BASICS OF ~MOLECULAR DOCKING~

SATARUPA DEB ROLL- 10

Docking is a structure-based technique which attempts to find the “best” match, between two molecules.

WHAT IS MOLECULAR DOCKING????• In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex.

• Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using for example scoring functions.

RECEPTOR LIGANDLIGAND-RECEPTOR COMPLEX

WHY IS DOCKING IMPORTANT? Signal Transduction :- The associations between biologically relevant molecules such as proteins, nucleic acids, carbohydrates, and lipids play a central role in signal transduction. Furthermore, the relative orientation of the two interacting partners may affect the type of signal produced (e.g., agonism vs antagonism). Therefore docking is useful for predicting both the strength and type of signal produced.

Drug-Designing:- Docking is frequently used to predict the binding orientation of small molecule drug candidates to their protein targets in order to in turn predict the affinity and activity of the small molecule. Hence docking plays an important role in the rational design of drugs.

Receptor or host or lock: The "receiving" molecule, most commonly a protein or other biopolymer.

Ligand or guest or key: The complementary partner molecule which binds to the receptor. Ligands are most often small molecules but could also be another biopolymer.

Docking: Computational simulation of a candidate ligand binding to a receptor.

Binding mode: The orientation of the ligand relative to the receptor as well as the conformation of the ligand and receptor when bound to each other.

Pose : A candidate binding mode.

Scoring : The process of evaluating a particular pose by counting the number of favorable intermolecular interactions such as hydrogen bonds and hydrophobic contacts.

Ranking : The process of classifying which ligands are most likely to interact favorably to a particular receptor based on the predicted free-energy of binding.

DOCKING GLOSSARY

DEFINITION OF THE PROBLEMOne can think of molecular docking as a problem of “lock-and-key”, in which one wants to find the correct relative orientation of the “key” which will open up the “lock” (where on the surface of the lock is the key hole, which direction to turn the key after it is inserted, etc.)

However, since both the ligand and the protein are flexible, a “hand-in-glove” analogy is more appropriate than “lock-and-key”. During the course of the docking process, the ligand and the protein adjust their conformation to achieve an overall "best-fit" and this kind of conformational adjustment resulting in the overall binding is referred to as "induced-fit“.

DOCKING APPROACHESSHAPE COMPLEMENTARITY:- One approach uses a matching technique that describes the protein and the ligand as complementary surfaces.

SIMULATION:- The second approach simulates the actual docking process in which the ligand-protein pairwise interaction energies are calculated. Both approaches have significant advantages as well as some limitations.

CALCULATE:-Hydrophilic and hydrophobic interactions.Hydrogen bond donated.Hydrogen bond accepted.Ligand orientation with best complementarity score.Binding affinities.Ionic interaction.Aromatic Interaction.Vander Waals’ forcesElectrostatic forcesFree energies.

STEPS OF DOCKINGStep 1: Start with Crystal Co-ordinates with target receptor.

For example,-HIV-1 protease is the target receptor- Aspartyl groups are its active sites

Step 2: Generate molecular surface for receptors.

Step 3: Generate spheres to fill the active site of the receptor: The spheres become potential locations for ligand atoms.

Step 4: Sphere centres are then matched with the ligand atoms, to determine possible orientations for the ligand.

Three scoring schemes:o Shape scoring, o Electrostatic scoring ando Force-field scoring.

Step 5: Find the top scoring or the best ranking.

APPLICATIONS OF MOLECULAR DOCKING

Determination of the lowest free energy structures for the receptor-ligand complex.Calculate the differential binding of a ligand to two different macromolecular receptors.Study the geometry of a particular complex.Propose modification of lead molecules to optimize potency or other properties.De novo design for lead generation.Library design.Screening for the side effects that can be caused by interactions with other molecules.To check the specificity of the potential drug against homologous proteins through docking.Docking is also a widely used tool for predicting protein-protein interaction.Knowledge of the molecular associations aid in understanding a variety of pathways taking place in the living and in revealing of the possible pharmacological targets.Protein-ligand docking can also be used to predict pollutants that can be degraded by enzymes.

COMMON SOFTWARES USED FOR DOCKING PURPOSE

1. UCSF DOCK- USA (1988)

2. AUTODOCK- USA (1990)

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.Current distributions of AutoDock consist of two generations of software: AutoDock 4 and AutoDock Vina.

3. FlexX- Germany (1996)

Receptor is treated as rigid.Incremental construction algorithm:

Break Ligand up into rigid fragmentsDock fragments into pocket of receptorReassemble ligand from fragments.Energy conformations

4. GOLD- UK (1995)

Performs automated docking with full acyclic ligand flexibility, partial cyclic ligand flexibility and partial protein flexibility in and around active site.

Scoring: includes H-bonding term, pairwise dispersion potential (hydrophobic interactions), molecular and mechanics term for internal energy

OTHER SOFTWARES

AADS- India (2011)

ADAM- Japan (1994)

BetaDock- South Korea (2011)

DARWIN- USA (2000)

DIVALI- USA (1995)

DockVision- Canada (1992)

EADock- Switzerland (2007)

Understanding the ruling principles whereby protein receptors recognize, interact, and associate with molecular substrates and inhibitors is of paramount importance in drug discovery efforts. Protein-ligand docking aims to predict and rank the structure(s) arising from the association between a given ligand and a target protein of known 3D structure. Despite the breathtaking advances in the field over the last decades and the widespread application of docking methods, several downsides still exist. In particular, protein flexibility-a critical aspect for a thorough understanding of the principles that guide ligand binding in proteins-is a major hurdle in current protein-ligand docking efforts that needs to be more efficiently accounted for. In this review the key concepts of protein-ligand docking methods are outlined, with major emphasis being given to the general strengths and weaknesses that presently characterize this methodology. Despite the size of the field, the principal types of search algorithms and scoring functions are reviewed and the most popular docking tools are briefly depicted.

CONCLUSION

REFERENCES

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2. Jorgensen WL (1991). "Rusting of the lock and key model for protein-ligand binding".Science 254 (5034): 954–5. doi:10.1126/science.1719636. PMID 1719636

3. http://www.crcnetbase.com/doi/abs/10.1201/9781420028775.ch3

4. http://www.ccdc.cam.ac.uk/Solutions/GoldSuite/Pages/GOLD.aspx

5. Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK (2004). "Testing a flexible-receptor docking algorithm in a model binding site". J. Mol. Biol. 337 (5): 1161–82.doi:10.1016/j.jmb.2004.02.015. PMID 15046985

6. http://autodock.scripps.edu/

7. http://www.ibms.kmu.edu.pk/sites/ibms.kmu.edu.pk/files/downloads/Dr.%20Abdul%20Wadood.pdf