Molecular Docking for Ligand-Receptor Binding Process Based on Heterogeneous Computing

Molecular docking aims to predict possible drug candidates for many diseases, and it is computationally intensive. Particularly, in simulating the ligand-receptor binding process, the binding pocket of the receptor is divided into subcubes, and when the ligand is docked into all cubes, there are many molecular docking tasks, which are extremely time-consuming. In this study, we propose a heterogeneous parallel scheme of molecular docking for the binding process of ligand to receptor to accelerate simulating. The parallel scheme includes two layers of parallelism, a coarse-grained layer of parallelism implemented in the message-passing interface (MPI) and a fine-grained layer of parallelism focused on the graphics processing unit (GPU). At the coarse-grain layer of parallelism, a docking task inside one lattice is assigned to one unique MPI process, and a grouped master-slave mode is used to allocate and schedule the tasks. Meanwhile, at the fine-gained layer of parallelism, GPU accelerators undertake the computationally intensive computing of scoring functions and related conformation spatial transformations in a single docking task. The results of the experiments for the ligand-receptor binding process show that on a multicore server with GPUs the parallel program has achieved a speedup ratio as high as 45 times in flexible docking and as high as 54.5 times in semiflexible docking, and on a distributed memory system, the docking time for flexible docking and that for semiflexible docking gradually decrease as the number of nodes used in the parallel program gradually increases. The scalability of the parallel program is also verified in multiple nodes on a distributed memory system and is approximately linear.

Exploring aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction: an in silico study

Some of the main challenges faced in drug discovery are pocket flexibility and binding mode prediction. In this work, we explored the aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction by means of in silico approaches. We first investigated the Spindlin1 aromatic cage plasticity by analyzing the available crystal structures and through molecular dynamic simulations. Then we assessed the ability of rigid docking and flexible docking to rightly reproduce the binding mode of a known ligand into Spindlin1, as an example of a reader protein displaying flexibility in the binding pocket. The ability of induced fit docking was further probed to test if the right ligand binding mode could be obtained through flexible docking regardless of the initial protein conformation. Finally, the stability of generated docking poses was verified by molecular dynamic simulations. Accurate binding mode prediction was obtained showing that the herein reported approach is a highly promising combination of in silico methods able to rightly predict the binding mode of small molecule ligands in flexible binding pockets, such as those observed in some reader proteins.

Structural and functional insights into esterase-mediated macrolide resistance

Macrolides are a class of antibiotics widely used in both medicine and agriculture. Unsurprisingly, as a consequence of their exensive usage a plethora of resistance mechanisms have been encountered in pathogenic bacteria. One of these resistance mechanisms entails the enzymatic cleavage of the macrolides’ macrolactone ring by erythromycin esterases (Eres). The most frequently identified Ere enzyme is EreA, which confers resistance to the majority of clinically used macrolides. Despite the role Eres play in macrolide resistance, research into this family enzymes has been sparse. Here, we report the first three-dimensional structures of an erythromycin esterase, EreC. EreC is an extremely close homologue of EreA, displaying more than 90% sequence identity. Two structures of this enzyme, in conjunction with in silico flexible docking studies and previously reported mutagenesis data allowed for the proposal of a detailed catalytic mechanism for the Ere family of enzymes, labeling them as metal-independent hydrolases. Also presented are substrate spectrum assays for different members of the Ere family. The results from these assays together with an examination of residue conservation for the macrolide binding site in Eres, suggests two distinct active site archetypes within the Ere enzyme family.

Allergen fragrance molecules: a potential relief for COVID-19

Background The latest coronavirus SARS-CoV-2, discovered in China and rapidly spread Worldwide. COVID-19 affected millions of people and killed hundreds of thousands worldwide. There are many ongoing studies investigating drug(s) suitable for preventing and/or treating this pandemic; however, there are no specific drugs or vaccines available to treat or prevent SARS-CoV-2 as of today. Methods Fifty-eight fragrance materials, which are classified as allergen fragrance molecules, were selected and used in this study. Docking simulations were carried out using four functional proteins; the Covid19 Main Protase (MPro), Receptor binding domain (RBD) of spike protein, Nucleocapsid, and host Bromodomain protein (BRD2), as target macromolecules. Three different software, AutoDock, AutoDock Vina (Vina), and Molegro Virtual Docker (MVD), running a total of four different docking protocol with optimized energy functions were used. Results were compared with the five molecules reported in the literature as potential drugs against COVID-19. Virtual screening was carried out using Vina, molecules satisfying our cut-off (− 6.5 kcal/mol) binding affinity was confirmed by MVD. Selected molecules were analyzed using the flexible docking protocol of Vina and AutoDock default settings. Results Ten out of 58 allergen fragrance molecules were selected for further docking studies. MPro and BRD2 are potential targets for the tested allergen fragrance molecules, while RBD and Nucleocapsid showed weak binding energies. According to AutoDock results, three molecules, Benzyl Cinnamate, Dihydroambrettolide, and Galaxolide, had good binding affinities to BRD2. While Dihydroambrettolide and Galaxolide showed the potential to bind to MPro, Sclareol and Vertofix had the best calculated binding affinities to this target. When the flexible docking results analyzed, all the molecules tested had better calculated binding affinities as expected. Benzyl Benzoate and Benzyl Salicylate showed good binding affinities to BRD2. In the case of MPro, Sclareol had the lowest binding affinity among all the tested allergen fragrance molecules. Conclusion Allergen fragrance molecules are readily available, cost-efficient, and shown to be safe for human use. Results showed that several of these molecules had comparable binding affinities as the potential drug molecules reported in the literature to target proteins. Thus, these allergen molecules at correct doses could have significant health benefits.

Modeling and docking studies of Keratinase from Bacillus Tequilensis MBR 25 against CYP51A of Aspergillus ৒lavus for inhibition: Insilico studies

Aspergillus flavus, which are common types of 'weedy' molds that are typically distributed in nature, are formed by aflatoxins. The existence of these molds does not always show that the aflatoxin levels are dangerous but shows an important danger. The molds may colonize and contaminate food before harvest or during storage, especially after prolonged exposure to high moisture or too stressful conditions such as dryness. Using 5EQB as a template for Modeler 9v7, a three-dimensional model of CYP51A from Aspergillus flavus was developed. After energy reduction, the structures of CYP51A 3D were compared with the prototype, and the final models were obtained using molecular mechanics and molecular dynamic methods. For flexible docking tests, a highly expressed CYP51A with keratinase from Bacillus tequilensis MBR 25 was used. The results showed that the LEU126, ALA153 and ILE165 binding steps of CYP51A are important determinant residues because hydrogen is closely linked to these compounds. These interactions with hydrogen bonding play an important role in stabilizing the complex.

In Silico Exploration of Efficacious Inhibitors for SARS-CoV-2’s Papain-like Protease

We applied the flexible docking method to rank-order all FDA-approved drugs as inhibitors for the papain-like protease (PLpro) of SRAS-CoV-2. We also evaluated these results using molecular dynamics (MD) simulations. From MD simulations, we unveiled the molecular mechanism for a known inhibitor rac5c's binding with PLpro. <br>

In Silico Exploration of Efficacious Inhibitors for SARS-CoV-2’s Papain-like Protease

We applied the flexible docking method to rank-order all FDA-approved drugs as inhibitors for the papain-like protease (PLpro) of SRAS-CoV-2. We also evaluated these results using molecular dynamics (MD) simulations. From MD simulations, we unveiled the molecular mechanism for a known inhibitor rac5c's binding with PLpro. <br>

Allergen Fragrance Molecules: A Potential Relief for COVID-19

Background: The latest coronavirus SARS-CoV-2, discovered in China and rapidly spread Worldwide. COVID-19 affected millions of people and killed hundreds of thousands worldwide. There are many ongoing studies investigating drug(s) suitable for preventing and/or treating this pandemic; however, there are no specific drugs or vaccines available to treat or prevent SARS-CoV-2 as of today.Methods: 58 fragrance materials, which are classified as allergen fragrance molecules, were selected and used in this study. Docking simulations were carried out using four functional proteins; the Covid19 Main Protase (Mpro), Receptor binding domain (RBD) of spike protein, Nucleocapsid, and host Bromodomain protein (BRD2), as target macromolecules. Three different software, AutoDock, AutoDock Vina (Vina), and Molegro Virtual Docker (MVD), running a total of four different docking protocol with optimized energy functions were used. Results were compared with the five molecules reported in the literature as potential drugs against COVID-19. Virtual screening was carried out using Vina, molecules satisfying our cut-off (-6.5 kcal/mol) binding affinity was confirmed by MVD. Selected molecules were analyzed using the flexible docking protocol of Vina and AutoDock default settings. Results: Ten out of 58 allergen fragrance molecules were selected for further docking studies. Mpro and BRD2 are potential targets for the tested allergen fragrance molecules, while RBD and Nucleocapsid showed weak binding energies. According to AutoDock results, three molecules, Benzyl Cinnamate, Dihydroambrettolide, and Galaxolide, had good binding affinities to BRD2. While Dihydroambrettolide and Galaxolide showed the potential to bind to Mpro, Sclareol and Vertofix had the best calculated binding affinities to this target. When the flexible docking results analyzed, all the molecules tested had better calculated binding affinities as expected. Benzyl Benzoate and Benzyl Salicylate showed good binding affinities to BRD2. In the case of Mpro, Sclareol had the lowest binding affinity among all the tested allergen fragrance molecules. Conclusion: Allergen fragrance molecules are readily available, cost-efficient, and shown to be safe for human use. Results showed that several of these molecules had comparable binding affinities as the potential drug molecules reported in the literature to target proteins. Thus, these allergen molecules at correct doses could have significant health benefits.

Molecular Modeling of Structures and Interaction of Short Peptides and Sortase Family Protein of Enterococcus Faecalis: Basis for Developing Peptide-Based Therapeutics Against Multidrug Resistant Strains

<p>The <i>Enterococcus faecalis</i> (<i>E. faecalis</i>) infection starts with initial adhesion to a host cell or abiotic surface by multiple adhesions on its cell membrane. The pathogenicity is due to virulence factors SrtA, SrtC, EbpA, EbpB, EbpC, and Aggregation Substance. <i>E. faecalis</i> developed resistance to the majority of standard therapies. Additionally, a notable key feature of <i>E. faecalis</i> is its ability to form biofilm <i>in vivo</i>. <i>E. faecalis</i> strains show resistance to aminoglycosides and β-lactam antibiotics with different degree of susceptibility. Sortases (SrtA and SrtC) are enzymes spatially localized at the septal region in majority of gram-positive bacteria during the cell cycle, which in-turn plays an important role in proper assembling of adhesive surface proteins and pilus on cell membrane. The studies have also proved that the both SrtA and SrtC were focally localized in <i>E. faecalis</i> and essential for efficient bacterial colonization and biofilm formation on the host tissue surfaces Using homology modeling and protein-peptide flexible docking methods, we report here the detailed interaction between peptides and <i>Ef</i>Srt (Q836L7) enzyme. Plausible binding modes between <i>Ef</i>Srt and the selected short biofilm active peptides were revealed from protein-peptide flexible docking. The simulation data further revealed critical residues at the complex interface and provided more details about the interactions between the peptides and <i>Ef</i>Srt. The flexible docking simulations showed that the peptide-<i>Ef</i>Srt binding was achieved through hydrogen bonding, hydrophobic, and van der Waals interaction. The strength of interactions between peptide-<i>Ef</i>Srt complexes were calculated using standard energy calculations involving non-bonded interactions like electrostatic, van der Waals, and hydrogen bonds.</p>