docking
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Bringing a new drug to the market is a lengthy, risky and expensive endeavor. Money spent on developing new drugs keeps going up each year, which is disproportional to the number of drugs brought to the market. Therefore, it is important to find ways to reduce costs and improve the effectiveness of drug discovery and development. Underlined by fast-paced developments in algorithms and processing power of modern hardware, computational methods have shown great potential in achieving this goal and molecular docking is an important tool in this toolbox. In this work, we briefly introduce the very basic principles of molecular docking and review some important contemporary challenges and developments in this field.
- Klíčová slova
- skórování, změna vazebné energie,
- MeSH
- algoritmy MeSH
- počítačová simulace MeSH
- racionální návrh léčiv MeSH
- simulace molekulového dockingu * metody trendy MeSH
- termodynamika MeSH
- vazba proteinů MeSH
- Publikační typ
- práce podpořená grantem MeSH
G protein-coupled receptors (GPCRs) are hard to crystallize. However, attempts to predict their structure have boomed as a result of advancements in crystallographic techniques. This trend has allowed computer-aided molecular modeling of GPCRs. We analyzed the performance of four molecular modeling programs in pose evaluation of re-docked antagonists / inverse agonists to 11 original crystal structures of aminergic GPCRs using an induced fit-docking procedure. AutoDock and Glide were used for docking. AutoDock binding energy function, GlideXP, Prime MM-GB/SA, and YASARA binding function were used for pose scoring. Root mean square deviation (RMSD) of the best pose ranged from 0.09 to 1.58 Å, and median RMSD of the top 60 poses ranged from 1.47 to 3.83 Å. However, RMSD of the top pose ranged from 0.13 to 7.33 Å and ranking of the best pose ranged from the 1st to 60th out of 60 poses. Moreover, analysis of ligand-receptor interactions of top poses revealed substantial differences from interactions found in crystallographic structures. Bad ranking of top poses and discrepancies between top docked poses and crystal structures render current simple docking methods unsuitable for predictive modeling of receptor-ligand interactions. Prime MM-GB/SA optimized for 3NY9 by multiple linear regression did not work well at 3NY8 and 3NYA, structures of the same receptor with different ligands. However, 9 of 11 trajectories of molecular dynamics simulations by Desmond of top poses converged with trajectories of crystal structures. Key interactions were properly detected for all structures. This procedure also worked well for cross-docking of tested β2-adrenergic antagonists. Thus, this procedure represents a possible way to predict interactions of antagonists with aminergic GPCRs.
A comparative study of interaction between chicken egg white lysozyme (Lyz) with two hexavalent chromate ions; chromate and dichromate; which are prevalently known for their toxicity, was investigated using different spectroscopic techniques along with a molecular docking study. Both steady-state and time-resolved studies revealed that the addition of chromate/dichromate is responsible for strong quenching of intrinsic fluorescence in Lyz and the quenching is caused by both static and dynamic quenching mechanisms. Different binding and thermodynamic parameters were also calculated at different temperatures from the intrinsic fluorescence of Lyz. The conformational change in Lyz and thermodynamic parameters obtained during the course of interaction with chromate/dichromate were well-supported by the molecular docking results.
MOTIVATION: Protein tunnels and channels are key transport pathways that allow ligands to pass between proteins' external and internal environments. These functionally important structural features warrant detailed attention. It is difficult to study the ligand binding and unbinding processes experimentally, while molecular dynamics simulations can be time-consuming and computationally demanding. RESULTS: CaverDock is a new software tool for analysing the ligand passage through the biomolecules. The method uses the optimized docking algorithm of AutoDock Vina for ligand placement docking and implements a parallel heuristic algorithm to search the space of possible trajectories. The duration of the simulations takes from minutes to a few hours. Here we describe the implementation of the method and demonstrate CaverDock's usability by: (i) comparison of the results with other available tools, (ii) determination of the robustness with large ensembles of ligands and (iii) the analysis and comparison of the ligand trajectories in engineered tunnels. Thorough testing confirms that CaverDock is applicable for the fast analysis of ligand binding and unbinding in fundamental enzymology and protein engineering. AVAILABILITY AND IMPLEMENTATION: User guide and binaries for Ubuntu are freely available for non-commercial use at https://loschmidt.chemi.muni.cz/caverdock/. The web implementation is available at https://loschmidt.chemi.muni.cz/caverweb/. The source code is available upon request. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Spectroscopic analysis, density functional theory (DFT) studies and surface enhanced Raman scattering (SERS) of antimycobactetial 4-[3-(4-acetylphenyl)ureido]-2-hydroxybenzoic acid (AUHB) have been studied on different silver sols. For Raman and SERS wavenumbers, very large changes are observed. Observed variations in the modes of ring may be due to surface π-electron interactions and presence of this indicated that poly substituted ring is more inclined than para substituted phenyl ring and assumes a inclined position for concentration 10-3 M. Changes in orientation are seen in SERS spectra depending on concentration. In order to find electron-rich and poor sites of AUHB, molecular electrostatic potential was also constructed. The molecular docking results show that binding affinity and interactions with the receptor DprE1 may be supporting evidence for further studies in design further AUHB pharmaceutical applications. Based on antitubercular activity of 4-aminosalicylic acid (PAS) and urea derivatives we designed, synthesized and investigated mutual PAS-urea derivatives as potential antimycobacterial agents.
In this work, the new diaminochromenes: 2,5-dimono-8-methoxychromeno[4,3,2-de][1,6]naphthyridine-4-carbonitrile (4), 8-ethoxy-2-imino-3,4-dihydro-2H-chromene-3-carbonitrile-4-malononitrile (5), 2,5-diamino-8-ethoxychromene[4,3,2-de][1,6]naphthyridine-4-carbonotrile (6), were synthesized and fully characterized through 600 MHz using 1H, 13C, APT, gHSQC, gHMBC, ROESY-1D and gated decoupling 13C. Further docking studies suggested that these compounds are capable of intercalating with the Drew-Dickerson Dodecamer DNA and, therefore, be candidates to work as effective compounds to decrease the cancer radiotherapy.Communicated by Ramaswamy H. Sarma.
A series of twenty-five novel salicylanilide N-alkylcarbamates were investigated as potential acetylcholinesterase inhibitors. The compounds were tested for their ability to inhibit acetylcholinesterase (AChE) from electric eel (Electrophorus electricus L.). Experimental lipophilicity was determined, and the structure-activity relationships are discussed. The mode of binding in the active site of AChE was investigated by molecular docking. All the discussed compounds expressed significantly higher AChE inhibitory activity than rivastigmine and slightly lower than galanthamine. Disubstitution by chlorine in C'(₃,₄) of the aniline ring and the optimal length of hexyl-undecyl alkyl chains in the carbamate moiety provided the most active AChE inhibitors. Monochlorination in C'(₄) exhibited slightly more effective AChE inhibitors than in C'(₃). Generally it can be stated that compounds with higher lipophilicity showed higher inhibition, and the activity of the compounds is strongly dependent on the length of the N-alkyl chain.
- MeSH
- acetylcholinesterasa metabolismus MeSH
- cholinesterasové inhibitory chemie farmakologie MeSH
- Electrophorus metabolismus MeSH
- fenylkarbamáty metabolismus MeSH
- galantamin metabolismus MeSH
- karbamáty chemie farmakologie MeSH
- katalytická doména MeSH
- molekulární modely MeSH
- salicylanilidy chemie farmakologie MeSH
- simulace molekulového dockingu MeSH
- vazebná místa MeSH
- vztahy mezi strukturou a aktivitou MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The series of symmetrical and unsymmetrical isoquinolinium-5-carbaldoximes was designed and prepared for cholinesterase reactivation purposes. The novel compounds were evaluated for intrinsic acetylcholinesterase (AChE) or butyrylcholinesterase (BChE) inhibition, when the majority of novel compounds resulted with high inhibition of both enzymes and only weak inhibitors were selected for reactivation experiments on human AChE or BChE inhibited by sarin, VX, or paraoxon. The AChE reactivation for all used organophosphates was found negligible if compared to the reactivation ability of obidoxime. Importantly, two compounds were found to reactivate BChE inhibited by sarin or VX better to obidoxime at human attainable concentration. One compound resulted as better reactivator of NEMP (VX surrogate)-inhibited BChE than obidoxime. The in vitro results were further rationalized by molecular docking studies showing future directions on designing potent BChE reactivators.
- MeSH
- acetylcholinesterasa účinky léků MeSH
- butyrylcholinesterasa účinky léků MeSH
- cholinesterasové inhibitory farmakologie MeSH
- isochinoliny chemická syntéza chemie farmakologie MeSH
- lidé MeSH
- reaktivátory cholinesterasy farmakologie MeSH
- simulace molekulového dockingu MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Ricin is a potent cytotoxin with no available antidote. Its catalytic subunit, RTA, damages the ribosomal RNA (rRNA) of eukaryotic cells, preventing protein synthesis and eventually leading to cell death. The combination between easiness of obtention and high toxicity turns ricin into a potential weapon for terrorist attacks, urging the need of discovering effective antidotes. On this context, we used computational techniques, in order to identify potential ricin inhibitors among approved drugs. Two libraries were screened by two different docking algorithms, followed by molecular dynamics simulations and MM-PBSA calculations in order to corroborate the docking results. Three drugs were identified as potential ricin inhibitors: deferoxamine, leucovorin and plazomicin. Our calculations showed that these compounds were able to, simultaneously, form hydrogen bonds with residues of the catalytic site and the secondary binding site of RTA, qualifying as potential antidotes against intoxication by ricin.Communicated by Ramaswamy H. Sarma.
Growing evidence of antibiotic-resistant pathogens is a serious medical issue that has to be addressed. Our antimicrobial research is focused on searching for novel small molecules that differ from the most clinically used antibiotics by chemical structure and mechanism. However, this fundamental research is like looking for a needle in a haystack. In addition, in vitro methods are time-consuming and expensive to screen large number of compounds in reasonable time. Off-target screening can represent a solution to find novel and effective antimicrobial agents that can eliminate these problems. Accordingly, molecular docking in the family of selected frentizole derivatives predicted their potential to inhibit bacterial nicotinate mononucleotide adenylyltransferase (NadD). This bacterial-essential specific enzyme has an important role in NAD metabolism. Thus, underlying mechanism of antimicrobials derived from frentizole would be interference with this biochemical process. Unfortunately, broth microdilution assay did not display any antimicrobial activity of tested compounds. On the other hand, herein we propose that off-target screening can facilitate searching for new drugs and that NadD could be a relevant target for antimicrobials.
- MeSH
- antiinfekční látky * chemie MeSH
- Bacteria MeSH
- benzothiazoly chemie MeSH
- indikátorové diluční techniky MeSH
- inhibitory enzymů chemie MeSH
- lidé MeSH
- nikotinamidnukleotidadenylyltransferasa * antagonisté a inhibitory MeSH
- simulace molekulového dockingu MeSH
- techniky in vitro MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
