Ligand-protein docking with water molecules

The presence of water molecules plays an important role in the accuracy of ligand-protein docking predictions. Comprehensive docking simulations have been performed on a large set of ligand-protein complexes whose crystal structures contain water molecules in their binding sites. Only those water molecules found in the immediate vicinity of both the ligand and the protein were considered. We have investigated whether prior optimization of the orientation of water molecules in either the presence or absence of the bound ligand has any effect on the accuracy of docking predictions. We have observed a statistically significant overall increase in accuracy when water molecules are included during docking simulations and have found this to be independent of the method of optimization of the orientation of water molecules. These results confirm the importance of including water molecules whenever possible in a ligand-protein docking simulation. Our findings also reveal that prior optimization of the orientation of water molecules, in the absence of any bound ligand, does not have a detrimental effect on the improved accuracy of ligand-protein docking. This is important, given the use of docking simulations to predict the binding modes of new ligands or drug molecules.     

Molecular docking with ligand attached water molecules

A novel approach to incorporate water molecules in protein-ligand docking is proposed. In this method, the water molecules display the same flexibility during the docking simulation as the ligand. The method solvates the ligand with the maximum number of water molecules, and these are then retained or displaced depending on energy contributions during the docking simulation. Instead of being a static part of the receptor, each water molecule is a flexible on/off part of the ligand and is treated with the same flexibility as the ligand itself. To favor exclusion of the water molecules, a constant entropy penalty is added for each included water molecule. The method was evaluated using 12 structurally diverse protein-ligand complexes from the PDB, where several water molecules bridge the ligand and the protein. A considerable improvement in successful docking simulations was found when including flexible water molecules solvating hydrogen bonding groups of the ligand. The method has been implemented in the docking program Molegro Virtual Docker (MVD).     

An anchor-dependent molecular docking process for docking small flexible molecules into rigid protein receptors

A molecular docking method designated as ADDock, anchor- dependent molecular docking process for docking small flexible molecules into rigid protein receptors, is presented in this article. ADDock makes the bond connection lists for atoms based on anchors chosen for building molecular structures for docking small flexible molecules or ligands into rigid active sites of protein receptors. ADDock employs an extended version of piecewise linear potential for scoring the docked structures. Since no translational motion for small molecules is implemented during the docking process, ADDock searches the best docking result by systematically changing the anchors chosen, which are usually the single-edge connected nodes or terminal hydrogen atoms of ligands. ADDock takes intact ligand structures generated during the docking process for computing the docked scores; therefore, no energy minimization is required in the evaluation phase of docking. The docking accuracy by ADDock for 92 receptor-ligand complexes docked is 91.3%. All these complexes have been docked by other groups using other docking methods. The receptor-ligand steric interaction energies computed by ADDock for some sets of active and inactive compounds selected and docked into the same receptor active sites are apparently separated. These results show that based on the steric interaction energies computed between the docked structures and receptor active sites, ADDock is able to separate active from inactive compounds for both being docked into the same receptor.     

Comparing ligand interactions with multiple receptors via serial docking

Standard uses of ligand-receptor docking typically focus on the association of candidate ligands with a single targeted receptor, but actual applications increasingly require comparisons across multiple receptors. This study demonstrates that comparative docking to multiple receptors can help to select homology models for virtual compound screening and to discover ligands that bind to one set of receptors but not to another, potentially similar, set. A serial docking algorithm is furthermore described that reduces the computational costs of such calculations by testing compounds against a series of receptor structures and discarding a compound as soon as it fails to satisfy specified bind/no bind criteria for each receptor. The algorithm also realizes substantial efficiencies by taking advantage of the fact that a ligand typically binds in similar conformations to similar receptors. Thus, once detailed docking has been used to fit a ligand into the first of a series of similar receptors, much less extensive calculations can be used for the remaining structures.     

Polymer and organic molecules ordered via epitaxy: geometrical and molecular interactions

Control of structural order at the molecular level for both conventional linear polymers and conjugated polymers with valuable opto‐electronic properties has major consequence on the macroscopic properties of these polymers. Though the traditional means of orientation of polymer was mechanical deformation, presently extensive works are concerned with a more controlled way of orientation: epitaxial crystallisation. Most of the first documented examples of epitaxial growth of conventional polymers on single crystals followed the well‐established geometrical rules of best matching. However, recent examples show off more subtle rules of selection. Analogous cases, following or breaking the matching rules, have been observed for diacetylenes ordered via epipolymerisation on single crystals. Hereafter, representative examples of the structural matching rules are depicted first, and then recent examples, which depart from the simple geometrical fitting, are described. The analysis of the former leads to define the subtle matching rules applying for polymers linked to their conformational adaptability. The analysis of the latter gives the opportunity to discuss the relative influence of geometrical and molecular interactions between the deposit and the substrate.     

ELECT++: Faster conformational search method for docking flexible molecules using molecular similarity

We have developed a program, ELECT++ (Effective LEssening of Conformations by Template molecules in C++), to speed up the conformational search for small flexible molecules using the similar property principle. We apply this principle to molecular shape and, importantly, to molecular flexibility. After molecules in a database are clustered according to flexibility and shape (FCLUST++), additional reagents are generated to screen the conformational space of molecules in each cluster (TEMPLATE++). We call these representative reagents of each cluster template reagents. Template reagents and clustered reagents produce, after reaction, template molecules and clustered molecules, respectively (tREACT++). The conformations of a template molecule are searched in the context of a macromolecular target. Acceptable conformational choices are then applied to all molecules in its cluster, thus effectively biasing conformational space to speed up conformational searches (tSEARCH++). In our incremental search method, it is necessary to calculate the root-mean-square deviations (RMSD) matrix of distances between different conformations of the same molecule to reduce the number of conformations. Instead of calculating the RMSD matrix for all molecules in a cluster, the RMSD matrix of a template molecule is chosen as a reference and applied to all the molecules in its cluster. We demonstrate that FCLUST++ clusters the primary amine reagents from the Available Chemicals Directory (ACD) successfully. The program tSEARCH++ was applied to dihydrofolate reductase with virtual molecules generated by tREACT++ using clustered primary amine reagents. The conformational search by the program tSEARCH++ was about 4.8 times faster than by SEARCH++, with an acceptable range of errors. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1834–1852, 1998     

Mutation effects of neuraminidases and their docking with ligands: a molecular dynamics and free energy calculation study

A systematic study has been performed on neuraminidase (NA) mutations and NA-inhibitor docked complexes, with the aim to understand protein–ligand interactions and design broad-spectrum antiviral drugs with minimal resistances. The catalytic D151 residue is likely to mutate while others are relatively conserved. The NA active-site conformations are altered by mutations, but more alterations do not necessarily result in larger deviations to the binding properties. The effects of all related mutations have been discussed; e.g., for the arginine triad (R118, R292 and R371), it is found that residue R118 plays the most significant role during ligand binding. Generally, the calculated binding free energies agree well with the experimental observations. Susceptibility of influenza virus to NA inhibitors can be reinforced by some mutations; e.g., the binding free energies of ligands with N2 subtype increase from ?18.0 to ?42.1 kcal mol^?1 by the E119D mutation. Mutations of the various NA subtypes often cause similar conformational and binding changes, explaining the occurrence of cross resistances; nonetheless, differences can be detected in some cases that correspond to subtype-specific resistances. For all NA subtypes, the electrostatic contributions are the major driving force for ligand binding and largely responsible for the binding differences between the wild-type and mutated NA proteins.     

Organoruthenium (II) complexes featuring pyrazole‐linked Schiff base ligands: Crystal structure,DNA/BSA interactions,cytotoxicity and molecular docking

Half‐sandwiched ruthenium (II) arene complexes with piano stool‐like geometry with the general formula [(p‐cymene)RuClL¹] and [(p‐cymene)RuClL²] [where L¹ = (Z)‐N′‐((1,3‐diphenyl‐1H‐pyrazol‐4‐yl)methylene)furan‐2‐carbohydrazide and L² = (Z)‐N′‐((1,3‐diphenyl‐1H‐pyrazol‐4‐yl)methylene)thiophene‐2‐carbohydrazide] were synthesized and characterized. The single crystal X‐ray data revealed that the complexes belong to the same crystal system (monoclinic) with octahedral geometry, where the ruthenium atom is surrounded by hydrazone ligand coordinated through ON atoms, one chloride labile co‐ligand and the remaining three coordination sites covered by an electron cloud of p‐cymene moiety. The interaction between the complexes and DNA/bovine serum albumin (BSA) was evaluated using absorption and emission titration methods showing intercalative modes of interaction. The DNA cleavage ability of the complexes was checked by agarose gel electrophoresis method exhibiting the destruction of DNA duplex arrangement. To understand the interaction between ruthenium complex and DNA/BSA molecule, molecular docking studies were performed. In vitro cytotoxicity of the complexes was examined by the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) assay on human lung cancer cell line, A549, and found that at lower IC₅₀, cell growth inhibition has occurred. Similarly, the IC₅₀ values of the complexes treated with cancerous cell lines have produced a significant amount of lactase dehydrogenase and nitrite content in the culture medium, which were evaluated as apoptosis‐inducing factors, suggesting that the ruthenium (II) arene hydrazone complexes with pyrazole ligands have promising anticancer activities.     

Comparison of clinically approved molecules on SARS-CoV-2 drug target proteins: a molecular docking study

The new type of coronavirus, SARS-CoV-2 has affected more than 22.6 million people worldwide. Since the first day the virus was spotted in Wuhan, China, numerous drug design studies have been conducted all over the globe. Most of these studies target the receptor-binding domain of spike protein of SARS-CoV-2, which is known to bind to the human ACE2 receptor and SARS-CoV-2 main protease, vital for the virus’ replication. However, there might be a third target, human furin protease, which cleaves the virus’ S1-S2 domains playing an active role in its entry into the host cell. In this study, we docked five clinically used drug molecules, favipiravir, hydroxychloroquine, remdesivir, lopinavir, and ritonavir onto three target proteins, the receptor-binding domain of SARS-CoV-2 spike protein, SARS-CoV-2 main protease, and human furin protease. Results of molecular docking simulations revealed that human furin protease might be targeted by COVID-19. Remdesivir, a nucleic acid derivative, strongly bound to the active site of this protease, suggesting that this molecule can be used as a template for designing novel furin protease inhibitors to fight against the disease. Protein-drug interactions revealed in this study at the molecular level, can pave the way for better drug design for each specific target.     

Tripod molecules build molecular networks and open-dimer capsules by weak interactions

Three tripod molecules, tris(2-methoxy-5-nitrobenzyl)phosphine oxide (1), tris(2-butoxy-3-methyl-5-nitrobenzyl)phosphine oxide (2), and tris(3-nitrobenzyl)amine (TNBA), were synthesized and crystallized. The structures of 1, 2, and their comparison (TNBA) were determined by X-ray crystallography. It is noteworthy that compound 1 interacted with adjacent molecules via π-π stacking and C-H···π interactions to yield an open supramolecular network with the porosity P in 8.9%, whereas compound 2 gathered closely...     

A computational study of interactions between acetic acid and water molecules

Density functional theory calculations were performed for the title reactions to elucidate the difference between the strong cyclic hydrogen bond of (Me-COOH)(2) and the electrolytic dissociation, MeCOOH <==> Me-COO(-) + H(+), as a weak acid. The association of water clusters with acetic acid dimers strengthens the cyclic hydrogen bond. A nucleophilic attack of the carboxylic carbon by a water cluster leads to a first zwitterionic intermediate, MeCOO(-) + H(3)O(+) + (HO)(3)C-Me. The intermediate is unstable and is isomerized to a neutral interacting system, MeCOOH...(HO)(3)C-Me + H(2)O. The ethanetriol, (HO)(3)-CMe is transformed to an acetic acid monomer. The monomer may be dissociated to give a second zwitterionic intermediate with reasonable proton-relay patterns and energy changes. In proton relay reaction channels, H in MeCOOH is not an acidic proton but is always a hydroxy proton.     

Predicting conformations and orientations of guests within a water soluble host: a molecular docking approach

In this study we have examined conformations and orientations of guests within a water-soluble host known by the trivial name Octa Acid (OA). Docking program Vina, which was originally developed for screening drug-like molecules, has been used to identify binding modes and affinities of select guest molecules with OA. Hydrophobic guests were encapsulated into the nonpolar cavity of OA capsule owing to solvophobic interactions. Amphiphilic guests were bound by keeping the nonpolar part within the cavity of OA, while pointing the polar anionic group out of the cavity. All these results obtained from the docking study were in accord with experimental findings. The post-complexation attributes of the guests were regulated by available free space and the specific interactions between guest–OA pair, which led to unusual conformations and orientations. This study showed that scoring function available with Vina, which was derived from protein–ligand data set, could successfully predict post-complexed structural features of guests within OA, thus opening opportunities to modulate physical and chemical behavior of guest molecules.     

Theoretical treatment of multiple site reactivity in large molecules

The method of electrostatic potentials is generalized via a double perturbation theory to describe the simultaneous attack of a large molecule by two or more charged species. The interaction term is found to reproduce accurately the full “super-molecule” calculation. The scheme is illustrated by treating the diprotonation of adenine and N7-methyladenine. For adenine, the most stable diprotonated species is found to be the N1, N7 combination, while the N3, N9 couple is predicted for the N7 substituted derivative if N3 is the first protonation site.     

A general synthetic route for the preparation of high-spin molecules: Replacement of bridging hydroxo ligands in molecular clusters by end-on azido ligands

A general method of increasing the ground-state total spin value of a polynuclear 3d-metal complex is illustrated through selected examples from cobalt(II) and nickel(II) cluster chemistry that involves the dianion of the gem-diol form of di-2-pyridyl ketone and carboxylate ions as organic ligands. The approach is based on the replacement of hydroxo bridges, that most often propagate antiferromagnetic exchange interactions, by the end-on azido ligand, which is a ferromagnetic coupler.     

Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach

A combined molecular dynamics simulation and multiple ligand docking approach is applied to study the binding specificity of acetylcholinesterase (AChE) with its natural substrate acetylcholine (ACh), a family of substrate analogues, and choline. Calculated docking energies are well correlated to experimental k(cat)/K(M) values, as well as to experimental binding affinities of a related series of TMTFA inhibitors. The "esteratic" and "anionic" subsites are found to act together to achieve substrate binding specificity. We find that the presence of ACh in the active site of AChE not only stabilizes the setup of the catalytic triad but also tightens both subsites to achieve better binding. The docking energy gained from this induced fit is 0.7 kcal/mol for ACh. For the binding of the substrate tailgroup to the anionic subsite, both the size and the positive charge of the tailgroup are important. The removal of the positive charge leads to a weaker binding of 1 kcal/mol loss in docking energy. Substituting each tail methyl group with hydrogen results in both an incremental loss in docking energy and also a decrease in the percentage of structures docked in the active site correctly set up for catalysis.     

Unsupervised guided docking of covalently bound ligands

Summary An approach for docking covalently bound ligands in protein enzymes or receptors was implemented in MacDOCK, a similarity-driven docking program based on DOCK 4.0. This approach was tested with a small number of covalent ligand–protein structures, using both native and non-native protein structures. In all cases, MacDOCK was able to generate orientations consistent with the known covalent binding mode of these complexes, with a performance similar to that of other docking programs. This method was also applied to search for known covalent thrombin inhibitors in a medium-sized molecular database (ca. 11,000 compounds). Detection of functional groups suitable for covalent docking was carried out automatically. A significant enrichment in known active molecules in the first 5% of the database was obtained, showing that MacDOCK can be used efficiently for the virtual screening of covalently bound ligands.