As you have asked about the syllabus of the Medicinal Chemistry subject in MS (Pharm) course offered by National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad, I am giving you information about it, check below for the details
Medicinal Chemistry

Semester-I

Basics of Drug Action
Spectral Analysis
Logic in Organic Synthesis
Separation Techniques
Chemotherapy of Parasitic and Microbial Infections
Industrial Process and Scale-up Techniques
Biostatistics
Seminar
General Laboratory Experience

Semester- II

Drug Design
Logic in Organic Synthesis
Structure and Function of Biomolecules
Stereochemistry and Drug Action
Drug Metabolism
Pharmacological Screening and Assays
Seminar
General Laboratory Experience in the area of Specialization

Semester- III

Synopsis
Presentation

Semester- IV
Thesis
Defence of thesis

NIPER Hyderabad Medicinal Chemistry syllabus
Semester-I
MC-510 Basics of Drug Action (2 credits)
1. Inter and intramolecular interactions: Weak interactions in drug molecules; Chirality and drug action;
Covalent, ion, ion-dipole, hydrogen bonding, C-H hydrogen bonding, dihydrogen bonding, van der
Waals interactions and the associated energies.
2. Energy concept and its importance in drug action; First, second and third laws of thermodynamics
and the principles derived from these laws which are of significance to drug action; Free energy and
relationship between thermodynamics and statistics; Importance of chemical potential in drug action;
Thermodynamic cycle.
3. Statistical thermodynamics in predicting the structure of biomolecules and their interaction with drug
molecules; Macromolecular vs. micromolecular correlation using thermodynamics and statistical
thermodynamics.
4. Receptorology: Drug-receptor interactions, receptor theories and drug action; Occupancy theory, rate
theory, induced fit theory, macromolecular perturbation theory, activation-aggregation theory.
Topological and stereochemical consideration
5. Kinetics, enzyme kinetics in drug action. Do all molecules of an enzyme have same kinetics?
Mechanisms of enzyme catalysis; Electrostatic catalysis and desolvation; Covalent catalysis, acidbase
catalysis, strain / distortion in enzyme catalysis; Coenzyme catalysis; Example based on
hemoglobin; Theories of enzyme inhibition and inactivation; Enzyme activation of drugs-prodrugs.
6. Nucleic acids (NA) as targets for drug action; NA-interactive agents; Classes of drugs that interact
with nucleic acids; Intercalation, NA-alkylation, NA-strand breaking and their importance in drug
action.
7. Drug like molecules and theories associated with the recognition of drug like properties.
8. Physical organic chemistry of drug metabolism, drug deactivation and elimination;
Phase-I and phase-II transformations; Concept of hard and soft drugs; Chemistry of ADME and
toxicity properties of drugs.
MC-511 Spectral Analysis (2 credits)
1. Ultra violet and visible spectroscopy: Energy levels and selection rules, Woodward-Fieser and
Fieser-Kuhn rules; Influence of substituent, ring size and strain on spectral characteristics; Solvent
effect; Stereochemical effect; Non-conjugated interactions. Spectral correlation with structure
2. Infrared spectroscopy (IR): Characteristic regions of the spectrum. Influence of substituents, ring
size, hydrogen bonding, vibrational coupling and field effect on frequency. Determination of
stereochemistry; Spectral interpretation with examples
3. Nuclear magnetic resonance spectrometry (NMR): Magnetic nuclei, chemical shift and shielding,
relaxation processes, chemical and magnetic non-equivalence, local diamagnetic shielding and
magnetic anisotropy, spin-spin splitting, Pascal’s triangle, coupling constant, mechanism of coupling,
quadrupole broadening and decoupling, effect of conformations and stereochemistry on the
spectrum, diastereomeric protons, virtual coupling, long range coupling-epi, peri, bay effects. Shift
reagents-mechanism of action, spin decoupling and double resonance.
4. Mass Spectrometry (MS): Molecular ion and metastable peak, fragmentation patterns, nitrogen and
ring rules, McLafferty rearrangement, electron and chemical ionization modes, applications.
MC-520 Logic in Organic Synthesis-I (3 Credits)
1. Organic reaction mechanism : Methods of determining reaction mechanisms (kinetic and non-kinetic
methods); Energy profile diagrams, reaction intermediates, crossover experiments and isotopic
labelling; Order of reactions, reversible, consecutive and parallel reactions, solvent, ionic strength
and salt effects; Acid-base catalysis; Nucleophilic substitution reactions; Uni- and bimolecular
reactions, attacking and leaving groups, steric and electronic effects; Neighbouring group
participation; Formation and hydrolysis of esters, amides and acyl halides; Different mechanisms.
Electrophilic substitution reactions; Aromatic electrophilic substitutions including Friedel-Crafts
reactions; Addition and elimination reactions.
2. Principles of synthetic planning : Logic-centered molecular synthesis; Dislocation, synthetic tree,
synthons, logical imposition of boundary conditions, direct associated approach; Structurefunctionality
relationships, functionality and unsaturation levels; Polar reactivity analysis; Control
elements, consonant and dissonant circuits; Protocol for synthetic design.
3. Alkylation : Enolates; Regio- and stereo-selective enolate generation, “O” versus “C”- alkylation,
effects of solvent, counter cation and electrophiles; Symbiotic effect; Thermodynamically and
kinetically controlled enolate formations; Various transition-state models to explain stereoselective
enolate formation; Enamines and metallo-enamines; Regioselectivity in generation, applications in
controlling the selectivity of alkylation.
4. Reaction of ylides: Phosphorous ylides; Structure and reactivity, stabilized ylides, effects of ligands
on reactivity, Wittig, Horner–Wadsworth–Emmons (HWE) reactions- mechanistic realizations; E/Z
selectivity for olefin formation, Schlosser modification; Petersons olefin synthesis. Sulphur Ylides;
Stabilized and non-stabilized ylides; Thermodynamically and kinetically controlled reactions with
carbonyl compounds, regio- and stereo-selective reactions.
5. Hydroboration : Control of chemo-, regio- and stereo-selectivity, rearrangement of alkylboranes;
Alkylboranes as organometallic reagents, e.g., 9-BBN, thexylboranes, siamylborane, chiral boranes-
Ipc2BH IpcBH2 etc.
NP-510 Separation Techniques (1 Credit)
1. Chromatography: General principles, classification of chromatographic techniques, normal and
reversed phase, bonded phase, separation mechanisms.
2. Column chromatography: Merits and demerits, short-column chromatography and flash
chromatography, vacuum liquid chromatography (VLC), medium pressure liquid chromatography,
high pressure liquid chromatography (HPLC).
3. TLC, HPTLC, over pressure layer chromatography (OPLC), centrifugal chromatography.
4. Counter-current chromatography, droplet counter-current chromatography, ion-exchange, affinity,
size exclusion and ion-pair chromatography.
5. Gas chromatography, introduction to GC-MS and LC-MS techniques.
PC-540 Chemotherapy of Parasitic and Microbial Infections (1 Credit)
1. Introduction to parasitic and infectious diseases.
2. Biology of tuberculosis.
3. Mechanism of action of antituberculosis drugs.
4. Targets for anti-tuberculosis drug development.
5. Mechanism of drug-resistance in tuberculosis.
6. Biology of human amoebiasis.
7. Mechanism of action anti-amoebic drugs.
8. Biology of filarial infections.
9. Mechanism of action of anti-filarial drugs.
10. Targets of anti-filarial drug development.
11. Biology of viral infection.
12. Mechanism of action of anti-HIV drugs.
13. Targets for anti-HIV drug development.
14. Biology of malaria.
15. Mechanism of action of anti-malarial drugs.
16. Targets for anti-malarial drug development.
17. Mechanism of drug-resistance in malaria.
18. Biology of leishmaniasis.
19. Mechanism of action of anti leishmanial drugs.
20. Targets for anti-leishmanial drug development.
21. Drug-resistance in leishmaniasis.
PT-510 Industrial Process and Scale up Techniques (1 credit)
1. Status of pharmaceutical industry (bulk drugs, natural products and formulations) in India vis-a-vis
industrialized nations.
2. Scale-up techniques for process optimization, maximization of productivity, in process control
techniques with examples.
3. Chemical technology of selected bulk drugs; Case studies with emphasis on rationale for selection of
routes, raw materials, process control methods, pollution control procedures etc. (examples depicting
novel routes); Data collection during pilot plant trails, preparations of flow diagrams, material balance
sheets and technical data sheets.
4. Isolation techniques for natural products from plants, animals, marine and microbial sources.
5. Process technologies for some selected natural products of commercial interest.
6. Scale-up techniques for industrial pharmacy, typical standard operating procedures for different
dosage forms; In-process control procedures.
7. Pharmaceutical manufacturing equipment in bulk drugs and formulations.
GE-510 Biostatistics (2 credits)
1. Statistics: Introduction, its role and uses. Collection; Organization; Graphics and pictorial
representation of data; Measures of central tendencies and dispersion. Coefficient of variation.
2. Probability: Basic concepts; Common probability distributions and probability distributions related to
normal distribution.
3. Sampling: Simple random and other sampling procedures. Distribution of sample mean and
proportion.
4. Estimation and hypothesis testing: Point and interval estimation including fiducial limits.Concepts of
hypothesis testing and types of errors. Student- t and Chi square tests.Sample size and power.
5. Experimental design and analysis of variance: Completely randomized, randomized blocks. Latin
square and factorial designs. Post- hoc procedures.
6. Correlation and regression: Graphical presentation of two continuous variables; Pearson’s product
moment correlation coefficient, its statistical significance. Multiple and partial correlations. Linear
regression; Regression line, coefficient of determination, interval estimation and hypothesis testing
for population slope. Introduction to multiple linear regression model. Probit and logit transformations.
7. Non-parametric tests: Sign; Mann-Whitney U; Wilcoxon matched pair; Kruskal wallis and Friedman
two way ANOVA tests. Spearman rank correlation.
8. Statistical techniques in pharmaceutics: Experimental design in clinical trials; Parallel and crossover
designs. Statistical test for bioequivalence. Dose response studies;Statistical quality control.
GE-511 Seminar (1 credit)
1. Introduction, information retrieval systems.
2. Writing term papers and reports.
3. Organization of scientific material, thesis, dissertation and references.
4. Reading research papers.
5. Skill in oral presentation.
Each student has to present a seminar before end of the semester.
LG-510 General Laboratory Experience 15 hours/week (3 credits)
1. Analytical Techniques (75 hours)
a. Spectral Analysis workshop (45 hours)
b. Separation Techniques (30 hours)
2. Computer and application in pharmaceutical sciences (100 hours): Introduction to computers, basic
unit and functions, H/W and S/W, operating systems, word processing, spread sheet, graphic
programs, dbase, windows, statistical S/W programs and packages. Steps involved in S/W
development, computer languages with emphasis to FORTRAN language and programming, hands
on experience in pharmaceutical software systems. Use of computers in information retrieval
systems
3. Specialization (95 hours): Two to three step synthesis involving Wittig reaction, glycidic ester
condensation, etc. Purification by chromatographic technique and identification by IR, NMR, and MS
Semester-II
MC-610 Drug Design (2 credits)
1. Structure Activity Relationships in drug design: Qualitative versus quantitative approaches,
advantages and disadvantages; Random screening, nonrandom screening, drug metabolism studies,
clinical observations, rational approaches to lead discovery; Homologation, chain branching, ringchain
transformations, bioisosterism; Insights into molecular recognition phenomenon; Structure
based drug design, ligand based drug design.
2. Molecular Modeling: Energy minimization, geometry optimization, conformational analysis, global
conformational minima determination; Approaches and problems; Bioactive vs. global minimum
conformations; Automated methods of conformational search; Advantages and limitations of
available software; Molecular graphics; Computer methodologies behind molecular modeling
including artificial intelligence methods.
3. QSAR: Electronic effects; Hammett equation, Lipophilicity effects; Hansch equation, Steric Effects;
Taft Equation; Experimental and theoretical approaches for the determination of physico-chemical
parameters, parameter inter-dependence; Case studies; Regression analysis, extrapolation versus
interpolation, linearity versus non-linearity; The importance of biological data in the correct form; 2D –
QSAR; 3D-QSAR-examples CoMFA and CoMSIA.
4. Molecular docking and dynamics: Rigid docking, flexible docking, manual docking; Advantages and
disadvantages of flex-X, flex-S, autodock and dock softwares with successful examples; Monte Carlo
simulations and molecular dynamics in performing conformational search, docking etc.
5. Pharmacophore: Concept, pharmacophore mapping, methods of conformational search used in
pharmacophore mapping; Comparison between the popular pharmacophore methods like
catalyst/HipHop, DiscoTech, GASP, etc. with practical examples.
6. Electronic structure methods and quantum chemical methods: Semi-empirical and ab initio methods;
Conformational analysis, energy minimization, comparison between global minimum conformation
and bioactive conformation; Predicting the mechanism of organic reactions using electronic structure
methods; Complete and constrained conformational search methods their advantages and
disadvantages; Theoretical aqueous solvation calculations for the design of ligands. Conformational
interconversion, transition-state determination and their role in designing rigid analogs
7. De novo drug design techniques.
8. Informatics methods in drug design: Bioinformatics, cheminformatics, genomics, proteomics,
chemogenomics, pharmainformatics; ADME databases, chemical biochemical and pharmaceutical
databases; Drug design techniques using these databases.
MC-620 Logic in Organic Synthesis-II (3 credits)
1. Metal/ammonia reduction: Reduction of mono-, bi- and tri-cyclic aromatic systems and various
functional groups, reductive alkylation, regio- and stereo- selectivity; Reduction of alkynes; Complex
metal hydrides and selectrides.
2. Reaction of electron-deficient intermediates: Carbene-nitrene and free radical-structure, stability and
modes of generation; Addition and insertion reactions of carbenoids and nitrenoids - regio- and
stereoselectivity, role of the metal catalysts in the transition-metal catalyzed reactions, other types of
reaction of carbenoids, e.g., ylide generation, 1,3-dipolar addition, rearrangement etc.; Intramolecular
radical trapping process leading to ring annulation - Baldwin’s rule.
3. Organometallics: Applications of organo-lithium, cadmium and cerium reagents, heteroatom directed
lithiation; Oxy- and amido-mercurations; Gilman reagent, mixed and higher order cuprates, uses in
nucleophilic substitution, cleavage of epoxides and conjugate addition reactions; Mechanism of
action; Spiro-annulation; Wacker oxidation, Wilkinson’s catalyst, carbonylation/hydroformylation
reactions; Heck arylation; Role of metal- ligands in controlling regio- and stereo-selectivity; Catalytic
and stoichiometric oxidation reactions; Homogeneous and heterogenous processes; Chemoselective
reactions; Bio-mimicking processes.
4. Umpolung and umpoled sythons: Concept, acyl and glycine cation/anion, homoenolate anion, vicinyl
dicarbonian, carbonyl dication equivalence etc.
5. Asymmetric synthesis: Chiral induction-factors controlling facial selectivity; Chiral reagents/catalysts,
auxiliaries, enzymes and antibodies; Kinetic resolution, double asymmetric induction, acyclic
diastereoselection, asymmetric amplification; Asymmetric synthesis of amino acids and beta lactams.
6. Concerted reactions and photochemistry: Molecular orbital symmetry, frontier orbitals of 1,3-
butadiene, 1,3,5- hexatrienes, allyl system, classification of pericyclic reactions; FMO approach,
Woodward-Hoffman correlation diagram method and PMO approach to pericyclic
reactions;Electrocyclic reactions- conrotatory and disrotatory motions, [4n], [4n+2] and allyl systems,
secondary orbiatl interaction; Cycloaddition- antarafacial and suprafacial additions, [4n] and [4n+2]
sytems with stereo chemical effects, 1,3 -dipolar cycloadditions, chelotropic reactions; Sigmatropic
rearrangements-supra and antarafacial shifts of H, sigmatropic shifts of carbon moiety, retention and
inversion of configuration, [3,3] and [3,5] sigmatropic rearrangements, fluxional tautomerism, ene
reactions; Franck-Condon principle, Jablonski diagram, singlet and triplet states, photosensitization,
quantum efficiency; Photochemistry of carbonyl compounds, norish type-I and type-II cleavages,
Paterno-Büchi reaction, photoreduction, photochemistry of enones and para-benzoquinones.
7. Synthesis of complex molecules: Various approaches for the synthesis of Taxol, Forskolin, FK-506,
Gibberellines, Prostaglandins, Spatol, Aphidicolin etc. on the basis of disconnection and direct
associative approaches.

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