NSCBIP/Sem-VI/Med Chem III/ CADD and Combinatorial Chemistry/Mr.
Samiran Sadhukhan/2025
Pharmacophore Modeling, Docking, and Combinatorial Chemistry
Syllabus:
• Pharmacophore modeling and docking techniques.
• Combinatorial Chemistry: Concept and applications of combinatorial chemistry: solid phase
and solution phase synthesis.
Pharmacophore modelling
In drug discovery, it's not always possible to test thousands of compounds experimentally. Instead,
we use computer-based models to predict which molecules might work as drugs. One such useful
approach is pharmacophore modelling.
A pharmacophore is like a “molecular fingerprint” — it describes the minimum essential features
a compound must have to bind to a biological target (like a receptor or enzyme) and produce a
desired biological effect (like lowering blood sugar in diabetes).
Definition: "A pharmacophore is the ensemble of steric and electronic features that is necessary to
ensure the optimal interactions with a specific biological target and to trigger (or block) its
biological response."
Key Features in a Pharmacophore:
• Hydrogen bond donors (HBD) – e.g., –OH, –NH₂
• Hydrogen bond acceptors (HBA) – e.g., =O, –N
• Aromatic rings
• Hydrophobic regions – e.g., alkyl chains
• Positive or negative ionizable groups
Types of Pharmacophore Modelling:
1. Ligand-Based Pharmacophore Modelling
• Used when the structure of the target is unknown.
• Built from known active ligands by identifying common features.
2. Structure-Based Pharmacophore Modelling
• Used when the 3D structure of the target protein is known.
• Built by analyzing interactions between the ligand and the protein's active site.
Steps in Pharmacophore Modelling:
1. Dataset Collection
• A set of biologically active compounds is selected.
• Compounds must have known activity against a particular target.
• Inactive compounds may also be included for validation purposes.
2. Molecular Alignment
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NSCBIP/Sem-VI/Med Chem III/ CADD and Combinatorial Chemistry/Mr. Samiran Sadhukhan/2025
• All active compounds are aligned in 3D space to identify common features.
• Alignment can be rigid or flexible depending on the software.
• Proper alignment ensures meaningful comparison of molecular features.
3. Feature Identification
Common chemical features such as:
• Hydrogen bond donors (HBD)
• Hydrogen bond acceptors (HBA)
• Aromatic rings
• Hydrophobic regions
• Ionizable groups
These features are assumed to be responsible for biological activity.
4. Pharmacophore Hypothesis Generation
• A 3D model is built showing the spatial arrangement of key features.
• This model serves as the "pharmacophore" – the essential features for activity.
• Inter-feature distances and angles are recorded.
5. Model Validation
• The model is tested to check its accuracy in distinguishing active from inactive molecules.
Techniques used:
• Test set validation
• Decoy set screening
• A validated model ensures reliable virtual screening.
6. Virtual Screening
• The pharmacophore model is used to screen large compound libraries.
• Compounds matching the model are considered potential drug candidates (hits).
• Helps in lead identification and optimization.
7. Hit Optimization
Hits obtained are further evaluated for:
• Drug-likeness
• ADMET properties
• Chemical diversity
• Selected hits can be modified and optimized into lead compounds.
Optional: Structure-Based Pharmacophore Modelling
If the target protein structure is known:
• Ligand is docked into the protein active site.
• Key interaction points are extracted (H-bonds, hydrophobic pockets).
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NSCBIP/Sem-VI/Med Chem III/ CADD and Combinatorial Chemistry/Mr. Samiran Sadhukhan/2025
• A receptor-based pharmacophore is created from these features.
Application
• Virtual screening for drug discovery
• Lead identification and optimization
• Understanding SAR (Structure-Activity Relationship)
• De novo drug design
• Scaffold Hopping
Docking
Molecular docking is one of the most regularly used computational methods in structure-based drug
design, due to its ability to predict the binding conformation of small molecules (ligands) to the
appropriate target (protein) binding site. In the process of "docking", a ligand to a binding site
mimics the natural course of interaction of the ligand and its receptor via the lowest energy
pathway. This interaction involves many types of non-covalent intermolecular interactions such as;
hydrogen bonds, ionic bonds, hydrophobic interactions, Van der Waals forces, etc. A molecular
docking study can also be possible between protein-protein and protein-nucleotide.
Definition: Docking is a computer-aided drug design (CADD) technique used to predict how
a small molecule (ligand) fits and binds into the active site of a target protein or enzyme.
• Binding site (or "active site"): The part of the protein where the ligand binds. Generally, a
cavity on the protein surface can be identified by looking at the crystal structure of the protein-
bound with a known inhibitor.
• Pose (or "binding mode"): The geometry of the ligand in the binding site.
Geometry = location, orientation, and conformation.
Types of molecular docking
a. Rigid Docking: This method was based on the lock-and-key hypothesis. In rigid docking, both
the ligand and the receptor are treated as rigid bodies. No conformational changes are allowed
during the docking process. The molecules will be correlated as rigid objects that cannot alter their
spatial shape. This type of docking is computationally less intensive and faster compared to flexible
docking. However, its accuracy is limited since it does not account for the flexibility of the
molecules, which can be crucial for realistic binding scenarios. Rigid docking is often used in initial
screening processes.
b. Flexible Docking: Flexible docking allows for the flexibility of the ligand and sometimes the
receptor during the docking process. This approach acknowledges that the ligand might change
shape when binding to the receptor, or the receptor might undergo slight conformational changes
(induced fit hypothesis). It is a more realistic approach than rigid docking.
Types of Flexible Docking:
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NSCBIP/Sem-VI/Med Chem III/ CADD and Combinatorial Chemistry/Mr. Samiran Sadhukhan/2025
i. Ligand-Flexible Docking:
• The ligand is allowed to rotate and adopt different conformations.
• The receptor remains rigid.
• Example: AutoDock (flexible ligand mode).
ii. Receptor-Flexible Docking:
• The ligand and some receptor residues are flexible.
• Only key amino acids in the binding site (side chains) move.
• Example: Induced Fit Docking (IFD) in Schrödinger.
iii. Fully Flexible Docking:
• Both the ligand and receptor undergo global conformational changes.
• Very computationally expensive.
• Example: Molecular dynamics-based docking (e.g., using AutoDock with MD simulations).
c. Extra Precision (XP) Docking: Extra Precision (XP) docking is a more accurate and refined
version of docking, focusing on improving the precision of binding mode prediction through more
stringent scoring functions and rigorous evaluation of possible binding modes and affinities. This
method is particularly significant in situations where traditional docking methods may fail to
distinguish between true binders and false positives effectively. This method is used in Glide XP
docking (Schrödinger) for highly accurate pose predictions.
Key differences
Extra-Precision Docking
Parameter Rigid Docking Flexible Docking
(XP)
Both protein and ligand Ligand (and sometimes Flexible ligand; advanced
Target and Ligand
are treated as rigid protein side chains) are treatment of receptor-ligand
Flexibility
bodies flexible interactions
Fast; less Slower due to Slower than standard
Speed computationally conformational docking; more refined
intensive sampling scoring
Higher accuracy due to
Moderate; lacks Very high; used to rank top
Accuracy better binding mode
conformational realism hits with better selectivity
prediction
AutoDock (rigid mode), AutoDock, GOLD, Glide-XP (Schrödinger),
Tools/Software
DOCK FlexX, Glide-SP GOLD-XP
Empirical + knowledge-
Scoring Function Simple, empirical Advanced scoring;
based; accounts for
Complexity scoring penalizes false positives
flexibility
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NSCBIP/Sem-VI/Med Chem III/ CADD and Combinatorial Chemistry/Mr. Samiran Sadhukhan/2025
Extra-Precision Docking
Parameter Rigid Docking Flexible Docking
(XP)
Medium-throughput
High-throughput initial Lead optimization and
Best Used For screening and hit
screening detailed SAR analysis
optimization
Neglects induced-fit May not handle full
Computationally expensive;
Limitation effects; low binding receptor flexibility;
not ideal for large libraries
mode accuracy slower
Applications of Molecular Docking
1. Drug Discovery & Development
• Helps identify potential drug candidates by screening large compound libraries.
• Predicts the binding affinity of ligands to target proteins, allowing for lead optimization.
Example: Screening phytochemicals from Indian traditional plants for antidiabetic activity.
• Helps in de novo drug design, where new molecules are created based on receptor binding
sites.
• Molecular docking helps in high-throughput virtual screening (HTVS), filtering large
databases of compounds.
• Determines the binding mode of ligands in the active site. Thus, helps in understanding the
mechanism of action (MOA) of drugs.
2. Computational Toxicology & ADMET Prediction
• Helps predict off-target binding and toxic effects of drug candidates. Thus, reduces failure rates
in clinical trials.
• Docking helps understand drug metabolism by simulating interactions with cytochrome P450
enzymes.
3. Biomolecular Interaction Studies & biomedication
• Used to study interactions between two or more proteins, such as enzyme-substrate or antibody-
antigen interactions. Example: Understanding insulin-receptor binding.
• Studies how microbial enzymes interact with pollutants for environmental cleanup.
Combinatorial Chemistry
Definition: Combinatorial chemistry is a technique where multiple different compounds are
synthesized simultaneously by systematically combining different sets of building blocks (e.g.,
molecules or functional groups) in all possible ways.
• Introduced to speed up drug discovery.
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NSCBIP/Sem-VI/Med Chem III/ CADD and Combinatorial Chemistry/Mr. Samiran Sadhukhan/2025
• Instead of synthesizing one compound at a time, it allows the synthesis of hundreds to thousands
of compounds in parallel.
• The set of compounds produced is called a compound library or chemical library.
Purpose: To identify lead molecules (potential drug candidates) by screening large numbers of
related compounds for biological activity.
Principle of Combinatorial Chemistry
• Uses a modular approach: Combine building blocks like A, B, C with X, Y, Z to generate
combinations like AX, AY, AZ, BX, BY, BZ, etc.
• Reduces the time and cost required to synthesize and test individual molecules.
• Utilized with automated robotic systems for high-throughput synthesis and screening.
Key Approaches to Combinatorial Synthesis
There are two major strategies:
1. Solid-Phase Synthesis
2. Solution-Phase Synthesis
Solid-Phase Synthesis
Solid-phase synthesis is a method where the initial reactant is anchored to an insoluble solid
support, and subsequent reactions are performed on this bound substrate.
Origin:
• Introduced by Bruce Merrifield in 1963 for peptide synthesis.
• Revolutionized combinatorial chemistry due to its ease of purification.
Solid Support:
• Commonly used supports: Polystyrene resin, Wang resin, Rink amide resin.
• These beads are chemically inert, but can anchor molecules through a linker.
Key Steps:
Step Description
1. Loading Attach the starting molecule to the resin via a linker.
2. Reaction Add reagents in sequence. Reaction occurs on resin.
3. Washing Unreacted reagents and by-products are washed away.
4. Repetition Steps 2 and 3 are repeated to elongate the molecule.
5. Cleavage Final compound is cleaved from the resin using specific reagents (e.g., TFA).
Advantages:
• Easy purification (just washing).
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NSCBIP/Sem-VI/Med Chem III/ CADD and Combinatorial Chemistry/Mr. Samiran Sadhukhan/2025
• Ideal for automation and parallel synthesis.
• Small amount of solid support can yield many compounds.
• Reduces loss of material.
Disadvantages:
• Difficult to monitor reaction progress (requires test cleaving).
• Limited to reactions compatible with solid-phase conditions.
• Costly resins and linkers.
• Sometimes lower reaction yields.
Solution-Phase Synthesis
Solution-phase synthesis involves carrying out reactions entirely in liquid solution, without using
any solid support.
This is the classic approach to organic synthesis, now adapted to combinatorial techniques using
micro-scale, parallel, and high-throughput setups.
Key Features:
• Reagents and substrates are dissolved in suitable organic or aqueous solvents.
• Reactions are typically batch-based or parallel.
• Use of microreactors and multi-well plates in modern setups.
Key Steps:
Step Description
1. Preparation Reactants and solvents are selected and dissolved in suitable reaction vessels.
Reactants are stirred and reacted under controlled conditions (e.g., heat,
2. Reaction
catalysts).
3. Monitoring Reaction progress is monitored using techniques like TLC, HPLC, or NMR.
Reaction mixture is subjected to extraction, filtration, or precipitation to isolate
4. Work-up
the crude product.
5. Purification The desired compound is purified using chromatography or recrystallization.
Steps are repeated in parallel or series with different reactants to generate a
6. Repetition
compound library.
Advantages:
• Better reaction kinetics due to free movement of molecules.
• Easier to monitor and analyze intermediates using TLC, NMR, etc.
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NSCBIP/Sem-VI/Med Chem III/ CADD and Combinatorial Chemistry/Mr. Samiran Sadhukhan/2025
• Scalable to gram or kilogram level (suitable for production).
• Broad compatibility with various types of reactions.
Disadvantages:
• Purification is more complex (requires chromatography, filtration, etc.).
• Automation is harder and less efficient.
• Cross-contamination risk if reactions are done in parallel.
• Time-consuming for large libraries.
Application of combinatorial chemistry
• Drug discovery: Rapid identification of lead compounds for new drugs.
• Peptide libraries: Design of diverse peptides for biological screening.
• Antibody development: Creation of antibody libraries for therapeutic and diagnostic uses.
• Catalyst design: Discovery of novel catalysts for chemical reactions.
• Material science: Synthesis of new materials with tailored properties.
• Agricultural chemistry: Development of new pesticides and herbicides.
• Protein-protein interaction studies: Screening of small molecules targeting protein interactions.
• Enzyme inhibitors: Identification of inhibitors for various enzymes related to diseases.
• Natural product analogs: Synthesis of synthetic analogs of natural products for optimization.
