Molecular modelling of the differential interaction between several non-steroidal anti-inflammatory drugs and human prostaglandin endoperoxide H synthase-2 (h-PGHS-2)

The prostaglandin endoperoxide H synthase-1 (PGHS-1) and prostaglandin endoperoxide H synthase-2 (PGHS-2) are the targets of non-steroidal anti-inflammatory drugs (NSAIDs). The high degree of selectivity for inhibition of PGHS-2 shown by certain compounds appears to stem from two mechanisms (time-dependent, time-independent inhibition) by which they interact with each isoform. Molecular models of the complexes between indomethacin, fenamates, 2-phenylpropionic acids and the selective cyclooxygenase-2 (COX-2) inhibitors, with the cyclooxygenase active site of human PGHS-2 have been built by combining homology modelling, conformational searching and automated docking techniques. The stability of the resulting complexes has been assessed by molecular dynamics simulations combined with extended linear response calculations. The results allow us to identify regions of biological significance consistent with both X-ray crystallographic and kinetic results. The selective PGHS-2 inhibitors exploit the extra space of a side-pocket in the active site of PGHS-2 that is not found in PGHS-1. The results obtained point out a marked relationship between the experimental affinity and the electrostatic interaction energy alone for a series of NSAIDs. Analysis of the structural and the energetic data provides evidence supporting that network of hydrogen bonds between Tyr355, Glu524, Arg120 and Arg513 might be involved in mediating the binding of the time-dependent inhibitors of PGHS-2.     

新型二芳基取代-1,2,4-三唑类化合物的抗炎构效关系和分子对接研究

目的:建立新型二芳基取代-1,2,4-三唑类化合物的定量构效关系,设计新型COX-2抑制剂.方法:采用PM3半经验量子化学法全优化18种二芳基取代-1,2,4-三唑类选择性环氧合酶(COX-2)抑制剂的结构,从数据中搜寻或计算它们的226种参数,利用逐步回归法,建立经典结构-活性关系(2D-QSAR);用Autodock对接软件研究二芳基取代-1,2,4-三唑类化合物与环氧合酶(COX-2)的对接,分析该类化合物与环氧合酶在复合物的立体结构以及分子对接自由能与抑制活性的关系.结果:建立合理二芳基取代-1,2,4-三唑类化合物COX-2抑制剂定量构效关系,表明活性二芳基取代-1,2,4-三唑类选择性环氧合酶(COX-2)抑制剂具有类似塞来昔布等三环类环氧合酶-2抑制剂的立体结构,并且对接自由能与抑制剂活性有较好的相关性.结论:所得的模型可以解释已有的构效关系,而且预测同类化合物能力较好,可指导设计新抑制剂.     

The structure of human serotonin 2c G-protein-coupled receptor bound to agonists and antagonists

We used the MembStruk computational procedure to predict the three-dimensional (3D) structure for the serotonin 5-HT_2C G-protein-coupled receptor (GPCR). Using this structure, we used the MSCDock computational procedure to predict the 3D structures for bound ligand–protein complexes for agonists such as serotonin and antagonists such as ritanserin, metergoline, and methiothepin. In addition, we predicted the SAR data for a series of psilocybin analogs, both agonists and antagonists. We performed molecular dynamics (MD) on serotonin bound to 5-HT_2C and we find the protein and binding site to be stable after 5 ns. We find good agreement with the currently known experimental data and we predict a number of new mutations which could be used to validate further our predicted structures. This agreement between theory and experiment suggests that our 3D structure is sufficiently accurate for use in drug design. We also compare a preliminary prediction for 5-HT_2B with our prediction for 5-HT_2C and find a difference in TM5 that contributes to different serotonin binding modes in 5-HT_2B and 5-HT_2C.     

A CoMFA study of COX-2 inhibitors with receptor based alignment

A diverse set of 53 cyclooxygenase-2 (COX-2) inhibitors which were aligned in two different ways were subjected to CoMFA analysis. The first method of alignment of the molecules was based on the binding information sourced from the crystallographic study, from which CoMFA Model 1 was derived. The second mode of alignment was generated by docking the inhibitors in the binding pocket using the DOCK and AFFINITY suite of programs; this gave a second model. The CoMFA Model 2 was slightly better than Model 1 in terms of the statistical parameters r(2) and q(2). The two models could predict very well the activity of a test set of diverse molecules, with a predictive r(2) of 0.593 and 0.768, respectively. Besides the QSAR results, the docking studies give a deep insight into the H-bonding interactions between the inhibitors and residues in the active site of the enzyme, which can be exploited in designing better inhibitors. Useful ideas on activity improvement could be gleaned from these models.     

Differential binding mode of diverse cyclooxygenase inhibitors

Non-steroidal anti-inflammatory drugs (NSAIDs) are competitive inhibitors of cyclooxygenase (COX), the enzyme that mediates biosynthesis of prostaglandins and thromboxanes from arachidonic acid. There are at least two different isoforms of the enzyme known as COX-1 and -2. Site directed mutagenesis studies suggest that non-selective COX inhibitors of diverse chemical families exhibit differential binding modes to the two isozymes. These results cannot clearly be explained from the sole analysis of the crystal structures of COX available from X-ray diffraction studies. With the aim to elucidate the structural features governing the differential inhibitory binding behavior of these inhibitors, molecular modeling studies were undertaken to generate atomic models compatible with the experimental data available. Accordingly, docking of different COX inhibitors, including selective and non-selective ligands: rofecoxib, ketoprofen, suprofen, carprofen, zomepirac, indomethacin, diclofenac and meclofenamic acid were undertaken using the AMBER program. The results of the present study provide new insights into a better understanding of the differential binding mode of diverse families of COX inhibitors, and are expected to contribute to the design of new selective compounds.     

Analysis of CYP2D6 substrate interactions by computational methods

Cytochrome P450 CYP2D6 is involved in the oxidation of well over 150 drugs and, in general, those which contain a basic nitrogen atom in the molecule. To clarify how the residues of CYP2D6 are utilized for orientating a wide range of its specific substrates and distinguishing them from a variety of other organic compounds, docking studies by AutoDock and molecular dynamics (MD) simulations were conducted. Specific ligands were docked to both the homology model and crystal structures optimally to estimate the site of reaction on the ligand molecule and the binding energy for the complex, which were generally in good agreement with the experimental data. MD simulation for the CYP2D6-propranolol complex was then carried out to reveal the amino acid residues interacting with the substrate at the active site. Phe-120, Glu-216, Asp-301, and Phe-483 are identified as the substrate-binding residues in agreement with previously reported site-directed mutagenesis data and the crystal structure reported recently (PDB code: 2F9Q). As well as these residues, our theoretical prediction suggests that Phe-219 and Glu-222 are also important residues for mediating oxidation of substrates, especially propranolol.     

Toward the three-dimensional structure and lysophosphatidic acid binding characteristics of the LPA4/p2y9/GPR23 receptor: A homology modeling study

Lysophosphatidic acid (LPA) is a naturally occurring phospholipid that initiates a broad array of biological processes, including those involved in cell proliferation, survival and migration via activation of specific G protein-coupled receptors located on the cell surface. To date, at least five receptor subtypes (LPA_1–5) have been identified. The LPA_1–3 receptors are members of the endothelial cell differentiation gene (Edg) family. LPA₄, a member of the purinergic receptor family, and the recently identified LPA₅ are structurally distant from the canonical Edg LPA_1–3 receptors. LPA₄ and LPA₅ are linked to G_q, G_12/13 and G_s but not G_i, while LPA_1–3 all couple to G_i in addition to G_q and G_12/13. There is also evidence that LPA₄ and LPA₅ are functionally different from the Edg LPA receptors. Computational modeling has provided useful information on the structure–activity relationship (SAR) of the Edg LPA receptors. In this work, we focus on the initial analysis of the structural and ligand-binding properties of LPA₄, a prototype non-Edg LPA receptor. Three homology models of the LPA₄ receptor were developed based on the X-ray crystal structures of the ground state and photoactivated bovine rhodopsin and the recently determined human β₂-adrenergic receptor. Docking studies of LPA in the homology models were then conducted, and plausible LPA binding loci were explored. Based on these analyses, LPA is predicted to bind to LPA₄ in an orientation similar to that reported for LPA_1–3, but through a different network of hydrogen bonds. In LPA_1–3, the ligand polar head group is reported to interact with residues at positions 3.28, 3.29 and 7.36, whereas three non-conserved amino acid residues, S114(3.28), T187(EL2) and Y265(6.51), are predicted to interact with the polar head group in the LPA₄ receptor models.     

Insight into structural and biochemical determinants of substrate specificity of PFI1625c: Correlation analysis of protein-peptide molecular models

Bioinformatics and sequence comparison indicate PFI1625c as a putative metalloprotease present in plasmodium genome. The structure of PFI1625c consists of two domains with nearly identical folding topology. The active site of PFI1625c is located in a large central cavity between the two domains. Substrate binding regions of PFI1625c are lined by E-136, D-140 which provides negatively charged patches whereas F-53 facilitates binding of bulky hydrophobic residues of substrates. Probing PFI1625c active site with 199 different peptides from a combinatorial peptide library indicates preference of PFI1626c toward hydrophobic residue substituted peptides. Correlation analysis of each position of the peptide indicates that Ser 2 is the most crucial residue and no significant improvement was observed until it is mutated to a hydrophobic residue. The peptide P550 (LVIVAKRA) exhibits significantly better interaction within the active site than a template peptide (LSRVAKRA). The molecular dynamic's simulation studies confirms integrity of the complex, with all structures well within the qualitative limit of compactness and stability during the simulation time. There are structural and biochemical differences between PFI1625c with human metalloprotease and these are sufficient enough to allow us to exploit PFI1625c as drug targets. These computationally obtained insights provided clues about substrate selectivity in PFI1625c and it can be used to exploit PFI1625c as a target for future anti-malarial development.     

External and internal electrostatic potentials of cholinesterase models

The electrostatic potentials for the three-dimensional structures of cholinesterases from various species were calculated, using the Delphi algorithm, on the basis of the Poisson–Boltzmann equation. We used structures for Torpedo californica and mouse acetylcholinesterase, and built homology models of the human, Bungarus fasciatus, and Drosophila melanogaster acetylcholinesterases and human butyrylcholinesterase. All these structures reveal a negative external surface potential, in the area around the entrance to the active-site gorge, that becomes more negative as the rim of the gorge is approached. Moreover, in all cases, the potential becomes increasingly more negative along the central axis running down the gorge, and is largest at the base of the gorge, near the active site. Ten key acidic residues conserved in the sequence alignments of AChE from various species, both in the surface area near the entrance of the active-site gorge and at its base, appear to be primarily responsible for these potentials. The potentials are highly correlated among the structures examined, down to sequence identities as low as 35%. This indicates that they are a conserved property of the cholinesterase family, could serve to attract the positively charged substrate into and down the gorge to the active site, and may play other roles important for cholinesterase function.     

Effects of protein flexibility on the site of metabolism prediction for CYP2A6 substrates

Structure-based prediction for the site of metabolism (SOM) of a compound metabolized by human cytochrome P450s (CYPs) is highly beneficial in drug discovery and development. However, the flexibility of the CYPs’ active site remains a huge challenge for accurate SOM prediction. Compared with other CYPs, the active site of CYP2A6 is relatively small and rigid. To address the impact of the flexibility of CYP2A6 active site residues on the SOM prediction for substrates, in this work, molecular dynamics (MD) simulations and molecular docking were used to predict the SOM of 96 CYP2A6 substrates. Substrates with known SOM were docked into the snapshot structures from MD simulations and the crystal structures of CYP2A6. Compared to the crystal structures, the protein structures obtained from MD simulations showed more accurate prediction for SOM. Our results indicated that the flexibility of the active site of CYP2A6 significantly affects the SOM prediction results. Further analysis for the 40 substrates with definite K_m values showed that the prediction accuracy for the low K_m substrates is comparable to that by ligand-based methods.     

Perspectives for the structure-based design of acetylcholinesterase reactivators

Rational design of active molecules through structure-based methods has been gaining adepts during the last decades due to the wider availability of protein structures, most of them conjugated with relevant ligands. Acetylcholinesterase (AChE) is a molecular target with a considerable amount of data related to its sequence and 3-dimensional structure. In addition, there are structural insights about the mechanism of action of the natural substrate and drugs used in Alzheimer’s disease, organophosphorus compounds, among others. We looked for AChE structural data useful for in silico design of potential interacting molecules. In particular, we focused on information regarding the design of ligands aimed to reactivate AChE catalytic activity. The structures of 178 AChE were annotated and categorized on different subsets according to the nature of the ligand, source organisms and experimental details. We compared sequence homology among the active site from Torpedo californica, Mus musculus and Homo sapiens with the latter two species having the closest relationship (88.9% identity). In addition, the mechanism of organophosphorus binding and the design of effective reactivators are reviewed. A curated data collection obtained with information from several sources was included for researchers working on the field. Finally, a molecular dynamics simulation with human AChE indicated that the catalytic pocket volume stabilizes around 600 ų, providing additional clues for drug design.     

Molecular modeling study on the effect of residues distant from the nucleotide-binding portion on RNA binding in Staphylococcus aureus Hfq

Hfq is an abundant RNA-binding bacterial protein that was first identified in E. coli as a required host factor for phage Qβ RNA replication. The pleiotrophic phenotype resulting from the deletion of Hfq predicates the importance of this protein. Two RNA-binding sites have been characterized: the proximal site which binds sRNA and mRNA and the distal site which binds poly(A) tails. Previous studies mainly focused on the key residues in the proximal site of the protein. A recent mutation study in E. coli Hfq showed that a distal residue Val43 is important for the protein function. Interestingly, when we analyzed the sequence and structure of Staphylococcus aureus Hfq using the CONSEQ server, the results elicited that more functional residues were located far from the nucleotide-binding portion (NBP). From the analysis seven individual residues Asp9, Leu12, Glu13, Lys16, Gln31, Gly34 and Asp40 were selected to investigate the conformational changes in Hfq–RNA complex due to point mutation effect of those residues using molecular dynamics simulations. Results showed a significant effect on Asn28 which is an already known highly conserved functionally important residue. Mutants D9A, E13A and K16A depicted effects on base stacking along with increase in RNA pore diameter, which is required for the threading of RNA through the pore for the post-translational modification. Further, the result of protein stability analysis by the CUPSAT server showed destabilizing effect in the most mutants. From this study we characterized a series of important residues located far from the NBP and provide some clues that those residues may affect sRNA binding in Hfq.     

Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction

The structural features of helical transmembrane (TM) proteins, such as helical kinks, tilts, and rotational orientations are important in modulation of their function and these structural features give rise to functional diversity in membrane proteins with similar topology. In particular, the helical kinks caused by breaking of the backbone hydrogen bonds lead to hinge bending flexibility in these helices. Therefore it is important to understand the nature of the helical kinks and to be able to reproduce these kinks in structural models of membrane proteins. We have analyzed the position and extent of helical kinks in the transmembrane helices of all the crystal structures of membrane proteins taken from the MPtopo database, which are about 405 individual helices of length between 19 and 35 residues. 44% of the crystal structures of TM helices showed a significant helical kink, and 35% of these kinks are caused by prolines. Many of the non-proline helical kinks are caused by other residues like Ser and Gly that are located at the center of helical kinks. The side chain of Ser makes a hydrogen bond with the main chain carbonyl of the i − 4th or i + 4th residue thus making a kink. We have also studied how well molecular dynamics (MD) simulations on isolated helices can reproduce the position of the helical kinks in TM helices. Such a method is useful for structure prediction of membrane proteins. We performed MD simulations, starting from a canonical helix for the 405 TM helices. 1 ns of MD simulation results show that we can reproduce about 79% of the proline kinks, only 59% of the vestigial proline kinks and 18% of the non-proline helical kinks. We found that similar results can be obtained from choosing the lowest potential energy structure from the MD simulation. 4–14% more of the vestigial prolines were reproduced by replacing them with prolines before performing MD simulations, and changing the amino acid back to proline after the MD simulations. From these results we conclude that the position of the helical kinks is dependent on the TM sequence. However the extent of helical kinking may depend on the packing of the rest of the protein and the lipid bilayer.     

Molecular modeling of the catalytic domain of serine/threonine phosphatase-1 with the Zn2+ and Mn2+ di-nuclear ion centers in the active site

Catalytic domains of the metalloenzymes protein phosphatases (PPP) 1, 2A and 2B (PP1, PP2A and PP2B, respectively) are homologous to approximately 45%, with the residues in the enzymatic centers strictly conserved. PP1, PP2A and PP2B are abundant in cells and they dephosphorylate serine and/or threonine residues in a variety of proteins serving as cellular phospho switches. The active enzymes work as invariant catalytic subunits PP1c, PP2Ac and PP2Bc, respectively, complexed with diverse regulatory subunits, dependent on the enzymes' specific location and biological function. The crystal structures of PP1c and PP2B (calcineurin) heterotetramer calcineurinA x calcineurinB x FKBP x FK506 have been determined. A comparison of the catalytic subunits of both enzymes indicates their significant structural homology and virtual identity within the catalytic centers, each including a set of conservative amino acids, two metal ions and a phosphate; thus confirming a hypothesis on their common enzymatic mechanisms. The elongated substrate cleft at the active centre is kinked by approximately 120 degrees at the active center in its middle and thus divided into a pre-phospho-Ser/Thr (ligand N-terminal) and a post-phospho-Ser/Thr (ligand C-terminal) section. In PP1c the N-terminal section is highly acidic while in PP2Bc is not. This feature is likely pertinent but not sufficient to the enzymes' selectivity, which is also controlled by regulatory subunits, diverse in various tissues. The metalloenzymes in general and PPP in particular are hard to deal with using theoretical simulations due to parameterization problems for the metal cations. In fact, there are only a few PP1c simulations reported, with the metal di-cations treated quite crudely. This is a preliminary work, in which we introduce and test against some experimental evidence a concept of pseudomolecules of proper geometry, composed of double metal (2Zn2+ or 2Mn2+) cation, and the OH- nuclephile incorporated into the PP1c catalytic site. Both models are associated with either the phosphate (a free enzyme) or the phosphorylated dodecapeptide RRRRPpTPAMLFR, an active fragment (residues 29-40) of a regulatory subunit DARPP-32 inhibitor (PP1c-inhibitor complex); four models total. We have parameterized both pseudomolecules within the AMBER force field. Subsequently, using molecular dynamic in water, we have found the free PP1c subunits to be less stable than the complexed ones and we have speculated on possible reasons for this feature.     

Structural determinants of the alpha2 adrenoceptor subtype selectivity

Alpha2-adrenergic receptor (α2-AR) subtypes, acting mainly on the central nervous and cardiovascular systems, represent important targets for drug design, confirmed by the high number of studies published so far. Presently, only a few α2-AR subtype selective compounds are known. Using homology modeling and ligand docking, the present study analyzes the similarities and differences between binding sites, and between extracellular loops of the three subtypes of α2-ARs. Several α2-AR subtype selective ligands were docked into the active sites of the three α2-AR subtypes, key interactions between ligands and receptors were mapped, and the predicted results were compared with the available experimental data. Binding site analysis reveals a strong identity between important amino acid residues in each receptor, the very few differences being the key toward modulating selectivity of α2-AR ligands. The observed differences between binding site residues provide an excellent starting point for virtual screening of chemical databases, in order to identify potentially selective ligands for α2-ARs.     

Arylhydrazone derivatives of naproxen as new analgesic and anti-inflammatory agents: Design,synthesis and molecular docking studies

A series of new arylidenehydrazone derivatives of naproxen were synthesized and evaluated for their analgesic and anti-inflammatory activities. Some of the synthesized analogues showed comparable activities when compared against naproxen for their analgesic and anti-inflammatory properties. 2-(6-methoxy-2-naphthyl)-N′-[(pyridine-4-yl)methylene]propanoic acid hydrazide 4j was found to be the most active analgesic agent. 2-(6-methoxy-2-naphthyl)-N′-[4-nitrobenzylidene]propanoic acid hydrazide 4g showed highest anti-inflammatory activity in comparison to the naproxen. Molecular modeling study of the synthesized compounds suggested that the designed molecules were well located and bound to the COX-1 and COX-2 active sites. Compound 4g showed the highest selectivity for COX-2 (R_{COX-2/COX-1 =} 1.94) and higher affinity rather than naproxen in COX-2 active site (R_{COX-2/naproxen =} 1.28). Moreover, the structural analyses confirmed that the E-ap rotamer is the preferred structure for the arylidenehydrazone derivatives.     

Prediction of three-dimensional structures and structural flexibilities of wild-type and mutant cytochrome P450 1A2 using molecular dynamics simulations

In this study, we investigated the effect of genetic polymorphism on the three-dimensional (3D) conformation of cytochrome P450 1A2 (CYP1A2) using molecular dynamics (MD) simulations. CYP1A2, a major drug-metabolizing enzyme among cytochrome P450 enzymes (CYPs), is known to have many variant alleles. The genetic polymorphism of CYP1A2 may cause individual differences in the pharmacokinetics of medicines. By performing 100 ns or longer MD simulations, we investigated the influence of amino acid mutation on the 3D structures and the dynamic properties of proteins. The results show that the static structures were changed by the mutations of amino acid residues, not only near the mutated residues but also in distant portions of the proteins. Moreover, the mutation of only one amino acid was shown to change the structural flexibility of proteins, which may influence the substrate recognition and enzymatic activity. Our results clearly suggest that it is necessary to investigate the dynamic property as well as the static 3D structure for understanding the change of the enzymatic activity of mutant CYP1A2.     

Effect of allosteric molecules on structure and drug affinity of HIV-1 protease by molecular dynamics simulations

Recent experiments show that small molecules can bind onto the allosteric sites of HIV-1 protease (PR), which provides a starting point for developing allosteric inhibitors. However, the knowledge of the effect of such binding on the structural dynamics and binding free energy of the active site inhibitor and PR is still lacking. Here, we report 200 ns long molecular dynamics simulation results to gain insight into the influences of two allosteric molecules (1H-indole-6-carboxylic acid, 1F1 and 2-methylcyclohexano, 4D9). The simulations demonstrate that both allosteric molecules change the PR conformation and stabilize the structures of PR and the inhibitor; the residues of the flaps are sensitive to the allosteric molecules and the flexibility of the residues is pronouncedly suppressed; the additions of the small molecules to the allosteric sites strengthen the binding affinities of 3TL-PR by about 12–15 kal/mol in the binding free energy, which mainly arises from electrostatic term. Interestingly, it is found that the action mechanisms of 1F1 and 4D9 are different, the former behaviors like a doorman that keeps the inhibitor from escape and makes the flaps (door) partially open; the latter is like a wedge that expands the allosteric space and meanwhile closes the flaps. Our data provide a theoretical support for designing the allosteric inhibitor.     

Structural insights into the camel milk lactoperoxidase: Homology modeling and molecular dynamics simulation studies

Lactoperoxodase (LPO) is a heme peroxidase enzyme present in mammalian milk. It is an antimicrobial protein with wide range of industrial applications. Although the three dimensional structure of LPO from various mammalian species has been reported, but its structure from camel source is still unknown. So far, the crystallization attempts have not been successful in determining camel LPO (cLPO) structure. Herein, we developed the three dimensional structure of cLPO by homology modeling approach using prime module available in Schrodinger suite. The developed model in complex with ligand hypothiocyanate (OSCN⁻) was further validated by Ramachandran plot followed by molecular dynamics (MD) simulation studies using Desmond module of Schrodinger. cLPO model exhibited overall structural similarity with template crystal structure, however, it displayed different interaction pattern of amino acid residues with ligand OSCN⁻ in comparison to template crystal structure. Moreover, the ligand binding site environment in cLPO is more polar, less hydrophobic, and harbours more number of charged residues than template crystal structure. The substrate binding pocket environment of cLPO shows a considerable difference from template crystal structure. This subsequently resulted in dissimilar behaviour of ligand during the course of MD simulation studies.     

An in silico approach to evaluate the polyspecificity of methionyl-tRNA synthetases

Residue-specific incorporation is a technique used to replace natural amino acids with their close structural analogs, unnatural amino acids (UAAs), during protein synthesis. This is achieved by exploiting the substrate promiscuity of the wild type amino acyl tRNA synthetase (AARS) towards the close structural analogs of their cognate amino acids. In the past few decades, seleno-methionine was incorporated into proteins, using the substrate promiscuity of wild type AARSs, to resolve their crystal structures. Later, the incorporation of many UAAs showed that the AARSs are polyspecific to the close structural analogs of their cognate amino acids and that they maintain fidelity for the 19 natural amino acids. This polyspecificity helps to expand the use of this powerful tool to incorporate various UAA residues specifically through in vivo and in vitro approaches. Incorporation of UAAs is expensive, tedious and time-consuming. For the efficient incorporation of UAAs, it is important to screen substrate selectivity prior to their incorporation. As an initial study, using a docking tool, we analyzed the polyspecificity of the methionyl-tRNA synthetases (MetRSs) towards multiple reported and virtually generated methionine analogs. Based on the interaction result of these docking simulations, we predicted the substrate selectivity of the MetRS and the key residues responsible for the recognition of methionine analogs. Similarly, we compared the active site residues of the MetRSs of different species and identified the conserved amino acids in their active sites. Given the close similarity in the active site residues of these systems, we evaluated the polyspecificity of MetRSs.