Docking | Protein-Protein Docking | Protein-Ligand Docking

Docking

• Protein-Protein

• Protein-Non Protein molecule

Docking as the name suggests implies the concept of dockyards constructed at sea parts the area constructed complementary to the shape of the ships where ships are allowed to rest. From the perspective of docking, it is seen that which molecules fit in the clefts or binding regions of protein it is seen that which molecules will be complementary to the surface.

Importance Of Docking

All the functions being performed normally can be known only when the abnormal is known as well.

Physiology  ➡️ Normal condition

Pathology  ➡️ Abnormal functioning

There are certain methods that are specific for only protein-protein docking & some for only protein-ligand docking. Some methods have the flexibility for both types.

A ligand as per definition can be proteins as well as a nonprotein molecule but in 90% of cases, it is a small molecule & binds to a large protein i.e. receptor.

In medical terms, the pathogen has a broad meaning. It can be even a molecule that allergic way as well. For example, formic acid can cause such hypersensitivity reactions that might be fatal/lethal if not treated.

Similar is the case with death bees or spiders (black spiders).

Thus, word pathology is used for malfunctioning what are the molecular details, whether the disease is metabolic, genetic, or infectious. These can be differentiated as the pathology of infectious disease & non-infectious diseases.

Physiology is studied to know about pathology. For example, in sickle cell anemia an amino acid replacement causes a change in structure which is not compatible with the binding of iron as there is no proper attachment of beam hence functioning gets affected. Thus, if normal and abnormal conditions are known then treatment can also be devised, drugs can be formed. Even in the case of immunology, it has to be seen against which target, the immune response will generate.

To perform any assay experimentally docking is performed. For example, an enzyme important for the survival of a pathogenic organism is targeted. Different antibiotics target different aspects if one aspect is blocked test will not occur. To inhibit the protein, a screening procedure is carried. Before docking, this was used to be done experimentally. A pool of compounds was taken and was reacted with the target. It was then run on a gel to see binding, binding affinity. This can further be checked by different methods.

Combinations of molecules are added with a natural ligand. The inhibitor should bypass natural ligand, it should have more affinity than it. Competitive inhibitor other methods of inhibition like allosteric inhibition may also be present. For this, structural details are required. The molecules have to be labeled to see which binding has occurred.

(Radiolabeling is not used much because of its drawbacks).

The complex is then isolated, purified and structure is determined either with NMR or x-ray crystallography. Complex with a ligand or is carried theoretically Virtual Screening. It is not actual. Through an algorithm it carries docking. A docking score is used for selection. The better the score, the better the binding. Virtual importance is actually not visible but it has its existence somewhere. Actually, docking is not being carried but through an algorithm, docking parameters are checked. Out of these, some are selected.

In virtual screening, it is seen that either some structures becoming fit or not and if so then what will be the extent of the effect of it. If there are some minor side effects then these are sacrificed for the main treatment.

In the case of some natural compounds to be used in binding as ligands they are isolated & then through mass spectrometry its structure is determined.

Bronchodilators are used in the case of bronchioles construction. It is targeted for B-adrenalin receptors. But these receptors are also present on the heart to which heartbeat increase such condition is called a side effect.

The task of bio-information is to carry experimentation on a focused area. Theoretical work reduces time consumption for experimental work. It provides a base for the work to be carried on an experimental level without wasting much time & trials.

Protein-Protein Docking

The molecular interaction details are obtained after docking. These help to understand how the mechanism of the reaction is being performed i.e. which atoms of which amino acids are involved. For example, functional traid 3 units ( amino acids in case of protein) performing the function in enzymes like hydrolytic enzymes consist of one electrophilic center one nucleophilic, and others as an electron donor. In order to find the triad even though there are chemical methods that do not require going into the detail but in order to know exactly how it is located in protein structure how it reacts i.e. enzymes & substrate interaction, docking is used. There is a bit difference between catalytic & binding site.

The orientation occurs in such a way that it can easily transfer the transferring group. Whatever the case is, the enzyme binds with the substrate on the binding region. The substrate binds so that transfer is easy. In this way, a complex i.e. enzymes-substrate complex forms through non-covalent interactions which are reversible.

Two things are involved in it.

1. The catalytic site of enzymes
2. The target site of protein

Docking algorithms basically search the surface complementary see complementary surfaces between both molecules. Docking complexes are formed which are higher in number because there are many possibilities and it is seen that which complex is close to the native complex. (Similar to BLAST search).

The problem which occurs is dynamicity. Protein molecules are flexible molecules. Flexibility is measured through dynamicity. They are finally to an extent only as protein has a 3-D structure which s stabilized through some interactions. The number & types of these interactions vary; these are not permanent, they change like hydrogen bonding, Van der Waal interactions, hydrophobic, etc (disulfide bridges are not included in these). The interactions change through the movement of electrons, charges move to and from the protein resulting in loss & making of bonds like hydrogen bonds will finish & molecules will move slightly apart.
Due to some modifying group carrying, there will be a disturbance in interactions in a particular area. A cleft may create and protein may get activated from an inactivated state. Bulky side chains causing instability in the local area of protein. Local changes continuously occur in protein structure which also called conformation changes.

It also depends on the amino acids present in this region. There are numerous possibilities in this case. Even at a single amino acid, alternation of the modifying group may occur, favorable environmental conditions, signaling activations (The molecules generating signals when a release will cause activation). For example, phosphate group & sugar may compete for a site. The result will be different there will be hydroxyl groups in both and the O & H of these hydroxyl groups will be the center of hydrogen bonding. Some ay break some may form. Thus, all of this depends on the modifying groups as well as built-in conformation. If distance was initially more not allowing the formation of hydrogen bond but due to modifying group, the distance reduced or lessened. Because of the narrowing of the cavity, the reactions that were not possible previously became possible.

By making these things as a base and to address dynamicity, molecules are considered as flexible entities in algorithms. The approaches are different in different programs

Rigid Receptor 〜 Rigid Ligand
Rigid Receptor 〜 Flexible Ligand
Rigid Receptor 〜 Rigid Ligand
Flexible Receptor 〜 Flexible Ligand

Flexibility is computed using different parameters, different biochemical, physicochemical &interactions are computed to see where interactions will be dynamic. First of all, surface complementarity is checked.

Programs compute all possibilities to see how much flexibility is there sometimes, complementarity distance/difference is more but it is reduced or minimized to see that at what level flexibility can com.
In some cases, usually, there seem to be hindrances in interaction but through docking, it fits in. Thus, through insilico analysis, invivo process is monitored although not completely but close to native conformation through labeled tags and fluorometry, dynamicity is seen. Through signals, it is seen what kinds of changes are occurring. As environmental changes are not known, one can be close but not exact to the original.

Just as X-ray crystallography has its limitation that it only tells about one of the proteins’ state but has many other benefits similarly docking complexes are useful although they have some limitations.

There are a number of protein ligands known which bind with cellular receptors. Sometimes anchored protein binds with receptor as the ligand.

Due to some outside changes, the domain becomes a ligand. The whole reaction does not have to be carried, it can be at any point or stage. Moreover, it's not necessary to be on the surface only. It can also happen inside.

In terms of docking, receptor & ligand can be defined as:

• A receptor is the one that provides a pocket.

• Ligand is the one which hind to the pocket.

A number of types of molecules can bind with proteins. For example, even metals can bind with proteins:

• In bioremediation in the process of phytoremediation, a metallothionine is a group of proteins that bind with metals. These proteins are present not in plants only but also in unicellular organisms (In fact these were discovered in the unicellular organisms).

• Lactoferrin absorbs all iron present in nutrition & provides it in milk. (In Herman bull, lactoferrin expression was increased).

Docking

1. Surface complementarity
2. Surface treated as rigid or flexible.

Requirements that form which angles molecules / amino acid can be flexible & up to what extent. Different combination of algorithms was developed for it.

Peptide Inhibitors

Inhibitors are not necessary to be single-molecule always. Sometimes inhibitors are peptides to stop an enzyme from its function. A protein whose ligand is also a protein can be used as peptide inhibitors.

Analysis of Docked Complexes

The activity of docking complexes is seen with the help of it.

In protein-ligand docking, it is seen that the protein is binding with ligand incorrect region or not with correct orientation or not. There will be different angles the surface is rotated to see that at which angle it will fit the most. Interaction is computed using different programs. The basic interactions involved are:

1. Hydrogen Bonding
2. Hydrophobic – Hydrophilic Interactions
3. Other Non-Bonded Covalent Contacts (Van Dar Waal, Atomic radii, Ionic radii, etc)

Separate programs as well as some containing different utilities are available.
Protein-Ligand        ➡️  Patch dock
Docking programs  ➡️  3-D jigsaw
The majority flow rigid surface docking.

Protein-Protein Docking Programs

• Auto dock (There are many versions of it. Some programs use it to carry docking as well as other functions.

• Auto dock vina (Carry screening procedures using docking screen chemical compounds from different databases)

• PyRx

• Hex

• Flex

• Z-Dock

• Cluspro

These programs carry protein-protein as well as protein-ligand docking. These are state of the art programs. They also compute flexibility in the whole molecule. These programs require specific file formats to be converted from PDB. (Protein-ligand programs take only a pdf file & give its surface complementarity only).
In Cluspro, both PDB files i.e. that of protein and that of the ligand are submitted and it produces docking. Cluspro uses Z-dock & other programs along with the features of Z-dock other features are also available.

Distance between ligand and receptor is computed which corresponds to an interaction distance i.e. whether hydrogen bond or hydrophobic-hydrophilic interactions will occur or not. Some analysis programs along with these interactions show covalent bonds, salt bridges, ionic bridges also. Even disulfide bridges are computed e.g if two cysteine residues are at such distance then by getting in proximity what will be the possibility of bond formation, the chance of disulfide bridge.

• Ligplot is an old method to compute the hydrogen bond between ligand and receptor i.e location of a hydrogen bond.

• An online server PDBsum, aport from protein-protein & protein-ligand interactions also views protein-nucleic acid interaction. It also tells about the possibility of a covalent bond along with others.

Thus dock complex can be analyzed by various means.
Analysis of the dock complex is important in the aspect that it tells about the correct position of interaction. Exact orientation and bonds in between are quite significant as in docking it happens sometimes that the best fit model may not be the required model, other models may be more close in actual.

Some standards are also very important to see interactions i.e. previously known details about interaction. For example, the position of a functional triad, etc.
If there is such a case in which there is no standard available then the standard is seen at sequence level e.g by Prosite etc, a motif is seen at sequence level is included in interaction or not.

If binding strength is known with a natural ligand then it can be seen whether it's correct or not. Binding strength is with respect to interactions the more the number and type of interactions the more will be the strength. Some are the case with its reverse. If there is an equal affinity of a ligand with a natural one then it will not be a good inhibitor. Binding strength should be more. Can be inhibitors or effector as well. It also has to be seen how severity level is more then it cannot be adopted as a drug. If the severity is more than drug severity then side effects can be sacrificed.

After docking it is seen that the protein can regulate which functions.

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