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What Is Docking?
• Docking is a method which predicts the preferred orientation of one
molecule to a second when bound to form a stable complex with
overall minimum energy.
Why Docking Is Important?
• It is of extreme relevance in cellular biology
• It is the key to rational drug design
• The results of docking can be used to find inhibition for specific target
proteins and thus to design new drug.
• It is gaining important as the number of proteins whose structure is
known increases.
Why We Do Docking?
• Drug discovery costs are too high
• Drugs interact with their receptors in a highly specific and
complementary manner.
• Core of the target-based structure-based drug design (SBDD) for lead
generation and optimization.
• Lead is a compound that
– shows biological activity,
– is novel, and
– has the potential of being structurally modified for improved
bioactivity, selectivity.
Drug Design
Traditional Drug Design Modern Drug Discovery Process
Factor Effecting Docking
1. Intramolecular forces. . . .
• bond length
• bond angle
• dihedral angle
2. Intermolecular forces. . . .
• electrostatic
• Dipolar
• hydrophobicity
• Vander walls forces
Types Of Docking
• There are 2 types of docking,
1.Rigid docking
2.Flexible docking
Rigid Docking
• In the rigid docking molecules are rigid, in 3D space of one of the
molecule which brings it to an optimal fit with the other molecules in
terms of a scoring function.
Flexible Docking
• In flexible docking molecules are flexible ,confirmations of the
receptor and the ligand molecules , as they appear in complex.
1) Protein-Protein Docking
• Both molecules are rigid Interaction produces no change in conformation Similar
to lock-and key model
2) Protein-Ligand Docking
• Ligand is flexible but the receptor protein is rigid. Interaction produces
conformational changes in ligand.
Mechanism Of Docking
Proton Detected Hetero nuclear NMR
Protein + Drug
Drug Fail to Combine
With Protein
NMR still be
detected
Drug bind to
protein
Nuclei will have
shorter relaxation
time
No NMR spectrum
Homologous modelling
• Align the amino acid sequence of protein with unknown structural
agent, the sequence of a homologous protein whose 3D structure has
already been determine.
• By converting structurally conserved region & structural variable
region, the core of the molecule can be identified.
Docking Software…..
1. DOCK (1982,2001)
2. FlexX(1996)
3. Hammerhead (1996)
4. Surflex (2003)
5. SLIDE(2002)
6. AutoDock(1990,1998)
7. ICM (1994)
8. MCDock (1999)
09. GOLD (1997)
10. GemDock (2004)
11. FRED (2002)
12. Glide (2004)
13. Yucca (2005)
14. vLife(Biopredicta)
15. MOLS 2.0 (2016)
16. Click Docking (2011)
Application Of Molecular Docking in Modern
Drug Discovery
• Determine the lowest free energy structures for the receptor ligand
complex.
• Search database and rank hits for lead generation.
• Calculate the differential binding of a ligand to two different
macromolecular receptors.
• Study the geometry of a particular complex.
• Propose modification of a lead molecules to optimize potency or other
properties.
• de novo design for lead generation.
• Library design.
• Case Study-
169000 compounds
(Pharmacophore
Based-screening)
300 compounds
(Molecular docking)
32 promising
compounds
Growing Evidence of Achievements....!!
 Molecular Docking has resulted in several breakthrough classes of
new drug.
01.Discovery of Indinavir, the HIV protease
inhibitor. (1992)
02.Identification of Haloperidol as a lead
compound in a structure- based design for
non-peptide inhibitor of HIV.
03.Neuraminidase (antiviral)
04.Elastase (treatment of emphysema)
Future Prospects(SAROGLITAZAR)
PPAR-alpha PPAR-gamma PPAR-delta
Binding energies:
1. Alpha = -6.98
2. Gamma = -6.87
3. Delta = -7.77
CONCLUSION:
As binding energy is indirectly proportional to binding affinity,
we can make future assumption of helping of PPAR-delta
receptors in treating MITOCHONDRIAL FATTY ACID &
OXIDATION DISORDERS(FAODS).

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Molecular Docking

  • 1. What Is Docking? • Docking is a method which predicts the preferred orientation of one molecule to a second when bound to form a stable complex with overall minimum energy.
  • 2. Why Docking Is Important? • It is of extreme relevance in cellular biology • It is the key to rational drug design • The results of docking can be used to find inhibition for specific target proteins and thus to design new drug. • It is gaining important as the number of proteins whose structure is known increases.
  • 3. Why We Do Docking? • Drug discovery costs are too high • Drugs interact with their receptors in a highly specific and complementary manner. • Core of the target-based structure-based drug design (SBDD) for lead generation and optimization. • Lead is a compound that – shows biological activity, – is novel, and – has the potential of being structurally modified for improved bioactivity, selectivity.
  • 4. Drug Design Traditional Drug Design Modern Drug Discovery Process
  • 5. Factor Effecting Docking 1. Intramolecular forces. . . . • bond length • bond angle • dihedral angle 2. Intermolecular forces. . . . • electrostatic • Dipolar • hydrophobicity • Vander walls forces
  • 6. Types Of Docking • There are 2 types of docking, 1.Rigid docking 2.Flexible docking Rigid Docking • In the rigid docking molecules are rigid, in 3D space of one of the molecule which brings it to an optimal fit with the other molecules in terms of a scoring function. Flexible Docking • In flexible docking molecules are flexible ,confirmations of the receptor and the ligand molecules , as they appear in complex.
  • 7. 1) Protein-Protein Docking • Both molecules are rigid Interaction produces no change in conformation Similar to lock-and key model 2) Protein-Ligand Docking • Ligand is flexible but the receptor protein is rigid. Interaction produces conformational changes in ligand.
  • 9.
  • 10. Proton Detected Hetero nuclear NMR Protein + Drug Drug Fail to Combine With Protein NMR still be detected Drug bind to protein Nuclei will have shorter relaxation time No NMR spectrum
  • 11. Homologous modelling • Align the amino acid sequence of protein with unknown structural agent, the sequence of a homologous protein whose 3D structure has already been determine. • By converting structurally conserved region & structural variable region, the core of the molecule can be identified.
  • 12. Docking Software….. 1. DOCK (1982,2001) 2. FlexX(1996) 3. Hammerhead (1996) 4. Surflex (2003) 5. SLIDE(2002) 6. AutoDock(1990,1998) 7. ICM (1994) 8. MCDock (1999) 09. GOLD (1997) 10. GemDock (2004) 11. FRED (2002) 12. Glide (2004) 13. Yucca (2005) 14. vLife(Biopredicta) 15. MOLS 2.0 (2016) 16. Click Docking (2011)
  • 13. Application Of Molecular Docking in Modern Drug Discovery • Determine the lowest free energy structures for the receptor ligand complex. • Search database and rank hits for lead generation. • Calculate the differential binding of a ligand to two different macromolecular receptors. • Study the geometry of a particular complex. • Propose modification of a lead molecules to optimize potency or other properties. • de novo design for lead generation. • Library design.
  • 14. • Case Study- 169000 compounds (Pharmacophore Based-screening) 300 compounds (Molecular docking) 32 promising compounds
  • 15. Growing Evidence of Achievements....!!  Molecular Docking has resulted in several breakthrough classes of new drug.
  • 16. 01.Discovery of Indinavir, the HIV protease inhibitor. (1992) 02.Identification of Haloperidol as a lead compound in a structure- based design for non-peptide inhibitor of HIV. 03.Neuraminidase (antiviral) 04.Elastase (treatment of emphysema)
  • 17. Future Prospects(SAROGLITAZAR) PPAR-alpha PPAR-gamma PPAR-delta Binding energies: 1. Alpha = -6.98 2. Gamma = -6.87 3. Delta = -7.77 CONCLUSION: As binding energy is indirectly proportional to binding affinity, we can make future assumption of helping of PPAR-delta receptors in treating MITOCHONDRIAL FATTY ACID & OXIDATION DISORDERS(FAODS).