GRT Institute of Pharmaceutical Education and Research, Thirutani.
Background-Molecular docking serves as an effective method for exploring the molecular targets of nutraceuticals in the treatment of diseases. Objectives-This review focuses on understanding the basics, types, approaches, applications, advantages and disadvantages of docking. Discussion-The basics of docking involve study of the ligands and proteins. The types of docking encompass Rigid Docking, Flexible-Rigid Docking and Flexible Docking. The approaches include determination of the energy profile for the docked conformer of the ligand target and determination of the complementarity of surfaces between the ligand and the target. Applications discussed in this review are Hit identification, Lead optimization, Bioremediation, Remediation, Binding site prediction, Protein – protein/ nucleic acid interactions, Searching for lead structures for protein targets, Mechanisms of enzymatic reactions, Protein engineering, Molecular dynamics simulation and Structure elucidation. The advantages of docking like easy understanding of the mechanism of action and disadvantages of docking like everchanging dynamic nature of protein-ligand interactions making it difficult to ascertain the conformational stabilities are also explained in this article. Conclusion-Docking study can include the preferred orientation of a molecule when bound to another molecule. This information can be used to predict the strength of the association between the two molecules.
What is docking?
Docking is a molecular modelling method (using a computer software) aimed at discovering the optimal fit between a ligand (Drug) and its binding site (receptor or protein) 1. Usually, a favorable binding or interaction with the receptor or protein initiates a positive response which is seen as cure of disease or its symptoms2.
Basics of Docking
Protein
Proteins are large, complex molecules that are essential to numerous bodily functions. They perform the majority of the work in cells and are necessary for the organs and tissues of the body to be regulated, functional, and structural.1 Although they can be depicted as primary, secondary, tertiary, and even quaternary structures, only the primary (amino acid) sequence is significant from a nutritional perspective. Similarly, while many substances in the body can be chemically classified as amino acids, we are only interested in the 20 canonical amino acids that are encoded in dna and the five others that have quantitatively significant functions in the body: taurine, ornithine, citrulline, γ-aminobutyrate, and β-alanine. 2 Since the body cannot generate their carbon skeletons, nine of the twenty amino acids found in proteins are regarded as nutritionally indispensable (essential) in adult humans. Leucine, valine, isoleucine, histidine, lysine, methionine, threonine, tryptophan, and phenylalanine are the nine amino acids in question. Moreover, two more are produced from their essential precursors: tyrosine from phenylalanine and cysteine from methionine. 2
Ligand
Ligands are neutral molecules or ions that form a connection with a central metal ion or atom. The core atom functions as a Lewis acid, which accepts electron pairs, while ligands function as Lewis bases, which give electron pairs. To establish covalent connections with the centre atom, ligands need at least one donor atom with an electron pair. 3 A ligand's structure and/or activity are changed when it interacts to its specific receptor, triggering a variety of biological reactions. In all multicellular animals, these cellular reactions are essential for cell motility, proliferation, survival, and differentiation.3 Ligands can be neutral molecules, cations, or anions. Ligands can be further categorized into tridentate, bidentate, and monodentate, among others. 4
Monodentate Ligands
The literal meaning of "monodentate" is "one tooth," signifying that the ligand binds to the centre via a single atom. Monodentate ligands include, for instance, hydroxide ions (called hydroxo when a ligand is present), ammonia (called ammine when a ligand is present), water (called aqua when a ligand is present), and chloride ions (called chloro when a ligand is present). 4
Bidentate Ligands
Bidentate ligands can attach to a central metal atom or ion at two different locations since they have two donor atoms. The oxalate ion (OX) and ethylenediamine (EN) are typical examples of bidentate ligands. The nitrogen (blue) atoms on the margins of the ethylenediamine diagram below each contain two free electrons that can be used to form a bond with a central metal atom or ion. 4
Polydentate Ligands
A central metal atom or ion can be bonded to by a variety of atoms in polydentate ligands. One type of polydentate ligand is EDTA, a hexadentate ligand, which contains six donor atoms with electron pairs that can form a connection with a central metal atom or ion.4 One well-known in silico structure-based technique that is frequently applied in drug development is molecular docking. Without knowing the chemical structure of other target modulators beforehand, docking makes it possible to identify new compounds of therapeutic relevance, anticipate ligand-target interactions at the molecular level, or define structure-activity correlations (sar). Docking's functions and applications in drug development have altered significantly over the past few years, despite the fact that it was initially created to aid in understanding the mechanics of molecular recognition between tiny and large molecules.5 Numerous molecular modeling techniques have been effectively integrated into pharmaceutical research to investigate intricate biological and chemical systems in a range of drug discovery initiatives. It has been very beneficial to identify and create new, promising chemicals by combining theoretical and experimental approaches. Modern drug design makes extensive use of molecular docking techniques to investigate the ligand conformations that are adopted within the binding sites of macromolecular targets. By assessing important occurrences in the intermolecular recognition process, this method also calculates the ligand-receptor binding free energy. Since there are many different docking algorithms available today, it is crucial to comprehend the benefits and drawbacks of each approach in order to create methods that work and produce outcomes that are pertinent.6 Molecular docking fundamentals in order to predict a small molecule's affinity and activity, docking is frequently utilized to predict how therapeutic small molecules would fit with their protein targets. 7 Docking is essential to logical medication design. The biological and pharmacological significance of docking investigations has led to a lot of work to enhance docking prediction systems. By using a mathematical technique called docking, one can predict the orientation a molecule will prefer when joined to form a stable complex. 7 Based on their preferred position, scoring functions can be used to determine the strength of the bond or binding affinity between two molecules. 7 Docking methodology is currently used as a standard computational tool in drug design for lead compound optimization and in virtual screening studies to find novel biologically active molecules. Its goal is to predict the experimental binding modes and affinities of small molecules within the binding site of specific receptor targets.8 Over the past few decades, many software programs have been created; some well-known examples include autodock, autodock vina, dockthor, gold, flexx, and molegro virtual docker.9
Types Of Docking
Based on the flexibility of the interacting molecules, receptor, and ligand, there are three types of docking studies: rigid docking, flexible-rigid docking, and flexible docking. 10 Flexible docking produces more accurate and dependable results because molecules' relative bond length and angle can change. 10 Receptor and ligand molecules are both regarded as rigid bodies in rigid type docking. Because of their unaltered shape, each molecule's internal geometry remains constant. Only the translational and rotational degrees of freedom are taken into consideration because of its positional flexibility. The results of this early docking technique, which can be performed between macromolecules like two protein molecules, are less accurate and dependable, which is why it is not as commonly used in modern docking studies. 10 This approach allows for the application of the lock-and-key principle. Both ligand and receptor molecules are regarded as rigid bodies in rigid type docking. Since their shape remains constant, each molecule's internal geometry remains unchanged. Since its position is changeable, only the translational and rotational degrees of freedom are taken into account.10
Rigid Docking
Both ligand and receptor molecules are regarded as rigid bodies in rigid type docking. Since their shape remains constant, each molecule's internal geometry remains unchanged. Since its position is changeable, only the translational and rotational degrees of freedom are considered. Since the results of this early docking method—which can be performed between macromolecules like two protein molecules—are less precise and dependable, it is not as commonly used in modern docking studies. This approach allows for the application of the lock-and-key principle. 10
Flexible-Rigid Docking
This docking technique is semi-flexible. Either the ligand or the receptor is viewed as a rigid body in this situation. Typically, the ligand's conformation varies while the receptor's shape remains constant. This approach is widely used because it produces more accurate and dependable results than the rigid docking method. 10
Flexible Docking
It is a completely flexible docking method where both the ligand and the receptor are regarded as flexible bodies. In other words, the rotations of the molecules—both the ligand and the receptor—are counted to find the best possible conformation and orientation for their interactions. By altering the rotatable bonds and torsion angles, the molecule's shape can be changed. This approach produces a highly accurate docked conformation prediction that most likely matches experimental findings, but it may take a lot of time and computational effort.10
Approaches Of Docking
There are two main methods for carrying out molecular docking. One method uses computer simulations to determine energy profile for the docked conformer of the ligand target. In contrast, the second strategy makes use of a method that determines the complementarity of surfaces between the ligand and the target.11Protein structure preparation is the first stage in molecular docking; the most popular method is to just eliminate all solvent molecules,ions,and other tiny molecular ligands, leaving a completely vacant binding pocket for docking.Although this method is straightforward to operate, it results in a difference between the pocket conditions for docking and physiological conditions. 12 On the one hand, certain water molecules may provide extremely potent hydrogen bonding interactions, that facilitate protein-ligand binding. These interactions are challenging to replace, as doing so could result in a false-positive docking result.12
Different Types of Interactions
Interaction forces are generally separated into four classes:
(1) electrostatic forces - dipole-dipole, charge-dipole and charge-charge.
(2) electrodynamics forces- van der waals interaction.
(3) steric forces - caused by entropy.
(4) solvent-related forces - hydrogen bond and hydrophobic interactions.13
Application Of Molecular Docking
While ligand binding can result in agonism or antagonism, molecular docking interactions can either activate or inhibit the protein. Perhaps using molecular docking to:
Hit Identification (Virtual Screening)
A successful drug discovery initiative starts with hit identification. The proper tiny molecules, often known as hits, that attach to the target and alter its function are found during this procedure. High-quality initial hits accelerate drug discovery projects and reduce attrition rates. In order to select the most promising hit series for the start of the hit-to-lead (h2l) process, a number of orthogonal approaches, including biophysical assays, are used for hit qualification and characterisation after a hit discovery campaign discovered multiple hit series.14 Virtual screening is the process of predicting which chemicals in a big library are most likely to bind to a target protein using computer methods like molecular docking and molecular dynamics simulations. 15
Lead Optimization (Drug Discovery)
The process of developing and enhancing a pre-identified lead compound is known as "lead optimization." it entails modifying various aspects of the molecule through chemical changes. Synthetic modifications are made throughout this procedure to maximize the compound's activity, potency, and selectivity as well as its ADMET characteristics (absorption, distribution, metabolism, excretion, and toxicity). 16
These ADMET characteristics include the compound's ability to enter the bloodstream (absorption), move throughout the body to its intended location (distribution), break down once inside the body (metabolism), expel the compound and any metabolites from the body (excretion), and have any adverse effects on the body (toxicity). Nevertheless, these characteristics are tracked throughout the earlier phases of drug development and are not just taken into account during the lead optimization phase.16
Remediation
Protein-ligand docking can be used to predict which pollutants are enzyme-degradable. The most efficient medication may be collected using it, as well as the intended location. 7 it is possible to identify enzymes and their mechanisms of action by molecular docking. It can also be used to ascertain the connections between proteins. Virtual screening of molecules is done using the remediation.17
Binding Site Prediction (Blind Docking)
Understanding the precise sequence areas that mediate contact, or binding sites, is essential to comprehending biological processes. Due to experimental limitations, computational approaches frequently require data that is not available at the proteome-scale, while experimental methods frequently report erroneous binding sites.18 When targeting places other than the initial substrate binding site, this technique is also crucial. One of the crucial objectives in drug discovery is identifying the allosteric binding site that regulates the target protein's activity.19
Protein – Protein/ Nucleic Acid Interactions
The movement of genetic information between DNA, RNA, and protein is negotiated by an astounding variety of protein–nucleic acid interactions. The range of gene expression is covered by the reviews in this section of current opinion in structural biology, including DNA packaging, unwinding and repair, RNA synthesis mechanisms and regulation, post-transcriptional modification, protein synthesis initiation, and targeting of emerging polypeptides for secretion or membrane insertion.20
Searching For Lead Structures for Protein Targets
The lead structure is where the hunt for a novel medication begins. Although such a chemical already has a desirable biological effect, certain qualities are still insufficient for its therapeutic application. The phrase "lead structure" also refers to the ability to create analogues by specific chemical modifications that result in analogues that are superior to the lead structure in terms of, say, potency or selectivity. Optimizing every feature until a finished product is prepared for therapeutic use is the aim.21
Protein Engineering
Protein engineering is the design of new enzymes or proteins with new or desirable functions. It is based on the use of recombinant DNA technology to change amino acid sequences. 22
Mechanisms Of Enzymatic Reactions
Quantum mechanical, classical mechanical, and statistical mechanical methods have been combined with site-directed mutagenesis, protein structure determination, and fast computers and algorithms to conduct enzymatic operations.23
Bioremediation
Molecular docking is used in bioremediation to predict the binding affinity of small molecules to enzymes involved in the degradation of environmental pollutants. Docking can help in designing inhibitors or activators of these enzymes to enhance bioremediation efficiency. 24
Molecular Dynamics Simulation
Molecular docking can be combined with molecular dynamic simulations to study the dynamic behavior of protein–ligand complexes. The simulations can help in understanding the conformational changes that occur upon ligand binding and the stability of the complex48. Several software tools combine molecular docking and dynamics simulation. These include frequently used software like autodock, vina, glide, and gold. In addition to molecular docking, they provide capabilities for conducting molecular dynamics simulations, allowing for the exploration of protein–ligand interactions over time and the analysis of their dynamic behavior. 24
Structure Elucidation
Molecular docking can also be used to elucidate the structure of proteins with unknown structures. Docking can be used to predict the binding modes of small molecules to the protein and generate a homology model of the protein based on the binding mode prediction. The generated model can then be refined using experimental data to obtain an accurate structure of the protein.24
Docking Software
There are many dockings program in that the many freely available docking programs are available like,
Autodock/Vina
Autodock tools (ADT), a graphical user interface application, was used to finish intermediate processes including creating grid boxes and preparing protein and ligand pdbqt files. The protein was given polar hydrogens, fragmental volumes, solvation parameters, and unified atom Kollman charges via ADT. The prepared file was saved in pdbqt format by autodock. Using a grid box, autogrid was utilized to create the grid map. The grid centre was identified with dimensions (x, y, and z) of -1.095, -1.554, and 3.894. The grid size was set to 60 × 60 × 60 XYZ points with a grid spacing of 0.375 å. The ligand structure is used to compute a scoring grid in order to reduce computing time. The configuration file's grid box attributes and protein and ligand information were used to dock using autodock/vina. Autodock/vina uses a global optimizer for iterated local search. Both the protein and the ligands are regarded as stiff during the docking process. The result with the most advantageous free energy of binding was used to represent the results with a positional root-mean-square deviation (RMSD) of less than 1.0 å. For additional examination, the position with the lowest binding energy or affinity was taken out and matched with the receptor structure. 26
Gold (Genetic Optimization for Ligand Docking)
Gold studies the ligand conformational flexibility and the rotational flexibility of receptor hydrogens using genetic algorithms. Docking was carried out in gold using the wizard with the following default settings: select-pressure (1.1), number of operations (10,000), number of islands (1), niche size (2), population size (100), and operator weights for migrate (0), mutate (100), and crossover (100). Choosing a protein active site residue allowed for the definition of an active site with a 10 å radius sphere. By default, ten solutions were kept for each ligand, and all computations were performed using the genetic algorithm settings. A goldscore fitness function utilizes gold. Goldscore is a function that resembles a molecular mechanism and has been refined for determining ligand binding sites. 26
Flexx
Flexx, now a component of lead it, is a flexible docking technique that places ligands into the active site using an incremental construction (ic) algorithm and a pure empirical scoring system akin to the one created by Bohm and teammates. Each molecule is first broken up into a series of hard pieces based on rotatable bonds by ic algorithms, which then gradually put the pieces back together around the binding pocket. A ligands library was created and the ligands' pdb files were converted to a sybyl mol2 file format for docking research. Using the flexx graphic interface, a receptor description file was created. By choosing the protein's residue, an active site was established. Protein residues with a radius of around 10 å and centred on the ligand's centre of mass make up the active site. Every ligand in the data set had its best ten ranking poses chosen for additional investigation based on energy values. 26
Dock
One of the most well-known and established ligand-protein docking programs is dock.
Rigid ligands were employed in the first version; flexibility was subsequently added by gradually building the ligand inside the binding pocket. As previously stated, dock is a fragment-based approach that uses complimentary chemical and morphological techniques for generating potential ligand orientations. Although there are three distinct scoring functions that can be used to score these orientations, their serious use is limited because none of them include explicit hydrogen-bonding, solvation/desolvation, or hydrophobicity terms. While dock is helpful for quick docking and appears to manage apolar binding sites well, it is not the most precise program on the market.25
Fred (Fast Rigid Exhaustive Docking)
The multi-conformer docking approach used by Fred creates a collection of low-energy conformers independently and then performs rigid docking for each conformer. Fred needed a ligand conformer library and a precisely generated receptor file in order to perform proper docking. While the ligand conformer library was made in omega 2.3.2 (open eye scientific software) with default parameters, the receptor file was constructed using the make-receptor file that was supplied in Fred. The receptor-centred docking box's volume was increased in all directions until it was roughly 31671 å3. The box's measurements were 28.10 å 32.91 å 34.25 å. A strong inhibitor against ASMT was obtained by docking ASMT with ligands conformer library using Fred with a gaussian type fitting score algorithm chemgauss4. The potentials between the chemically matching locations surrounding the ligand docked pose are used by chemgauss4. These chemical locations complement the receptor's adjacent specific groups. A favourable hydrogen bond score is achieved when a polar hydrogen site on one molecule overlaps a lone pair position on another molecule. Typically, the interactions are either hydrogen bond donors or acceptors. Steric, acceptor, donors, coordinating groups, metals, lone pairs, polar hydrogens, and chelator coordinating groups are among the interactions that can be scored using chemgauss functions. 26
ADVANTAGES
DISADVANTAGES
CONCLUSION
Docking study can include the preferred orientation of a molecule when bound to another molecule. This information can be used to predict the strength of the association between the two molecules.
REFRENCES
Bharathwaj J., Deepak Venkataraman N.*, Charumathi P., Lakshminarasimman S., Purushothaman V. M., Sudharsan S., An Overview of Basics, Types, Approaches, Applications, Advantages and Disadvantages of Docking, Int. J. of Pharm. Sci., 2025, Vol 3, Issue 3, 437-445. https://doi.org/10.5281/zenodo.14992121
10.5281/zenodo.14992121
