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Semester-wise structure for the
M.Pharm. in Pharmaceutical & Medicinal Chemistry (MPMC) programme
Semester I
No. Sub.
Code
Title of the
Course
Type of
Course
Credit
s
Contact
hours/week
ESE
(hour)
Weightage
(%)
CIE ESE
C/E/S L I.L P T P ST IA
1 MPMC
100
Communicati
on Skills
C 2 2 - - 2 - 30 20 50
2 MPMC
101
Biostatistics
and IPR
C 3 2 1 - 2 - 30 20 50
3 MPMC
102
Physical
Methods of
Analysis
C 3 2 1 - 2 - 30 20 50
4 MPMC
103 &
103P
Advanced
Organic
Chemistry I
C 3 + 3 2 1 4 2 4 30 20 50
5 MPMC
104 &
104P
Medicinal
Chemistry I
C 3 + 3 2 1 4 2 4 30 20 50
6 MPMC
151
Seminar 1 C 2 - 2 - 0.5 - - 20 80
7 MPMC
152
Lab Rotations S 2 2 - - - - - - -
Total Credits: Semester I 24 Credits
CIE Continuous Internal Evaluation; ESE End Semester Examination; ST Sessional Tests; IA
Internal Assessment, L Lectures, I.L. Integrated Learning involving Tutorials, Group
Discussions, Assignments, Field Work; P Practicals, Lab. work, Project, C Core, E Elective, S
Supportive.
In MPMC 152 Lab. Rotations, the student will rotate between different research laboratories
in his/her department and interact with the professor and the research students for a
period of total 30 hrs. At the end of the month the guide will be chosen based on mutual
consent of the student and professor. After selection of the research guide the student will
formulate his/her Seminar topic (MPMC 151).
Semester II
No. Sub.
Code
Title of the
Course
Type of
Course
Credit
s
Contact
hours/wee
k
ESE
(hour)
Weightage (%)
CIE ESE
C/E/S L I.L P T P ST IA
1 MPMC
201
Advanced
Organic
Chemistry II
C 3 2 1 - 2 - 30 20 50
2 MPMC
202
Medicinal
Chemistry II
C 3 2 1 3 2 - 30 20 50
3 MPMC
210 &
210P
Basic
Molecular
Biology
C 3 + 3 2 1 4 2 4 30 20 50
4 MPMC
221 or
222 or
223 or
224
Elective-I E 3 2 1 - 2 - 30 20 50
5 MPMC
221 or
222 or
223 or
224
Elective-II E 3 2 1 - 2 - 30 20 50
6 MPMC
251
Research
Seminar 2 -
Literature
Review and
proposed
research plan
S 3 - 3 - 0.5 - - 20 80
7 MPMC
252
Minor
Research
Project
S 3 - 3 - - - - - -
Total Credits: Semester II –24
Semester III
No. Sub.
Code
Title of the
Course
Type of
Course
Credit
s
Contact
hours/wee
k
ESE
(hour)
Weightage (%)
CIE ESE
C/E/S L I.L P T P ST IA
1 MPMC
300
Research
Methodology
C 3 2 1 - 2 - 30 20 50
The full time research work will commence from this Semester.
Total Credits: Semester III = 3 + 21 Research Credits = 24 Credits
Semester IV
This Semester is devoted totally to research which will culminate in the submission of a
thesis.
Total Credits: Semester IV = 24 Research Credits
Strong emphasis should be placed on the IPR value of the research work, beside
publications in peer reviewed journals of good impact factors. Students should be
encouraged to attend conferences, seminars where they will present their research work.
Detailed Syllabus
Theory Courses
Course No. MPMC 100 Title of the Course: Communication Skills Credits 2
Unit Course Content (Topics) Contact
Hours
Communication Skills
1.0 Grammar 6
1.1 Conditionals/Tenses, relative clauses, subject–verb agreement, passive voice
2.0 Written Communication 6
2.1 Discuss a topic of general interest, but related to science in about 300 words.
(Analyze, comment, argue, reflect, persuade, etc.) (can also be used for oral
presentations by the students, followed by discussion).
3.0 Oral Communication 3
3.1 Consulting a dictionary for correct pronunciation (familiarity with phonetics
symbols and stress-marks only)
3.2 (ii) Dialogue
4.0 Scientific Writing 6
4.1 Writing a Scientific Report on a project undertaken or an experiment
conducted (theory + practice)
5.0 Soft Skills
5.1 Gestures/ postures – Body language, gesture, posture. 2
5.2 Group discussion – Giving up of PREP, REP Technique, how body language
during group discussion.
2
5.3 Presentation skills: (i) How to make a Power Point presentation (ii) Body
language during presentation; Resume writing: Cover letter, Career
objectives, Resume writing (tailor made)
3
5.4 Mock Interview: Each student to face an interview and to demonstrate the
above taught skills.
2
Total 30
Course No MPMC 101. Title of the Course: Biostatistics and IPR Credits 3
Unit Course Content (Topics) Contact
Hours
Biostatistics
1.0 Collection and Organization of data 3
1.1 Graphical and pictorial presentation of data
1.2 Measures of central tendency and dispersion
1.3 Variance and standard deviation, relative error, coefficient of variation,
precision and accuracy
1.4 Sampling techniques: simple random sampling; stratification; estimation of
the mean and proportion.
2
2.0 Probability 6
2.1 Definition. Conditional probability and Bayes’ theorem. Probability
distributions: binomial, multinomial and Poisson distributions. Normal and
lognormal distributions. Use of normal distribution tables.
3.0 Regression 6
3.1 Linear regression and correlation, curvilinear regression, method of least
squares, curve fitting, Fiducial limits, probit and logit analysis
4.0 Parametric tests 6
4.1 Testing hypothesis, Types of error. Level of significance. Significance tests and
p-value
4.2 Tests of significance based on normal distribution, test of significance for
correlation coefficients, confidence interval for mean and regression
proportion.
5.0 Nonparametric tests 3
5.1 Nonparametric procedures: Chi square goodness of fit test, sign test, Mann-
Whitney test; Wilcoxon signed rank test.
6.0 Experimental designs 6
6.1 Randomization, completely randomized, randomized block and Latin square
designs, factorial design, cross over and parallel designs
6.2 Students should learn use of Minitab / R Software for data summary,
correlation, regression analysis, test of hypothesis and experimental design
Total of Biostatistics 32
IPR and Patents
7.0 Introduction to intellectual property rights: types of IP, patents, trademarks,
copyright and related rights, industrial design, traditional knowledge,
geographical indications, protection of new GMOs. International framework
for the protection of IP. IP as a factor in industry, relevance of IP to
biotechnology, and few case studies. Introduction to the history of GATT,
WTO, WIPO, and TRIPS.
7.1 Concept of prior art: invention in context of prior art, patent databases,
searching international databases, country wise patent searches (USPTO, EPO,
India etc.). Analysis and report formation.
7.2 Basics of Patents: types of patents, Indian Patent Act 1970, recent
amendments, filing of a patent application, precautions before patenting,
disclosure/non-disclosure. WIPO treaties, Budapest treaty, PCT and
implications, procedure for filing a PCT application
7.3 Patent filing and infringement: types of patent applications, provisional and
complete specifications, PCT and conventional patent applications,
international patenting requirements, procedure and costs, financial
assistance for patenting – introduction to existing schemes, publication of
patents – gazette of India, status in Europe and USA. Patenting by research
students, lecturers and scientists – university/organisation, rules in India and
abroad, credit sharing by workers, financial incentives.
Patent infringement – meaning, scope, litigation, case studies and examples.
Total of IPR and Patents 13
Total 45
Books
1. Pharmaceutical Statistics – Practical and Clinical Applications, Bolton S., Marcel Dekker,
Inc. N. Y. USA
2. Biostatistics: A Foundation for Analysis in Health Sciences, Wayne W Daniel, John Wiley &
Sons, Inc.
3. Introduction to Statistical Analysis, Dixon W. J. and Massey F. J., McGraw Hill, N.Y., USA.
4. Statistical Methods, Snedecor G. W. and Cochran W. G., Iowa State University Press,
Ames, Iowa.
Course No MPMC 102. Title of the Course: Physical Method of Analysis Credits 3
Unit Course Content (Topics) Contact
Hours
1.0 UV 4
1.1 Woodward-Fieser rules, UV spectra of aromatic and heterocyclic compounds,
optical rotatory dispersion and circular dichroism
2.0 IR and Raman Spectroscopy 6
2.1 FT technique, group frequencies, vibrational coupling, NIR spectroscopy,
scattering phenomena, Raman Spectroscopy, a brief of factors affecting
absorption frequencies
3.0 NMR and ESR 11
3.1 CW vs Pulse Experiments
3.2 Factors influencing chemical shift, coupling constant, types of couplings,
decoupling studies, shift reagents, spin-lattice and spin-spin relaxation,
nuclear Overhauser effect, spectral editing. Interpretation of NMR spectras.
CMR and factors affecting CMR shifts
3.2 Two-dimensional NMR
3.2 Proton-proton correlation through coupling, proton-heteronuclear
correlation, proton-proton correlation through space and chemical exchange,
carbon-carbon correlation
3.3 Theory and experimental techniques of ESR, hyperfine splitting, ESR
parameters
2
4.0 Mass Spectrometry 8
4.1 EI, CI, DI, MALDI, SELDI, SI and ESI
4.2 Mass analysis – TOF analysers, quadrupole mass filters, ion cyclotron
resonance, tandem mass spectrometers, HRMS
4.3 General Principles of fragmentation, energetic of dissociation, odd- and even-
electron ions, Stevenson’s rules, rearrangement vs simple cleavage, proximate
vs remote fragmentation, distonic ions, charge localization, characteristic
fragment ions and neutral fragments
4.4 Chemical analysis, molecular weight determination, molecular structure
determination, molecular formula determination
4.5 Isotopic analysis, quantitative analysis, mixture analysis
4.6 Chromatography-mass spectrometry, tandem mass spectrometry (MS-MS),
thermochemical determinations
5.0 X-Ray Diffraction 4
5.1 Introduction
5.2 Crystal Planes and miller indices
5.3 Bragg’s law of diffraction
5.4 Reciprocal Lattices
5.5 Powder method: Debye-Scherrer method, The powder diffractometer,
Indexing the powder patterns, use of X-ray powder patterns
5.0 Problems involving structure determination based on UV, IR, NMR and MS 10
Total 45
Books
1. Spectroscopy, Pavia D. L., Lapman G. M., Kritz G. S., Vyvyan J. R., Brooks/Cole Indian
Reprint.
2. Modern NMR Techniques for Chemistry Research, Derome A. E., Pergamon Press.
3. Spectroscopic Methods in Organic Chemistry, Williams D. H., Fleming I., Tata McGraw Hill.
4. Spectrometric Identification of Organic Compounds, Silverstein R. M., Bassler G. C.,
Morrill T. C., John Wiley.
Course No MPMC 103. Title of the Course: Advanced Organic Chemistry I Credits 3
Unit Course Content (Topics) Contact
Hours
1.0 Advanced Stereochemistry 24
1.1 Coverage of the basic concepts in stereochemistry – optical activity,
specific rotation, racemates and resolution of racemates, the Cahn-
Ingold-Prelog sequence rule, meso compounds, pseudo asymmetric
centres, pro-R, pro-S, axes of symmetry, Fischers D and L notation, cis-
trans isomerism, exo-endo, syn-anti nomenclature. Stereoselective and
stereospecific reactions. Conformational isomerism in acyclic systems.
Shape of six membered rings and effect of substituents and reactivity.
1.2 Chirality in systems lacking a stereogenic carbon atom
1.2.1 Point chirality – tertiary amines and phosphines
1.2.2 Axial chirality – allenes, biphenyls and binaphthyls
1.2.3 Helical structures – polynucleotides, polyamino acids, biaryls and
allenes
1.3 Methods for estimating ratios of stereoisomers in a mixture, separation
and identification of the individual components by NMR spectroscopy,
X-ray crystallography.
1.4 Nucleophilic attack on acyclic carbonyl compounds – Cram’s rule,
Felkin-Ahn rule. Locking effects in nucleophilic reactions at carbonyl
groups
1.5 Stereochemistry of important reactions leading to formation of alkenes
– Wittig and related reactions
1.6 Pericyclic Reactions: Electrocyclic, cylcoaddition, sigmatropic reactions.
Woodward Hoffmann rules, FMO approach, Hückels approach.
Stereochemical implications in pericyclic reactions.
2.0 Green Chemistry 5
2.1 History, need and the goals of green chemistry
2.2 Basic principles of green chemistry, illustrated with examples to discuss
issues of prevention of waste or minimize by-products, atom economy,
prevent and minimize formation of hazardous or toxic products, design
of safer chemical equivalents, selection of appropriate solvents, media,
separation agents, improve economy and efficiency of reactions by use
of microwaves, ultrasound etc., and use of renewable starting
materials.
3.0 Photochemistry 7
3.1 Interaction of radiation with matter, types of excitations, fate of excited
molecules, quantum yield, transfer of excitation energy
3.2 Determination of the rate constants of photochemical reactions, effect
of the intensity of light on the rate of photochemical reactions
3.3 Some photochemical reactions involving alkenes, carbonyl compounds
and aromatic compounds
4.0 Combinatorial Chemistry 9
4.1 Introduction, advantages and planning combinatorial synthesis
4.2 Solid phase and solution phase synthesis
4.3 Supports, linkers, and tags
4.4 Deconvolution and iteration
4.5 Parallel synthesis, multistep – convergent and sequential synthesis,
multicomponent reactions
Total 45
Books
1. Stereochemistry of carbon compounds, Eliel E, Wilen S H, Manden L N, Wiley.
2. Stereochemistry of Organic Compounds, Nasipuri D, Wiley Eastern.
3. Advanced Organic Chemistry, Carey FA and Sundberg RJ, Part A and B, Springer
4. Introduction to Green Chemistry, Ryan M. A., Tinnesand M., American Chemical Society
(Washington).
5. Combinatorial Chemistry; Synthesis and Application, Eds., Wilson S. R. Czarnik A. W.,
Wiley: New York.
6. Organic Chemistry, Clayden J, Greeves N, Warren S, Wothers P, Oxford University Press.
7. Stereoselective Synthesis, Atkinson R S, John Wiley & Sons.
8. Molecular Photochemistry, Turro N J, Publisher W A Benjamin.
9. Pericyclic Reactions, Mukherjee S M, McMillan Press.
Practical Courses
Course No MPMC 103P. Title of the Course: Advanced Organic Chemistry I Credits 3
Unit Course Content (Topics) Contact
Hours
1.1 Friedel crafts alkylation: t-butyl alcohol to t-butylchloride to t-butylbenzene
1.3 Friedel crafts acylation: phthalic anhydride to o-benzoylbenzoicacid to
anthraquinone
2.1 Wolff Kischner reduction: acetophenone to ethylbenzene
2.2 LAH reduction: cyclohexanone to cyclohexanol
2.3 Oxidation reduction: p-nitrotolune to p-nitrobenzoic acid to p-aminobenzoic acid
3.1 Hydroquinone to quinone to triacetoxybenzene
3.2 Hydroquinone to hydroquinone diacetate to 2,5-dihydroxyacetophenone
4.1 Napthalene to nitronapthalene to 4-nitronapthylamine
5.1 Mannich reaction of acetophenone
6.1 Anthranilic acid to o-chlorobenzoic acid to N-phenylanthranilic acid to acridone
7.0 Synthesis of heterocycles:
7.1 Aniline to quinoline
7.2 Urea to barbituric acid
7.3 Resorcinol to 7-hydroxy-4-methyl coumarin
7.4 Cyclohexanone to 1,2,3,4-tetrahydrocarbazole
7.5 o-phenylenediamine to benzimidazol
7.6 o-phenylenediamine to benzotriazole
7.7 Benzil to diphenylquinazoline
7.8 Acetylacetone to 3,5-dimethypyrazole
8.0 Grignard reaction, enamine synthesis and its acylation, NaBH4 reduction,
hydroboration oxidation, Green synthesis could also be easily incorporated in
the practical program
Total 60
Fifteen syntheses to be done during the Semester which will comprise 5 single stage
synthesis, 5 two stage synthesis and 5 hetereocycles.
Course No MPMC 104. Title of the Course: Medicinal Chemistry I
Credits 3
Unit Course Content (Topics) Contact
Hours
1.0 Drug Discovery 5
1.1 Historical perspective
1.2 Lead Discovery
1.3 Lead Modification – identification of the pharmacophore, functional
group modification, privileged structures and drug-like molecules,
modifications to increase potency and the therapeutic index,
modifications to increase oral bioavailability
2.0 Receptors 10
2.1 Basic ligand concepts – agonist, antagonist, partial agonist, inverse
agonist, efficiency and potency
2.2 Interactions (Forces) involved in drug-receptor complexes
2.3 Receptor theories – occupancy theory, rate theory and activation
theory
2.4 Receptor classification – the four superfamilies
2.5 Receptor binding assays- measurement of Kd, Bmax and IC50
2.6 Topographical and stereochemical considerations in drug –receptor
interactions
3.0 Prodrugs and Drug Delivery Systems 8
3.1 Enzyme activation of drugs, utility of prodrugs – aqueous solubility,
absorption and distribution, site specificity, instability, toxicity, poor
patient acceptability, formulation problems.
3.2 Carrier-linked prodrugs – carrier linkages for various functional groups,
carrier-linked bipartite prodrugs, macromolecular drug carrier systems,
tripartite prodrugs, mutualprodrugs, bioprecursor prodrugs (hydrolytic
activation, elimination activation, oxidative activation, reductive
activation, nucleotide activation, phosphorylation activation, sulfation
activation and decarboxylation activation).
4.0 Enzymes 8
4.1 Introduction to enzymes, binding site, specificity of enzyme catalyzed
reactions and rate acceleration, MichaelisMenten kinetics and methods
for plotting enzyme kinetic data
4.2 Mechanisms of enzyme catalysis – covalent catalysis, acid-base
catalysis, electrostatic catalysis, some examples of the mechanisms of
enzyme catalysis
4.3 Coenzyme catalysis – pyridoxal 5’-phosphate (racemases,
decarboxylases, aminotransferases), nictoinamide and flavin (two-
electron mechanism, carbanion followed by two one-electron transfers,
one-electron mechanism and hydride mechanism), folic acid and
thiamine (one carbon transfer reactions).
4.4 Enzyme therapy
5.0 Discovery, development and mechanistic aspects of selected classes
such as antibiotics, anticancer, antiviral, CVS, CNS, and GIT disorders
14
Total 45
Books
1. The Organic Chemistry of Drug Design and Drug Action, Silverman R. B., Academic Press.
2. Textbook of Drug Design and Discovery, Eds. Krogsgaard-Larsen P., Liljefors T., Madsen U.,
Taylor & Francis.
3. Drug Discovery – A History, Sneader W., Wiley.
4. Medicinal Chemistry: An Introduction, Thomas G, Wiley.
5. Drug Discovery – A History, Sneader W, John Wiley & Sons, Ltd.
Course No MPMC 104P. Title of the Course: Medicinal Chemistry I Credits 3
Unit Course Content (Topics) Contact
Hours
1.0 Measurement of logP of a poorly water soluble and a highly water soluble drug
2.0 Determination of the pKa of a drug (weak acid and weak base) by
potentiometric titration and by UV/visible spectroscopy
3.0 Determination of Km and Vmax for the esterase catalyzed hydrolysis of p-
nitrophenyl acetate by plasma esterases. Can also include inhibition of the
reaction by paraoxon and determination of IC50
4.0 Estimation of two drugs by simultaneous equation method and by absorbance
ratio method.
5.0 Synthesis of some drugs for e.g. thiazide and hydrothiazide derivatives
involving multistep reactions.(Students should learn to monitor the reaction by
TLC, separate the main product from impurities by column chromatography
and learn use of IR and 1H and
13C NMR to check the structures of the
intermediates and the final compounds). Comparison of microwave versus
conventional synthesis for two different reactions with respect to time
requirements and overall yield comparison
6.0 Resolution of racemic mixtures of acidic and basic compounds by formation of
diastereomers, e.g. RS-warfarin using (-) brucine
7.0 Synthesis of prodrugs of some common drugs and study of their decomposition
(kinetics) to the parent drug
8.0 Separation of drug and metabolites from plasma/urine. e.g. if volunteers are
given coumarin and 0-3 hrs urine is collected, it will have both coumarin and 7-
hydroxy coumarin (metabolite is present as glucuronide and has to be acid-
hydrolysed before HPLC injection)
9.0 Isolation of microsomes from liver tissue by calcium aggregation method.
Determination of protein content by Biuret method/Lowry method (BSA as
standard), determination of CYP content using CO binding by method of Omura
and Sato. Determination of catalytic competence using p-nitrophenol to p-
nitrocatechol reaction in presence of NADPH by RP-HPLC. Can also include
inhibition of the reaction by antipyrine or SKF-525 or chlorzoxazone.
10.0 Isolation of glutathione S-transferase fraction from liver tissue. Determination
of protein content (as above) and assay for 2,4-dichoronitrobenzene-
glutathione conjugate formation in the presence of reduced glutathione by
following change in absorbance with respect to time. Can also study inhibition
of reaction by ethacrynic acid or styrene oxide
11.0 Isolation of crude fraction of xanthine oxidase from rat liver. (involves heat
precipitation, solvent fractionation and ammonium sulfate precipitation) and
monitoring xanthine to uric acid formation by UV
Total 60
Any two from 9.0 to 11.0 to be conducted in a given Semester
Course No MPMC 151 Title of the Course: Seminar 1 Credits 2
The student in consultation with his/her research guide will choose a topic related to his/her
area of research and will deliver a Seminar at a date and time fixed by the department, that
should be attended by all students in the department, the research guide, the HOD and
other faculty of the Department. The Seminar will be of 25 minutes duration, followed by a
discussion. The student will be evaluated by all faculty members under the following
parameters: coverage of literature, presentation skills, defence and the seminar report (the
report should be handed in by the student the next day after the delivery of the seminar
and a copy of the seminar should be housed in the library). The final marks will be the
average of the marks given by the faculty.
In MPMC 152 Lab. Rotations, the student will rotate between different research
laboratories in his/her department and interact with the professor and the research
students for a period of total 30 hrs. At the end of the month the guide will be chosen
based on mutual consent of the student and professor. After selection of the research
guide the student will formulate his/her Seminar topic (MPMC 151).
Theory Courses for Semester II
Course No MPMC 201. Title of the Course:Advanced Organic Chemistry II Credits 3
Unit Course Content (Topics) Contact
Hours
1.0 Catalysis & Organometallics in Organic Synthesis 16
1.1 Types of catalysis, heterogeneous and homogenous catalysis,
advantages and disadvantages, catalytic cycles
1.2 Heterogeneous catalysis – preparation, characterization, kinetics,
supported catalysts, catalyst deactivation and regeneration, some
examples of heterogeneous catalysis used in synthesis of drugs.
1.3 Homogenous catalysis, hydrogenation, hydroformylation,
hydrocyanation, Wilkinson catalysts, chiral ligands and chiral induction,
Ziegler-Natta catalysts, some examples of homogenous catalysis used in
synthesis of drugs
1.4 Phase transfer catalysis - theory and applications
1.5 Introduction, Classification of organometallic compounds based on
hapticity and polarity of the M-C bond. Nomenclature and general
characters. Synthesis, stability and decomposition pathways.
1.6 Transition metal π-complexes with unsaturated organic molecules,
carbon monoxide, alkenes, alkynes, allyl, dienes, cyclopentadienyl,
arene complexes, preparation, properties, nature of bonding and
structural features, important reactions relating to nucleophilic attack
on ligands and to organic synthesis. Basic organometallic reactions
covering oxidative reactions, migratory reactions, insertions, extrusion,
additions, eliminations – their mechanisms and stereochemistry.
2.0 Synthon Approach and Applications 8
2.1 Retrosynthesis and its advantages, rules for dissection of molecules,
meaning of the term, disconnection, FGI, FGA and synthons, guidelines
for the order of events
2.2 C-X disconnections; C-C disconnections – alcohols and carbonyl
compounds; 1,2-, 1,3-, 1,4-, 1,5-, 1,6-difunctionalized compounds
2.3 Strategies for synthesis of three, four, five and six-membered rings
2.4 Strategies for synthesis of aromatic and saturated heterocycles
3.0 Protective Groups in Organic synthesis 4
3.1 Protective groups for hydroxyl, amino, carbonyl, carboxyl and thiol
functionalities
3.2 Synthetic equivalent groups
3.3 Protection and deprotection concepts
3.4 Selected applications
4.0 Asymmetric Synthesis 8
4.1 Introduction and need; chiral synthesis using chiral pool, chiral
auxiliaries, chiral catalysts
4.2 Enzymes, chiral solvents and whole organisms
4.3 Analytical methods of determining purity of stereoisomers
4.4 Applications in industry
5.0 Total synthesis of some drug molecules and natural products (like
reserpine, prostaglandins, taxol, estrone, epothiolone etc) as discussed
by Nicolaou and Sorensen in their books “Classics in Total Synthesis”.
9
Total 45
Books
1. The Organometallic Chemistry of the Transition Metals, Crabtree R. H., John Wiley
2. Transition Metals in Synthesis of Complex Organic Molecules, Hegedus L., University
Science Books.
3. Homogenous Transition Metal Catalysis, Masters C., Chapman & Hall.
4. Principles and Practice of Heterogenous Catalysis, Thomas J. M., Thomas M. J., John Wiley
5. Principles of Asymmetric Synthesis, Gawley R. E., Aubrey J, Elsevier.
10. Greene’s Protective Groups in Organic Synthesis, Wuts, P. G. M., Green T. W., Wiley
11. Organic Synthesis – The Disconnection Approach, Stuart, W., Wiley.
12. Classics in Total Synthesis, Nicolaou K C and Sorensen E J, Wiley-VCH.
13. The logic of chemical synthesis, Corey E J and Cheng X-M, John Wiley and Sons.
Course No: MPMC 202. Title of the Course : Medicinal Chemistry II Credits 3
Unit Course Content (Topics) Contact
Hours
1.0 Enzyme Inhibition 12
1.1 Coverage of basic aspects of enzyme kinetics, catalysis, transition-state
theory.
1.2 Drug Resistance through alterations of drug uptake, overproduction of
enzyme, alterations of the enzyme active site, overproduction of the
substrate or new pathways for formation of the product
1.3 Drug synergism, concepts and mechanisms.
1.4 Reversible enzyme inhibitors – competitive inhibition, non-competitive
inhibition, uncompetitive inhibition with suitable examples. Detection
of type of inhibition by suitable plotting methods. Concepts of IC50 and
Ki.
1.5 Slow-tight binding inhibitors, covalent enzyme inhibitors and
mechanism-based inhibitors with suitable examples. Concept of Kinact
and Ki for irreversible inhibitors
2.0 QSAR 14
2.1 Historical Aspects
2.2 Electronic Effects- the Hammett equation, lipophilic effects,
experimental measurement of lipophilicity, logP and logD, effect of
ionization on logP, calculation of logP and logD, Steric effects- the Taft
equation
2.3 Hansch Analysis, Free-Wilson method, Topliss operational scheme
2.4 Basics of regression analysis - linear and multilinear regression,
introduction to PCA, PCR, PLS, ANN and GFA. Correlation coefficients
(r2 and r
2pred), F-test, standard error, validation methods like cross-
validation by calculation of q2, boot-strap analysis and randomization.
Application domain for predictions using a QSAR model.
2.5 Design of training and test sets using factorial design
3.0 Peptides and Peptidomimetics 6
3.1 Coverage of peptide structure, biosynthesis of peptides and solid-
phase/solution synthesis of peptides.
3.2 Design of peptidomimetics by manipulation of the amino acids,
modification of the peptide backbone, incorporating conformational
constraints locally or globally, α-helix, β-sheet, β-and γ-turn mimetics
3.3 Examples of peptidomimetics for some enzymes and receptors like ACE,
CCK, bradykinin
4.0 Antisense therapeutic agents 6
4.1 History and principles
4.2 Design of antisense oligonucleotides and small interfering RNAs
(siRNAs) with some examples
5.0 Molecular Biology, Genetic engineering and Biotechnology in
production of biologicals as drugs.
7
Total 45
Books
1. The Organic Chemistry of Drug Design and Drug Action, Silverman R. B., Academic Press.
2. Textbook of Drug Design and Discovery, Eds. Krogsgaard-Larsen P., Liljefors T., Madsen U.,
Taylor & Francis.
3. Medicinal Chemistry: An Introduction, Thomas G, Wiley.
4. Peptide and Protein Design for Biopharmaceutical Applications, Ed Jensen K. J., Ch. 3
Aspects of Peptidomimetics by Maes V.,Tourwé D., John Wiley & Sons, Ltd, Chichester,
UK.
5. Comprehensive Medicinal Chemistry, Series Ed., Hansch C., Pergamon Press.
6. Burgers Medicinal Chemistry, Drug Discovery and Development, Wiley.
Course No. MPMC 210 Title of the Course: Basic Molecular Biology Credits 3
Unit Course Content (Topics) Contact
Hours
1.0 The beginnings of molecular biology 1
2.0 DNA Structure and Role of DNA 12
2.1 Organization of the genome, building from nucleotides to chromatin
2.2 The genetic code and its relationship to protein structure
2.3 DNA replication, Telomere maintenance, mechanisms of DNA repair, DNA
recombination
3.0 The versatility of RNA 16
3.1 Transcription and translation in prokaryotes; Transcription and translation in
eukaryotes
3.2 Epigenetics and monoallelic gene expression
3.3 RNA processing and post-transcriptional gene regulation
3.4 Mechanisms of translation
4.0 Genetically modified organisms: Use in basic and applied research 14
4.1 Recombinant DNA technology, molecular cloning, & some tools for analyzing
gene expression
4.2 Genome analysis: DNA typing; Genomics and beyond; Medical molecular
biology: applications in Cancer and Gene therapy; Genes and behaviour
5.0 Plant tissue culture and animal cell culture 2
Total 45
Books
1. Genes IX, Ed Benjamin Lewin. Oxford University Press.
2. Molecular Cell Biology, Lodish H, Berk A, Zipursky S L, Matsudaira P., Baltimore D, Darnell J,
Publisher W. H. Freeman.
3. Molecular Biology of the Cell, Alberts Publisher Garland Science.
4. Watson, J. D. Tania A. Baker, Stephen P. Bell, Alexander Gann, Michael Levine, Richard
Losick, Molecular Biology of the Gene, Benjamin Cummings; 6th Edition, 2007.
5. Molecular Biology in Medicinal Chemistry, Dingemann Th, Steinhilber D and Folkers G,
Wiley-VCH, Germany
6. Basic Principles of Gene Manipulation, Primrose SB, Twyman RM and Old RW, Blackwell.
7. Molecular Biology and biotechnology, Walker JM and Rapley R, Royal Society of Chemistry
Practical Courses
Course No. MPMC 210P Title of the Course: Basic Molecular Biology Credits 3
Unit Course Content (Topics) Contact
Hours
1.0 Experiments with cells – homogenization of the tissue, centrifugation,
marker enzyme assays, microscopy and microphotography of cells
2.0 Quantitative assays - enzyme assays, RIA, ELISA, assays for DNA, RNA &
proteins
3.0 Fractionation of proteins – salting out, , electrophoretic separation, gel
filtration, affinity based chromatography, ion-exchange, HPLC, SDS-
PAGE.
4.0 Enzymology – purification of enzyme & study of enzyme kinetics
5.0 Experiments on DNA –genomic and plasmid DNA isolation, cloning,
restriction enzyme digestion, ligation, transformation, electrophoresis,
PCR, real-time PCR.
6.0 Southern blotting, Western blotting and Northern blotting
7.0 Absorption & fluorescence spectroscopy
8.0 Plant tissue culture
9.0 Animal cell culture
Total 60
Books
1. Molecular Cloning- A Laboratory Manual. J. Sambrook, E.F. Fritsch and T. Maniatis.
Cold Spring, Harbor Laboratory Press.
2. Wilson, K. and Walker, J., Principles and Techniques of Practical Biochemistry and
Molecular Biology, 7th Edition, Cambridge Univ. Press, 2010
3. Christian, G. D., Analytical Chemistry, John Wiley & Sons (Asia) Pvt. Ltd., 2004
4. R. Ian Freshney, Culture of Animal Cells: A Manual of Basic Technique and Specialized
Applications, John Wiley and Sons, 2010.
5. C. Neal Stewart, Jr., Plant Biotechnology and Genetics: Principles, Techniques and
Applications, 2008
Elective Subjects
Course No: MPMC 221 Title of the Course: Drug Metabolism Credits 3
Unit Course Content (Topics) Contact
Hours
1.0 Introduction to xenobiotic/drug metabolism and its relation to other defence
systems (Physical barriers, excretion, immune system).
4
1.1 Types of reactions (I and II), consequences of drug metabolism (DM)
[inactivation, bioactivation, prodrugs], organs of DM, localization of drug
metabolizing enzymes, factors affecting drug metabolism.
2.0 Cytochrome P450s: Introduction to the family of enzymes, their classification
and nomenclature.
14
2.1 CYP450 catalytic cycle, different types of reactions catalyzed by CYP450s and
the mechanisms of catalysis.
2.2 Human CYP450s involved in DM, their distribution and properties, typical
substrates, specific probe substrates, specific inhibitors, induction of CYPs and
specific inducers
3.0 Discussion of glucuronosyltransferases, sulfotransferases, glutathione S-
transferases, N-acetyl transferases, and FMO [on lines similar to that specified
for CYPs as listed above].
14
4.0 Introduction to methods for studying DM. Discussion of in vitro and in vivo
tools, along with their advantages and limitations {recombinant enzymes,
subcellular fractions, hepatocytes, liver slices, perfused liver and whole animal
studies}.
5
5.0 Discussion of types of DM studies – metabolic stability, cross species
comparisons, metabolite profiling and identification, reaction phenotyping,
CYP inhibition and CYP induction studies.
6
6.0 Introduction to in silico drug metabolite predictions and associated
algorithms.
2
Total 45
Books
1. Comprehensive Medicinal Chemistry, Series Ed., Hansch C., Pergamon Press.
2. Wilson and Gisvold’s, Textbook of Organic Medicinal and Pharmaceutical Chemistry, Lippincott-
Raven
3. Foye’s Principles of Medicinal Chemistry, Lippincott Williams and Wilkins.
4. Drug Metabolizing Enzymes-Cytochrome P450 and Other Drug Metabolizing Enzymes in Drug
Discovery and Development, Lee JS, Obach SR and Fisher MB, Marcel Dekker, Fontis India, 2003
5. Pharmaceutical Profiling in Drug Discovery for Lead Selection, Borchardt RT, Kerns EH, Lipinski CA,
Thakker DR and Wang B, AAPS Press, 2004
6. Drug Metabolism – Current Concepts, Ionescu C and Caira MR, Springer International Edition
7. Handbook of Drug Metabolism, Woolf TF, Marcel Dekker, 1999.
Course No: MPMC 222 Title of the Course: Pharmacokinetics Credits 3
Unit Course Content (Topics) Contact
Hours
1.0 Introduction to pharmacokinetics and its utility in drug design and dosage regimen
design. Definitions of absorption, distribution, metabolism, excretion, elimination.
Different approaches for determination of pharmacokinetics of drugs – non-
compartmental, physiological, and compartmental modeling. Assumptions involved in
the evolution of single and multi-compartment models.
6
2.0 Discussion (including mathematical description and equations) of the pharmacokinetics
of drugs showing one compartment pharmacokinetics following intravenous bolus
dosing[blood/plasma/urine sampling]
20
2.1 Discussion (including mathematical description and equations) of the pharmacokinetics
of drugs showing one compartment pharmacokinetics following intravenous multiple
bolus dosing[blood/plasma]
2.2 Discussion (including mathematical description and equations) of the pharmacokinetics
of drugs showing one compartment pharmacokinetics following intravenous constant
infusion dosing [blood/plasma].
2.3 Discussion (including mathematical description and equations) of the pharmacokinetics
of drugs showing one compartment pharmacokinetics following extravascular bolus
dosing [blood/plasma]. Discussion of the concepts of bioavailability (absolute and
relative) and bioequivalence.
2.4 Discussion (including mathematical description and equations) of the pharmacokinetics
of drugs showing one compartment pharmacokinetics following extravascular multiple
bolus dosing [ blood/plasma].
2.5 Discussion of approaches to solve problems related to the analysis of pharmacokinetic
study data obtained after different types of dosing. Discussion of approaches to
problem solving involving data from bioavailability and bioequivalence studies.
Discussion of approaches to dosage regimen design
3.0 Discussion of the processes of absorption, distribution and elimination with respect to
how these processes impact the values of rate constants for
absorption/distribution/elimination and the values of bioavailability, volume of
distribution and clearance.
10
4.0 Introduction to drug transporters and their impact on the pharmacokinetics of drugs
and pharmacokinetic drug-drug interactions.
4
5.0 Brief introduction to the concept of dose- and time-dependent pharmacokinetics [non-
linear pharmacokinetics] and their impact on drug development and clinical use.
5
Total 45
Books
1. Clinical Pharmacokinetics and Pharmacodynamics-Concepts and Applications, Rowland M
and Tozer TN, Walters Kluwer – Lippincott Williams and Wilkins.
2. Applied Biopharmaeutics and Pharmacokinetics, Shargel L and Yu ABC, Appleton and
Lange, International Edition
3. Handbook of Basic Pharmacokinetics including clinical applications, Ritschel WA and
Kearns GL, APhA,
4. Basic Pharmacokinetics, Jambhekar SS and Breen PJ, Pharmaceutical Press.
5. Biopharmaceutics and Pharmacokinetics, Venkateshwarlu V, Pharma Book Syndicate
Course No. MPMC 223 Title of the Course: Rational Drug Design Credits 3
Unit Course Content (Topics) Contact
Hours
1.0 Molecular Mechanics and the forcefield. General form of a generic
force field, force field parametrization.
5
2.0 Energy minimization 5
2.1 Steepest descents, conjugate gradients, Newton Raphson method,
advantages and limitations of each method
3.0 Conformational analysis 10
3.1 Systematic search, Monte Carlo simulations, Molecular dynamics
simulations, distance geometry, strengths and limitations of each
method
4.0 Docking 6
4.1 Docking by energy minimization, superimposition, molecular dynamics,
Metropolis Monte Carlo, genetic algorithms, build-up approach.
Different types of scoring function, e.gs of successful application of
docking.
5.0 de novo ligand design 6
5.1 Classes of de novo ligand design – active site analysis methods, whole-
molecule methods, connection methods, random connection and
disconnection methods, e.gs of successful application of denovo ligand
design
5.2 Fragment based drug design
6.0 Pharmacophore modelling 6
6.1 Techniques of developing a pharmacophore map covering both ligand
based and receptor based approaches, incorporating additional
geometric features into a 3D pharmacophore, use of a pharmacophore
model in drug design, successful e.g. of pharmacophore maps in drug
design.
7.0 Virtual Screening based on similarity, docking, pharmacophore maps
and filters for drug-likeness and ADME
3
8.0 3D-QSAR 4
8.1 CoMFA and CoMSIA. Mention of other 3D-QSAR techniques and
introduction to the 4th
, 5th
and 6th
dimension in QSAR.
Total 45
Books
1. Molecular Modelling – Principles and Applications, Leach A. R., Prentice Hall.
2. Practical Application of Computer-Aided Drug Design, Ed. Charifson P., Marcel
Dekker Inc.
3. 3D QSAR in Drug Design: Theory, Methods and Applications, Ed. Kubinyi H., Ledien
ESCOM.
4. Molecular Modeling and Simulation -An Interdisciplinary Guide, Schlick T., Springer.
Course No. MPMC 224 Title of the Course: Advanced Biochemistry Credits 3
Unit Course Content (Topics) Contact
Hours
1.0 Proteins 15
1.1 Structure – primary, secondary, tertiary, quaternary; motifs, structural
and functional domains, protein families and macromolecular
assemblies
1.2 Mechanisms for regulating protein function: Protein-protein
interactions, interaction with ligands; Ca2+
and GTP as modulators,
cyclic phosphorylation and dephosphorylation, proteolytic cleavage.
1.3 Purification and characterisation of proteins: electrophoresis,
ultracentrifugation and liquid chromatography, use of biological assays,
use of radioisotopes; MS, X-ray crystallography, NMR and homology
modelling to determine structures; amino acid analysis; cleavage of
peptides; protein sequencing.
1.4 Protein biosynthesis: translation machinery in prokaryotic and
eukaryotic systems; comparison of similarities and differences, drug
affecting protein biosynthesis and protein function
2.0 DNA and nucleic acids 15
2.1 DNA, RNA structure, nomenclature, double helix, conformations, higher
order packing and architecture of DNA, transcription and replication of
DNA – mechanisms in prokaryotic and eukaryotic systems, DNA repair
mechanisms, drug affecting nucleotide biosynthesis, RNA and DNA
biosynthesis and RNA and DNA function
3.0 Carbohydrates 8
3.1 Mono, di and polysaccharides and their nomenclature,
stereochemistry, types of linkages; conjugates of carbohydrates with
other molecules – glycoproteins, glycolipids, proteoglycans,
lipopolysaccharides and their biological roles
4.0 Lipids 7
4.1 Classification, nomenclature, stereochemistry, storage lipids,
membrane lipids, lipids as secondary messengers and cofactors,
biological role of lipids, drug affecting lipid metabolism.
Total 45
Books
1. Principles of Biochemistry, Lehninger, Nelson D.L., C.B.S Publishers, New Delhi.
2. Biochemistry, Stryer L, W. H. Freyment& Co., New York.
3. Molecular Cell Biology, Lodish H, Darneu J, Scientific American Books, N.Y.
4. Biochemistry- The chemical reactions of living cells, Vol 1 &2, Metzler DE, Elsevier
Academic Press.
5. Biochemistry, Berg JM, Tymoczko JL and Stryer L, WH Freeman and Company and
Sumanas Inc.
6. Biomacromolecules- Introduction to structure, function and informatics, Stan Tsai C,
Wiley-Liss
7. Protein: Structure and Molecular properties, Thomas E Creighton, W. H. Freeman.
8. Physical Biochemistry- Principles and applications, Sheehan D, Wiley-Blackwell
Course No: MPMC 251 Title of the Course: Research Seminar 2 -Literature Review and
proposed research plan Credits: 3
The students will do a literature survey for the research work that is to be carried out in
Semesters III and IV and present a Seminar which should cover aspects of literature report,
plan of research work, methodology timelines, and expected outcome of the work before a
committee that will constitute the Research Work, Head of the Department and the other
faculty of the Dept. of Pharmaceutical and Medicinal Chemistry.
Course No: MPMC 252 Title of the Course: Minor Research Project Credits: 3
The students will do a Minor Research Project in an area of their choice and will not be
restricted to the Department. He/She will be evaluated by their respective Minor Research
Project Guide for satisfactory completion of the Minor Research Project.
Semester III
Course No MPMC 300. Title of the Course: Research Methodology Credits 3
Unit Course Content (Topics) Contact
Hours
1.0 Objectives and purposes of research, type of research (educational,
clinical, experimental, basic , applied, patent oriented research)
2
2.0 Literature Survey 3
2.1 Use of the library, books and journals, Medline, Internet, obtaining
patents and reprints of articles
3.0 Selecting a problem and preparing a research proposal for different
types of research mentioned in Unit 1.0
4
4.0 Methods and tools used in Research 10
4.1 Qualitative and quantitative studies, simple data organization,
descriptive data analysis, limitations and sources of errors, inquiries in
form of questionnaires, opinions or by interview, statistical analysis of
data including variance, standard deviation, standard error, mean,
student’s “t” test and Anova, correlation of data and its interpretation,
computer data analysis.
5.0 Documentation 5
5.1 Techniques and importance of documentation, uses of computer
packages in documentation
6.0 Scientific writing and reporting 5
6.1 Different types of research papers, title and author names, abstract,
key words, methodology,
7.0 Scientific Presentation 5
7.1 Importance, types, different skills, content, format of model,
introduction and ending, skills for oral presentation and types of visual
aids, questionnaire
8.0 Protection of Patents and trademarks, designs and copyrights 4
8.1 The patent system in India, present status of Intellectual Property
Rights (IPR), product patent, process patent, requirements and
preparation of patent proposals, registration of patents in foreign
countries
9.0 Cost Analysis of the project 5
9.1 Cost incurred on raw materials, cost incurred on procedure, cost
incurred on instrumentation, cost incurred on preclinical and/or clinical
studies, commercialization of patents
10.0 Industry-Institute Interaction, industry projects – feasibility studies 2
Total 45
Books
1. Research in Education, Best J. W., Khan J. V., Prentice Hall of India Pvt. Ltd.
2. Presentation Skills, Hatton, M., Indian Society for Technical Education.
3. Thesis and Assignment Writing, Jonathan A., Berry H D., Wiley Eastern Ltd.,
Bangalore.
4. Writing a Technical Paper, Menzel D. H., McGraw Hill Book Co., Inc.
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