possible that serves to guide the student's study in the
subject, as well as to know and develop their motivations and attitudes. In this case, the group
tutorials appear associated with the Chemical Laboratory
Number of hours of the • Calculation work and analysis of laboratory results: 30 hours
student's own work: • Independent study and preparation of work: 153 hours
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4.2. Methodological strategies, materials and teaching resources
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5. EVALUATION: Procedures, evaluation and qualification criteria
PROCEDURE
In each academic year the student will have the right to have two calls, one ordinary and one
extraordinary. The ordinary call will be based on continuous evaluation, except in those cases
contemplated in the evaluation regulations in force at the UAH, in which the student may
benefit from a final evaluation procedure. To benefit from this final evaluation procedure, the
student will have to request it in writing to the Dean or Center Director in the first two weeks of
teaching the subject, explaining the reasons that prevent him or her from following the
continuous evaluation system. In the case of those students who, for justified reasons, have
not formalized their registration on the start date of the course or the period of teaching of the
subject, the indicated period will begin to count from their incorporation into the degree.
Ordinary Call
Continuous assessment:
It will be governed according to the evaluation regulations in force at the UAH. Knowledge of
the subject will be assessed through two partial tests (Pharmaceutical Chemistry Partial I and
Pharmaceutical Chemistry Partial II), carried out in the middle of each semester and two
global tests (Pharmaceutical Chemistry Global Exam I and Pharmaceutical Chemistry Global
Exam II). , carried out at the end of them. The assessment of the skills and knowledge
acquired during the practical classes will be carried out through two exams, which will be
developed together with each global test of each semester, constituting part of the Global
Exam.
Students who have not completed and passed the practices, consisting of two periods of
experimental work in the laboratory (Pharmaceutical Chemistry Practices I and
Pharmaceutical Chemistry Practices II), one for each semester, and a practice period in Drug
Spectroscopy, to be completed before attending the second period of experimental work
(Pharmaceutical Chemistry Practices II) will not be able to pass the subject. Participating in
the continuous evaluation means consuming the ordinary call. If you do not pass the ordinary
call, as long as the practices have been carried out and approved, you will have the right to
take a final exam in the extraordinary call.
Final evaluation:
An exam will be carried out that will consist of questions, problems and/or practical exercises
that allow assessing the acquisition of the skills included in the teaching guide.
Extraordinary Call
An exam will be carried out that will consist of questions, problems and/or practical exercises
that allow assessing the acquisition of the skills included in the teaching guide.
EVALUATION CRITERIA:
- Active participation in the proposed classes and activities.
- Knowledge and understanding of concepts, foundations and methodologies.
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- Application and integration of content to specific situations and problems.
- Comprehensive resolution of exercises and questions.
- Critical sense and coherent argumentation of ideas.
- Study and planning of the practical sessions, prior to their implementation.
- Compliance with safety standards in the laboratory.
- Skill in carrying out laboratory practices, data analysis and reasoned interpretation of
the results.
QUALIFICATION CRITERIA:
As it is a subject of a markedly experimental and technical nature, the completion of
laboratory practices is mandatory for all students taking the subject, as well as passing the
corresponding exam, regardless of the type of exam they take.
Ordinary call
Continuous evaluation: the learning of each student will be assessed using objective data
from:
- Laboratory practices: 20%.
- Activities carried out by students, participation in seminars and/or written tests: 40%.
- Final overall test: 40%
Final evaluation: An in-person test will be carried out that will consist of questions, problems
and/or exercises that allow the student's acquisition of the skills included in the teaching
guide to be assessed. To pass the subject it is necessary to pass this part with a grade
equal to or greater than 5. Students who have passed the laboratory practices must take
a written test of the corresponding contents, which they must pass with a grade equal to
or greater than 5. The grade for the practices will count for 20% of the total grade.
Extraordinary call:
An in-person test will be carried out that will consist of questions, problems and/or exercises
that allow the student's acquisition of the skills included in the teaching guide to be assessed.
To pass the subject it is necessary to pass this part with a grade equal to or greater than 5.
Students who have passed the laboratory practices must take a written test of the
corresponding contents, which they must pass with a grade equal to or greater than 5. The
grade for the practices will count for 20% of the total grade.
If the Health Authorities consider it necessary to suspend the face-to-face teaching activity or
the circumstances of the subject require it, the teaching, or part of it, would continue with the
online methodology until the suspension is lifted, at which time it would be resumed. the face-
to-face modality.
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6. BIBLIOGRAPHY
Basic Bibliography:
[1] J. TO. Joule, K. Mills "Heterocyclic Chemistry" 5th Edition. John Wiley & Sons.
Oxford, 2010 . (Text available in the UAH libraries, BAF 547.7 JOU).
[2] J. TO. Joule, K. Mills Heterocyclic Chemistry at a Glance By John A. Joule and Keith
Mills. 2nd Edition John Wiley & Sons. Oxford, 2013 .
[3] T.L. Lemke and D. TO. Williams, V. F. Roche, S. W. Zito Eds “Foye's Principles of
Medicinal Chemistry" 7th Edition. Walters Kluwer/Lippincott Co. New York, 2013 .
(Text available in the UAH libraries, BAF 615. 7 FOY).
[4] g. L. Patrick “An Introduction to Medicinal Chemistry” 5th Edition. Oxford U. Press.
Oxford, 2013 . (Text available in the UAH libraries, BAF 615.7 PAT).
[5] c. g. Wermuth Ed. The Practice of Medicinal Chemistry 4th Edition. Academic Press,
London, 2015 .
[6] N. Dunlap and D. M. Huryn “Medicinal Chemistry” Garlan Science Group. Taylor &
Francis Group, NY. 2018
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