Biological properties and conformational studies of amphiphilic Pd(II) and Ni(II) complexes bearing functionalized aroylaminocarbo-N-thioylpyrrolinate units

• Samet Poyraz,
• Samet Belveren,
• Sabriye Aydınoğlu,
• Mahmut Ulger,
• Abel de Cózar,
• Maria de Gracia Retamosa,
• Jose M. Sansano and
• H. Ali Döndaş

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

• Luiz Claudio Ferreira Pimentel,
• Lucas Villas Boas Hoelz,
• Henayle Fernandes Canzian,
• Frederico Silva Castelo Branco,
• Andressa Paula de Oliveira,
• Vinicius Rangel Campos,
• Floriano Paes Silva Júnior,
• Rafael Ferreira Dantas,
• Jackson Antônio Lamounier Camargos Resende,
• Anna Claudia Cunha,
• Nubia Boechat and
• Mônica Macedo Bastos

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

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

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

• Peter Bayer,
• Anja Matena and
• Christine Beuck

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

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

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

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

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

• Abimelek Cortes-Pacheco,
• María Adelina Jiménez-Arellanes,
• Francisco José Palacios-Can,
• José Antonio Valcarcel-Gamiño,
• Rodrigo Said Razo-Hernández,
• María del Carmen Juárez-Vázquez,
• Adolfo López-Torres and
• Oscar Abelardo Ramírez-Marroquín

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

• Sivaraman Balasubramaniam,
• Sajith Vijayan,
• Liam V. Goldman,
• Xavier A. May,
• Kyra Dodson,
• Sweta Adhikari,
• Fatima Rivas,
• Davita L. Watkins and
• Shana V. Stoddard

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

• Man-Man Wang,
• Hao Huang,
• Lei Shu,
• Jian-Min Liu,
• Jian-Qiu Zhang,
• Yi-Le Yan and
• Da-Yong Zhang

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

• Hoang Huy Do,
• Saif Ullah,
• Alexander Villinger,
• Joanna Lecka,
• Jean Sévigny,
• Peter Ehlers,
• Jamshed Iqbal and
• Peter Langer

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

• Irina G. Tkachenko,
• Sergey A. Komykhov,
• Vladimir I. Musatov,
• Svitlana V. Shishkina,
• Viktoriya V. Dyakonenko,
• Vladimir N. Shvets,
• Mikhail V. Diachkov,
• Valentyn A. Chebanov and
• Sergey M. Desenko

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

• Christoph W. Grathwol,
• Nathalie Wössner,
• Sören Swyter,
• Adam C. Smith,
• Enrico Tapavicza,
• Robert K. Hofstetter,
• Anja Bodtke,
• Manfred Jung and
• Andreas Link

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

• Silvie Rimpelová,
• Michal Jurášek,
• Lucie Peterková,
• Jiří Bejček,
• Vojtěch Spiwok,
• Miloš Majdl,
• Michal Jirásko,
• Miloš Buděšínský,
• Juraj Harmatha,
• Eva Kmoníčková,
• Pavel Drašar and
• Tomáš Ruml

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

• Hajime Sato,
• Takaaki Mitsuhashi,
• Mami Yamazaki,
• Ikuro Abe and
• Masanobu Uchiyama

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

• Iwona E. Głowacka,
• Aleksandra Trocha,
• Andrzej E. Wróblewski and
• Dorota G. Piotrowska

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

• Stiliyana Pereva,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

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

Synthesis and biological evaluation of truncated derivatives of abyssomicin C as antibacterial agents

• Leticia Monjas,
• Peter Fodran,
• Johanna Kollback,
• Carlo Cassani,
• Thomas Olsson,
• Maja Genheden,
• D. G. Joakim Larsson and
• Carl-Johan Wallentin

Beilstein J. Org. Chem. 2019, 15, 1468–1474, doi:10.3762/bjoc.15.147

• docking of known and proposed ligands. The crystal structure contains a tryptophan molecule in the active site. Restrained molecular dynamics [20][21] was employed to position the active site cysteine (Cys-263) in a position that would allow covalent binding of the ligands in the active site. The

• resulting protein conformation was allowed to relax to ensure that the found conformation was an energy minimum. This protein structure was then used for docking of ligands using Glide [22][23][24]. Glide XP docking positioned both AbC and the analog atrop-O-benzyl-desmethyl-abyssomicin C with low energy

• conformations and with expected interaction points in the binding site, providing suitable docking scores (see Supporting Information File 1). The key interactions include a hydrogen bond to the backbone of Arg-45 and lipophilic interactions in the deep pocket defined by Phe-241 and Leu-34 (Figure 2). Our

Towards the preparation of synthetic outer membrane vesicle models with micromolar affinity to wheat germ agglutinin using a dialkyl thioglycoside

• Dimitri Fayolle,
• Nathalie Berthet,
• Bastien Doumeche,
• Olivier Renaudet,
• Peter Strazewski and
• Michele Fiore

Beilstein J. Org. Chem. 2019, 15, 937–946, doi:10.3762/bjoc.15.90

• 8 showed the highest inhibitory effect of this study with an IC50 of 11 µM corresponding to a 3000-fold improvement compared to the monomer control. This result suggests a higher participation of sugar units in the lectin binding for this compound. Docking calculation for model glycolipids To

• appreciate the possible binding of 4, 5, 7 and 8 onto WGA, a docking simulation was performed using the crystal structure of WGA obtained in the presence of GlcNAc (PDB 2UVO) and of other GlcNAc derivatives (PDB 2X52 and 4AML). The docking experiments were performed using analogous molecules bearing acetate

• and butanoate alkyl chains (namely 4C2, 4C4, 5C2, 5C4, 7C2, 7C4, 8C2 and 8C4 according to the alkyl length, see Figures S5 and S6 in Supporting Information File 1) instead of the long alkyl chains, for calculation simplicity. The docking protocol was validated using GlcNAc and Glc as ligands. In such

Stereochemical investigations on the biosynthesis of achiral (Z)-γ-bisabolene in Cryptosporangium arvum

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2019, 15, 789–794, doi:10.3762/bjoc.15.75

• resulting in (S)-A after ring closure (Scheme 1, path A) or via (S)-NPP, which would suggest involvement of (R)-A (Scheme 1, path B). This stereochemical link between NPP and A was also observed in a theoretical docking study with epi-isozizaene synthase suggesting (S)-NPP and (R)-A to be included in its

Back to the future: Why we need enzymology to build a synthetic metabolism of the future

• Tobias J. Erb

Beilstein J. Org. Chem. 2019, 15, 551–557, doi:10.3762/bjoc.15.49

• screened for new catalytic reactions in metabolic retrosynthesis. Further improvements in homology modeling and virtual docking are expected to increase accuracy and throughput, which will help to map and predict the substrate and reactions catalyzed by an enzyme superfamily and its individual members in

Design of indole- and MCR-based macrocycles as p53-MDM2 antagonists

• Constantinos G. Neochoritis,
• Maryam Kazemi Miraki,
• Eman M. M. Abdelraheem,
• Ewa Surmiak,
• Tryfon Zarganes-Tzitzikas,
• Beata Łabuzek,
• Tad A. Holak and
• Alexander Dömling

Beilstein J. Org. Chem. 2019, 15, 513–520, doi:10.3762/bjoc.15.45

• -pocket as shown by our docking studies (Figure 1A,B, Figure S4 in Supporting Information File 1). Thus, extending our previous work [13], the Leu26 subpocket was probed by utilizing the different ring sizes and the different heteroatoms (oxygen or sulfur) of our macrocyclic library. In addition, the

Protein–protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics

• Laura Carro

Beilstein J. Org. Chem. 2018, 14, 2881–2896, doi:10.3762/bjoc.14.267

• was screened by X-ray crystallography leading to the identification of four fragment hits. In an attempt to improve their binding affinities, another library was searched for compounds displaying similarity to these initial hits. After a docking-based screening followed by a fluorescence polarization

• database [82] was searched for structurally similar compounds leading to the identification of the meta-substituted tetrazole 33 (Figure 7), which was found to have a similar dissociation constant. Moreover, in order to predict the orientation of the fragments in the binding site, molecular docking of 33

Targeting the Pseudomonas quinolone signal quorum sensing system for the discovery of novel anti-infective pathoblockers

• Christian Schütz and
• Martin Empting

Beilstein J. Org. Chem. 2018, 14, 2627–2645, doi:10.3762/bjoc.14.241

• docking [51]. These inhibitors appeared to bind in the substrate channel in a slightly remote position from the active site cysteine and, hence, termed channel blockers [51]. Optimised hits exhibited a potency in the single-digit micromolar range (12, Figure 6). However, it has been found that similar

• tailor-made SPR experiment including truncated and elongated derivatives as well as nitrophenylmethanol-based active-site blockers of different size as competitors. These experiments combined with molecular docking (Figure 7) led to the postulation of a plausible binding pose characterising the

• , their potency in attenuating biofilm formation was more pronounced than ciprofloxacin and linezolid itself. A docking study suggested PqsD to be the target of these compounds like 23 (Figure 10), although this remains speculative. PqsE inhibitors The pathway-specific thioesterase PqsE is not only

Microwave-assisted synthesis of biologically relevant steroidal 17-exo-pyrazol-5'-ones from a norpregnene precursor by a side-chain elongation/heterocyclization sequence

• Gergő Mótyán,
• László Mérai,
• Márton Attila Kiss,
• Zsuzsanna Schelz,
• Izabella Sinka,
• István Zupkó and
• Éva Frank

Beilstein J. Org. Chem. 2018, 14, 2589–2596, doi:10.3762/bjoc.14.236

• hormones, and therefore, in the development of prostate cancer [1]. According to extensive structure–activity relationship and docking studies, a potent steroidal inhibitor should possess certain structural characteristics for efficient P45017α inhibition [1][2][3], such as (i) a five or six-membered non

Synthesis of 3-aminocoumarin-N-benzylpyridinium conjugates with nanomolar inhibitory activity against acetylcholinesterase

• Nisachon Khunnawutmanotham,
• Cherdchai Laongthipparos,
• Patchreenart Saparpakorn,
• Nitirat Chimnoi and
• Supanna Techasakul

Beilstein J. Org. Chem. 2018, 14, 2545–2552, doi:10.3762/bjoc.14.231

• potent activities with inhibitory concentration (IC50) values in the nanomolar concentration range. Among them, the 2,3-difluorobenzylpyridinium-containing compound was the most potent inhibitor with an IC50 value of 1.53 ± 0.01 nM. Docking studies revealed that the synthesized compounds inhibit the

• well as with benzylpyridinium moieties [12][13][14] have been reported as dual-binding site AChE inhibitors. Recently we have reported the AChE inhibitory activity of the coumarin derivative, scopoletin conjugated with a pyridinium side chain (Figure 1) [15] and a docking study revealed that the

• that may be useful for binding with this enzyme. Herein, we report our progress on the synthesis, biological evaluation, and molecular docking of 3-aminocoumarin linked with the benzylpyridinium moiety through an amide bond. Results and Discussion Chemistry The target 3-aminocoumarin-N-benzylpyridinium