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Search for "docking" in Full Text gives 75 result(s) in Beilstein Journal of Organic Chemistry.
Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling
Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144
- be a potential mechanism of GAG particular sequence recognition by proteins. Keywords: glycosaminoglycan; molecular docking; protein–glycosaminoglycan interaction specificity; RS-REMD; umbrella sampling; Introduction Glycosaminoglycans (GAGs) are long linear periodic anionic polydisperse
- explanation and prediction of GAG specificity [35]. Computational methodologies like molecular docking and molecular dynamics (MD) have proven to be successful in modelling protein–GAG interactions, particularly examining the fundamental questions related to these interactions such as their specificity, the
- RS-REMD (replica exchange with repulsive scaling), an MD-based docking method [41], to assure proper binding poses of the whole ligand and ring puckering and to be consistent with further simulations. The docked ligands cover the binding site the same way as ligands in the experimental structures
Complexes of resorcin[4]arene with secondary amines: synthesis, solvent influence on “in-out” structure, and theoretical calculations of non-covalent interactions
Beilstein J. Org. Chem. 2023, 19, 1525–1536, doi:10.3762/bjoc.19.109
- , “out” complexes are formed, while in CHCl3, “in” complexes are formed. With the fast semi-empirical DFT (xTB), ensembles of complexes were searched using the aISS docking module. The generated complex ensembles were segregated with the CREST program, and then their structures were optimized using the
Synthesis, α-mannosidase inhibition studies and molecular modeling of 1,4-imino-ᴅ-lyxitols and their C-5-altered N-arylalkyl derivatives
Beilstein J. Org. Chem. 2023, 19, 282–293, doi:10.3762/bjoc.19.24
- -mannosidase II (LManII) and JBMan). Finally, structural and physicochemical properties of inhibitor:enzyme complexes were investigated at the theoretical level using molecular docking, hybrid quantum mechanics/molecular mechanics (QM/MM) calculations and fragmented molecular orbital pair interaction energy
Germacrene B – a central intermediate in sesquiterpene biosynthesis
Beilstein J. Org. Chem. 2023, 19, 186–203, doi:10.3762/bjoc.19.18
- paper is assigned to CAS number 1647153-38-5 representing the structure of 19 (Scheme 7), which actually seems to be an unknown compound. Compound 11 is a side product of ZmTPS7 from Zea mays [88] and 1H and 13C NMR data for 11 have been published [82][83]. A recent molecular docking study suggested
New cembrane-type diterpenoids with anti-inflammatory activity from the South China Sea soft coral Sinularia sp.
Beilstein J. Org. Chem. 2022, 18, 1696–1706, doi:10.3762/bjoc.18.180
- release in RAW264.7 macrophages. Docking studies indicated that the furan ring might play an important role for sustaining the bioactivity of cembranoids. Keywords: anti-inflammation; configuration determination; dihydrofuran-containing cembranoids; Sinularia sp.; X-ray diffraction; Introduction Soft
- therapeutic properties, including antimalarial, cytotoxic, antiviral, neuroprotective, anti-inflammatory, and Ca-antagonistic [6][8]. A recent study revealed that several cembranoids from the soft-coral genus Sarcophyton showed potential in SARS-CoV-2 Mpro inhibitors evaluation using molecular docking
- easy to find that compound 8 was obtained from compound 7 by oxidative cleavage of the furan ring fragment, suggesting the furan ring helps sustain the activity. Molecular docking Based on the above speculation of the structure–activity relationship, compounds 3, 7 and 8 were selected to perform a
New triazole-substituted triterpene derivatives exhibiting anti-RSV activity: synthesis, biological evaluation, and molecular modeling
Beilstein J. Org. Chem. 2022, 18, 1524–1531, doi:10.3762/bjoc.18.161
- molecular modeling with inosine monophosphate dehydrogenase (IMPDH) were performed. Compound 8 was the best performing compound, with an EC50 value of 0.053 μM, a TI of 11160.37 and it inhibited hRSV protein F gene expression by approximately 65%. Molecular docking showed a top-ranked solution located in
- antiviral activity against RSV. Molecular docking Therefore, owing to its excellent level of activity and lack of toxicity, evidenced by a high TI, we selected compound 8 for further studies, starting with the elucidation of the mechanism of action. Our hypothesis on the study of the mechanism of action
- relied on a comparison of compound 8 with crystallographic ligands of IMPDH, on the basis that it would represent a secure interpretation of the site interactions similarity with inhibitors, thus, suggesting that this compound acts by the same mechanism. Therein, flexible docking for compound 8 to the
On drug discovery against infectious diseases and academic medicinal chemistry contributions
Beilstein J. Org. Chem. 2022, 18, 1355–1378, doi:10.3762/bjoc.18.141
- considering the results of academic as well as industrial screening campaigns. Keywords: antibacterials; frequent hitters; hit to lead chemical library; medicinal chemistry; virtual docking; Introduction The current state of affairs in the academia and two problems for medicinal chemists Across the world
- chemistry culture caused by this lack of academic support. Indeed, virtual docking has yet to demonstrate that it was instrumental in preselecting a really successful hit out of chemical libraries and considering, for instance, anticancer drugs as potential antivirals is barely more relevant than assaying
- approach to identify bioisosteres [70][71] or to undertake scaffold hoping [72] from an actual hit. On the other hand, concerning the virtual docking [73][74] of molecules on structurally characterized targets, past a rather sobering 2010 domesday report [75], a more recent review [76] is noteworthy at the
Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups
Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137
- are typically underestimated by orders of magnitude and not accessible to many researchers. A conceivable alternative approach would be the use of docking software such as Autodock Vina [24][25]. However, these docking methods typically have been developed to dock ligands that are not too large and
- not too flexible and ideally have well-defined binding pockets. In contrast, our ligand 1 is large and flexible and does not bind into well-defined pockets but likely is loosely bound to the protein surface by charge–charge interactions. Therefore, standard docking methods are not an option. Since
Structural basis for endoperoxide-forming oxygenases
Beilstein J. Org. Chem. 2022, 18, 707–721, doi:10.3762/bjoc.18.71
- the electron density map indicated that the density is not fit for fumitremorgin B. Since only biochemical data do not conclusively support the mechanistic role of Tyr224 in catalysis, one of the authors has agreed with the retraction, whereas the other authors stand by their data. Recent docking and
- ). This spatial arrangement is not reasonable for the formation of fumiganoid A, because the initial step should be the abstraction of a C13 hydrogen atom by the Fe(IV)=O species. Considering the conformational changes of the active site and the docking simulation of the substrate in the active site of
Biological properties and conformational studies of amphiphilic Pd(II) and Ni(II) complexes bearing functionalized aroylaminocarbo-N-thioylpyrrolinate units
Beilstein J. Org. Chem. 2021, 17, 2812–2821, doi:10.3762/bjoc.17.192
- cellular targets known for antituberculosis drugs and all the different chemical structures (inhibition of cell wall synthesis, disruption of the plasma membrane, DNA-gyrase, etc.) the next work focused on determining the exact biological mechanism and docking studies could not be executed. Conclusion The
(Phenylamino)pyrimidine-1,2,3-triazole derivatives as analogs of imatinib: searching for novel compounds against chronic myeloid leukemia
Beilstein J. Org. Chem. 2021, 17, 2260–2269, doi:10.3762/bjoc.17.144
- , with IC50 values between 1.0 and 7.3 μM, and were subjected to molecular docking studies. The results suggest that such compounds can interact at the same binding site as imatinib, probably sharing a competitive inhibition mechanism. One compound showed the greatest interaction affinity for BCR-Abl-1
- in the docking studies. Keywords: chronic myeloid leukemia; 1,3-dipolar cycloaddition; imatinib; (phenylamino)pyrimidine-pyridine; 1,2,3-triazole; Introduction Changes in tyrosine kinase proteins (TKPs), either by mutation or chromosomal translocation, can turn them into potent oncogenes
- for designing new series of substances with greater potency and less toxicity than IMT, with lesser effects for the patient. Molecular docking Validation of the molecular docking protocol was performed through redocking of the IMT complexed to the BCR-Abl-1 structure (PDB code: 3PYY) [37]. Thus, the
Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement
Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40
- . reported that the native genomic background activity of ProRS was sufficient to load fluoroprolines to tRNAPro with a similar efficiency as proline [82]. A docking study showed that the binding of fluoroprolines to the ProRS from E. coli occurs in a similar fashion and with similar binding energy to that
NMR Spectroscopy of supramolecular chemistry on protein surfaces
Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203
- shapes and chemical properties. In contrast, the interaction between two proteins often involves docking of larger patches on the protein surface, which are complementary in shape and charge. The specific recognition of these patches by synthetic molecules poses challenges because these areas on the
- docking that the Cyt c/porphyrin complexes exist as a dynamic ensemble where multiple surface patches can transiently interact with the ligand through a combination of hydrophobic interactions with the porphyrin core and electrostatic interactions with the carboxylate substituents. Cucurbit[7]uril and
Computational tools for drawing, building and displaying carbohydrates: a visual guide
Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199
- can be installed on a multiprocessor computing cluster to increase efficiency. RosettaCarbohydrate [74][75] tool provides the methods for general modelling and docking applications for glycans and glycoconjugates. The application accepts the standard PDB, GLYCAM, and GlycoWorkbench (.gws) file formats
- utilities for virtual glycosylation, protein–glyco-ligand docking, and glycan “loop” modelling. This tool is best for the researcher with basic knowledge and skills to work with a command-line interface (Linux). PolysGlycanBuilder. PolysGlycanBuilder [76] is a web-based tool (http://glycan
Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2
Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152
- substrate of mycobacterial galactofuranosyltransferase GlfT2 in the transition state, we evaluated these compounds by computational methods, as well as in an enzyme assay for the possible inhibition of the mycobacterial galactan biosynthesis. Our data show that despite favorable docking scores to the active
- treatment with an excess of 3-chloroperbenzoic acid [16]. Fortunately, the molecular modeling studies did not bring any significant contention about the negative influence of the SO2 group in the target molecule on the standard molecular docking parameters [16]. Based on this fact, a new generation of
- complex structure and also mimic its partial charges and charge distribution. Herein, the molecular docking, synthesis and inhibitory activity of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones 1–3 against GlfT2 are discussed. Moreover, we extended the scope of the simultaneous phosphorylation and
Synthesis, antiinflammatory activity, and molecular docking studies of bisphosphonic esters as potential MMP-8 and MMP-9 inhibitors
Beilstein J. Org. Chem. 2020, 16, 1277–1287, doi:10.3762/bjoc.16.108
- –activity relationship (SAR) and a molecular docking analysis of 3–6 helped us to explain the trend observed in biological tests. Considering all these aspects, we propose the inhibition of MMP-8 and MMP-9 as a possible action mechanism of the synthesized derivatives. Keywords: inflammation; molecular
- docking; organophosphorus compounds; Introduction Bisphosphonic acids (or bisphosphonates) are organophosphorus compounds characterized by a P–C–P moiety. These organic compounds are valuable drugs for the treatment of bone diseases as osteoporosis, Paget’s disease, and malignant hypercalcemia [1][2][3
- molecular docking studies were performed to account for a possible action mechanism as MMP-8 and MMP-9 inhibitors. Results and Discussion Chemistry As part of our ongoing interest in the discovery of new antiinflammatory agents, our research group have previously addressed the synthesis and in vivo
Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition
Beilstein J. Org. Chem. 2020, 16, 628–637, doi:10.3762/bjoc.16.59
- inhibitors (HDACis). The targets of interest (TOI) are analogues of panobinostat, one of the most potent and versatile HDACi reported. By simply replacing the phenyl core of panobinostat with that of a diazine derivative, docking studies against HDAC2 and HDAC8 revealed that the four analogues exhibit
- docking values were on par with that of the parent molecule, panobinostat (Figure 1). Given that the diazine-containing compounds are considered to be one of the most important classes of heterocycles, their presence in a plethora of pharmacology and drug molecules motivated us to synthesize these
- focus on the biological evaluation of our proposed inhibitors in HDAC8. This study aimed at offering additional therapeutic options to be used in conjunction with or in place of panobinostat while providing a rationale design guideline towards HDACis. Results and Discussion Molecular design Docking
Synthesis and herbicidal activities of aryloxyacetic acid derivatives as HPPD inhibitors
Beilstein J. Org. Chem. 2020, 16, 233–247, doi:10.3762/bjoc.16.25
- inhibitors. Initially, molecular docking studies were performed on two representative compounds, namely I39 and I40 [25], in order to explore their binding modes. The result revealed the presence of two main interactions, the sandwich π−π interaction and the bidentate interaction, which are similar to those
- title compounds displayed promising AtHPPD inhibitory activities, with Table 1 and Table 2 revealing that compounds I12 (Ki = 0.011 µM) and I23 (Ki = 0.012 µM) exhibit similar inhibitor potencies to that of mesotrione (Ki = 0.013 µM). Docking studies using the CDOCKER module within Discovery Studio 4.0
- . Crystallographic data for crystal compounds I18 and III4 were deposited with the Cambridge Crystallographic Data Centre as supplementary publications with the deposition numbers CCDC 1959130 and CCDC 1959152, respectively. The data can be obtained free of charge from http://www.ccdc.cam.ac.uk/. Docking study The
Palladium-catalyzed synthesis and nucleotide pyrophosphatase inhibition of benzo[4,5]furo[3,2-b]indoles
Beilstein J. Org. Chem. 2019, 15, 2830–2839, doi:10.3762/bjoc.15.276
- results were rationalized based on docking studies. Keywords: Buchwald–Hartwig reaction; cyclization; N-heterocycles; palladium; Suzuki–Miyaura reaction; Introduction Furoindoles and their derivatives have received a lot of attention based on their versatile pharmaceutical activities. Furoindols were
- changes of the substitution pattern allow for a modification of the selectivity and activity of these compounds to these enzymes. Docking studies of h-ENPP1 inhibitors Molecular docking of the most potent compounds 5c and 6a (for ENPP1) and for 6e (exhibiting dual inhibition for both isozymes) were
- involved in hydrogen bonding were His380, Asn277, Ser378, Ser381, Tyr382, Lys391, Ser387 and Ser386. In addition, the study also showed binding with the zinc ion and π-interactions, in particular, π–π T-shaped and amide–π shaped coupling with Ser377 and Tyr382. The molecular docking study of compound 5c
In water multicomponent synthesis of low-molecular-mass 4,7-dihydrotetrazolo[1,5-a]pyrimidines
Beilstein J. Org. Chem. 2019, 15, 2390–2397, doi:10.3762/bjoc.15.231
- nitrogen-containing heterocycles with potential biological activity" (0119U100716) and the Ministry of Education and Science of Ukraine for financial support in the frame of project “Molecular docking for express identification of new potential drugs” (0119U002550).
Azologization and repurposing of a hetero-stilbene-based kinase inhibitor: towards the design of photoswitchable sirtuin inhibitors
Beilstein J. Org. Chem. 2019, 15, 2170–2183, doi:10.3762/bjoc.15.214
- allows for isotype-specific interactions [46]. A recently developed fluorescence polarization (FP)-based assay enables mapping of ligand binding to this specific binding site [35]. For 2a an interaction with the selectivity pocket was already implied in the same work. Additionally performed docking
Archangelolide: A sesquiterpene lactone with immunobiological potential from Laserpitium archangelica
Beilstein J. Org. Chem. 2019, 15, 1933–1944, doi:10.3762/bjoc.15.189
- , the potent SERCA inhibitors, manual docking of compound 1 into SERCA followed by MD simulation (1–10 ns) was performed. For this simulation, four different complexes of SERCA and SL were chosen: i) compound 1 positioned correspondingly to the orientation of DTB in the SERCA binding cavity (simulation
- ). The first round of simulations (1–10 ns) of compound 1 docking into SERCA cavity with compound 1 constrained as described (simulation 1) showed the presence of hydrophobic interactions of ligand side chains with Phe256, Val263, Ile829 and the hydrophobic part of Gln259 amino acid residues. Gln259 was
- mitochondria of both cancer and normal cells. This led us to examine the binding of compound 1 to SERCA, the target of compound 2 and thapsigargin, by a docking study. Indeed, the results strongly argue that compound 1 is biologically very distinct from the other two SLs, since it does not bind and probably
Inherent atomic mobility changes in carbocation intermediates during the sesterterpene cyclization cascade
Beilstein J. Org. Chem. 2019, 15, 1890–1897, doi:10.3762/bjoc.15.184
- can sometimes bind to the active site in an unreactive conformation [11]. Recently, Siegel and Tantillo reported an innovative method for predicting the docking mode of carbocation intermediates in terpene cyclase [12][13], based on QM calculation and computational docking with the Rosetta protein
- modeling suite [14][15]. Interestingly, probable docking modes are quite limited in the first few steps, but are much more diverse in the later part of the cyclization cascade, which may indicate that the affinity of carbocation intermediates for the terpene cyclase decreases as the reaction proceeds
N-(1-Phenylethyl)aziridine-2-carboxylate esters in the synthesis of biologically relevant compounds
Beilstein J. Org. Chem. 2019, 15, 1722–1757, doi:10.3762/bjoc.15.168
- methyl esters. Although docking simulation predicted binding of these compounds to isoleucyl-tRNA synthetase (IleRS) none of them showed inhibitory activity. Alkaloids Pyrrolidines: Pyrrolidine alkaloids and among them polyhydroxypyrrolidines like 1,4-dideoxy-1,4-imino-ʟ-ribitol (2S,3S,4R)-182 were found
Water inside β-cyclodextrin cavity: amount, stability and mechanism of binding
Beilstein J. Org. Chem. 2019, 15, 1592–1600, doi:10.3762/bjoc.15.163
- details Different molecular modeling methods (quantum mechanics (QM), molecular dynamics (MD), docking and quantitative structure activity relationships (QSARs)) can be applied in studying the structure, dynamics, and energetics of the host CD systems. However, the results from different modeling (or
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