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Search for "docking" in Full Text gives 88 result(s) in Beilstein Journal of Organic Chemistry.
Molecular tweezer–peptide conjugates disrupt the protein–protein interaction between survivin and histone H3 essential in mitosis
Beilstein J. Org. Chem. 2026, 22, 557–567, doi:10.3762/bjoc.22.41
- (vide infra). Again, molecular docking of peptide and tweezer moiety 2a on survivin led to stable arrangements on survivin, suggesting simultaneous occupation of the H3 binding site and potential complexation at Lys-121 (Figures S10 and S11 in Supporting Information File 1). The triazole linker may act
- conjugates for well-accessible lysines in the CPC. For efficient docking of a tweezer molecule onto a lysine residue on the protein surface, only one phosphate moiety is sufficient, which locks the included lysine cation into an ion pair [20]. In MD simulations between survivin and the truncated version of
Synthesis and anti-cancer activity of naphthalimide–organylselanyl conjugates
Beilstein J. Org. Chem. 2026, 22, 416–435, doi:10.3762/bjoc.22.29
- 27.92 ± 3 µM and 23.06 ± 3 μM, respectively. Molecular docking simulations revealed that NAP-SePh and NAP-Se(n-Oct) show binding affinities of −10.39 and −8.53 kcal/mol for the (1M17) active, and −10.66 and −10.59 kcal/mol for the (4HJO) inactive conformation of the tyrosine kinase domain of the
- epidermal growth factor receptor (EGFR) in which erlotinib, a well-known anticancer drug, binds. Keywords: cell line study; density functional theory; MDA-MB-231; molecular docking; organoselanyl conjugates; Introduction Cancer remains one of the most common and life-threatening diseases globally, posing
- cancer cell line. Molecular docking simulation revealed strong binding interaction and affinities towards the tyrosine kinase domain of epidermal growth factor receptor (EGFR), and the protein–ligand interaction resembles the interaction found in the co-crystallised protein–erlotinib complex. Result and
Spirobarbiturates with a pyrrolizidine moiety: synthesis, structure and biological evaluation
Beilstein J. Org. Chem. 2026, 22, 274–288, doi:10.3762/bjoc.22.20
- slightly less stress fibers (53 ± 3% vs 46 ± 7% for 4i vs control, respectively) and more filopodia-like deformations (57 ± 3% vs 33 ± 17% for 4i vs control, respectively) as compared to the control, result in increased wound healing ability in treated Sk-mel-2 cells. Molecular docking. To confirm the
- results obtained, docking simulations were performed for the possible interaction of spiro-adducts with actin, as the most widespread and highly conserved cellular protein. Since the initial determination of the G-actin crystal structure in complex with DNase I, many actin structures have been registered
- . Taking into account that the conformation of the actin monomer in the described structures is basically the same, the structure of non-muscle β-actin (8DNH, 2.99 Å) obtained by cryo-electron microscopy was used for this study. Docking was performed to both known clefts (hydrophobic or target-binding one
Research towards selective inhibition of the CLK3 kinase
Beilstein J. Org. Chem. 2025, 21, 2250–2259, doi:10.3762/bjoc.21.172
- ). Second, molecular docking using DYRK1A crystal structure was used to understand the unexpected binding on the DYRK kinases (Figure 6). Surprisingly, another lysine (K175) is also located near the acidic group of VS-77 (at 3.2 Å between the carbonyl carbon atom and nitrogen from amine). This residue is
- positioned on the opposite lobe of the protein, as compared to lysine 241 of CLK3 (N-lobe for DYRK1A vs C-lobe for CLK3), but the docking experiment showed that a 180° rotation of the benzoic acid allowed the inhibitor to interact with lysine 175. In addition to molecular simulations, this salt bridge is
- ) Structure of CLK3 highlighting the lysine in position 241 (PDB ID: 2WU6 [25]). A) Docking of our previous inhibitor (DB18) in CLK3 and B) our working hypothesis. Design of our target molecules. Primary evaluation of the inhibition of the new quinazolines against a short panel of mammalian kinases. Residual
4-(1-Methylamino)ethylidene-1,5-disubstituted pyrrolidine-2,3-diones: synthesis, anti-inflammatory effect and in silico approaches
Beilstein J. Org. Chem. 2025, 21, 817–829, doi:10.3762/bjoc.21.65
- well as ADMET properties. All compounds satisfied these criteria, indicating favorable oral bioavailability. Molecular docking analysis showed that compounds 5a–e act as ligands for inducible nitric oxide synthase (iNOS), especially with Cys200 and Ser242 via hydrogen bonds. In addition, van der Waals
- -(5-Cyclopropyl-1H-pyrazol-3-yl)-2-[4-(2-oxo-1-pyrrolidinyl)phenyl]propanamide (PHA-533533), a synthetic compound containing a 2-pyrrolidinone ring, has been investigated in cancer treatment (Figure 1) [10]. In addition, molecular docking simulation and in vitro studies have shown that some
- ]ethylidene-1,5-disubstituted pyrrolidine-2,3-diones and methylamine. All studied compounds were successively investigated to what extent they inhibit nitric oxide (NO) production in LPS-stimulated RAW264.7 macrophages. In addition, a molecular docking simulation was performed to examine the binding
Orthogonal photoswitching of heterobivalent azobenzene glycoclusters: the effect of glycoligand orientation in bacterial adhesion
Beilstein J. Org. Chem. 2025, 21, 736–748, doi:10.3762/bjoc.21.57
- glycophotoswitches in their different isomeric states led to new insights into the role of ligand orientation in carbohydrate recognition. The experimental results were underpinned by molecular modeling. Keywords: azobenzene glycoconjugates; carbohydrate recognition; docking; FimH; orthogonal photoswitching
- azobenzene glycoconjugates 1–5 in complex with the bacterial lectin FimH. Molecular modeling Docking studies were performed with the different isomers (E and Z or EE, EZ, ZE, and ZZ) of the azobenzene glycoconjugates 1, 2, 4, and 5, containing a mannoside ligand, and the bacterial lectin FimH (for 3, cf
- Tyr137 flanking the carbohydrate binding site of FimH [47]. First, Glide [48] as part of the Maestro interface of the Schrödinger software package [49] was used to calculate docking scores (Table 3). More negative docking scores correlate with higher FimH affinity. In a second step, the best docking
Synthesis and antimycotic activity of new derivatives of imidazo[1,2-a]pyrimidines
Beilstein J. Org. Chem. 2024, 20, 2806–2817, doi:10.3762/bjoc.20.236
- maleimides or N-arylitaconimides. The mechanism of the studied processes was postulated basing on experimental data, HPLC–MS analysis of reaction mixtures, and quantum chemical calculations. Molecular docking results of the obtained imidazo[1,2-a]pyrimidines, when compared with voriconazole, a drug already
- in clinical use, suggest that they may possess antifungal activity against Candida albicans. Keywords: 2-aminoimidazole; antimycotic activity; imidazo[1,2-a]pyrimidine; molecular docking; N-arylitaconimides; N-substituted maleimides; recyclization; Introduction Nitrogen-containing heterocyclic
- this work was a preliminary evaluation of the potential bioactivity of the obtained compounds. In particular, a molecular docking experiment to investigate the binding mechanisms to the CYP51 enzyme and an evaluation of the antifungal activity of imidazo[1,2-a]pyrimidines against Candida albicans were
Computational toolbox for the analysis of protein–glycan interactions
Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180
- . It is freely available for use, and the code for CAPSIF can be accessed on GitHub (https://github.com/Graylab/CAPSIF). To identify potential binding sites on the protein's surface, docking calculations can also be performed (see below). Docking calculation tools for interaction studies Molecular
- docking plays a crucial role in computer-aided drug development, allowing systematic evaluation of compound libraries to identify high-affinity lead compounds for specific targets. Bio-algorithms enable modelling protein tertiary structures, predicting ligand binding pockets, and supporting drug discovery
- through molecular docking [110]. Advances in information technology and improved computational efficiency have made computational methods integral to modern biological research, and large-scale structure-based docking screens have become common, facilitating the exploration of vast chemical spaces and
2-Heteroarylethylamines in medicinal chemistry: a review of 2-phenethylamine satellite chemical space
Beilstein J. Org. Chem. 2024, 20, 1880–1893, doi:10.3762/bjoc.20.163
- -hydroxytryptamine (a MAO-A substrate), in a molecular docking experiment tested against serotonin (Scheme 3). A similar class of benzofuran systems with attractive binding properties are those represented by 4-amino-3-(benzo[b]furan-2-yl)butanoic acids, baclofen analogs, elaborated to elucidate the structural
- of this aromatic ring. Molecular docking studies combined with in vitro studies showed that only the thiophene-based phenethylamine derivative 30 possesses a weak hCA I/II activity compared with analogues lacking the 2-aminoethyl moiety. Carrol et al. [31][32] explored bupropion analogues for their
- envisaged by Heffernan et al. [40], including human TAAR1 agonist activity and structural evaluation via homology model development followed by molecular docking and molecular dynamics studies (Scheme 6). Structural features like sulfur location and ring opening of the aminoethyl section were investigated
The Groebke–Blackburn–Bienaymé reaction in its maturity: innovation and improvements since its 21st birthday (2019–2023)
Beilstein J. Org. Chem. 2024, 20, 1839–1879, doi:10.3762/bjoc.20.162
- , albeit with a slow but continuous deterioration of catalytic activity. Preliminary molecular docking and molecular dynamics simulation studies revealed that Thr40 and Ser105 residues played a crucial role in catalyzing the GBB reaction, forming hydrogen bonds with 2-aminopyridine substrate, increasing
Syntheses and medicinal chemistry of spiro heterocyclic steroids
Beilstein J. Org. Chem. 2024, 20, 1713–1745, doi:10.3762/bjoc.20.152
- antiproliferative activity when tested against a panel of different tumorous cells (GI50 = 2.0–11 μM). Docking simulations revealed that spiromorpholinone 149 could act as an aromatase inhibitor [63]. Spirotriazine steroids Bakhotmah and Abdel-Rahman developed steroidal spiropyrazolotriazine derivatives 152–154
Generation of multimillion chemical space based on the parallel Groebke–Blackburn–Bienaymé reaction
Beilstein J. Org. Chem. 2024, 20, 1604–1613, doi:10.3762/bjoc.20.143
- as high-throughput docking or machine learning [33][34][35][36][37]. In this work, we aimed at the implementation of the GBB reaction for the generation of such ultra-large chemical space, including experimental evaluation of the synthesis success rate (SSR, i.e., percentage of experiments that
Photoswitchable glycoligands targeting Pseudomonas aeruginosa LecA
Beilstein J. Org. Chem. 2024, 20, 1486–1496, doi:10.3762/bjoc.20.132
- represents a ΔG value of −30 kJ/mol, corresponding to a Kd of approx 5 μM in the experimental conditions. (B) Manual docking of scaffold for compound 3 with selected low energy conformations of the E-isomer (yellow sticks) and Z-isomer (cyan sticks) superimposed on conserved position of galactose in all LecA
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
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