X-ray Crystallography Research Articles

Development of a broad-spectrum therapeutic Fc-nanobody for human noroviruses.

Human norovirus was discovered more than five decades ago and is a widespread cause of outbreaks of acute gastroenteritis. There are no approved vaccines or antivirals currently available. However, norovirus inhibitors, including capsid-specific monoclonal antibodies (Mabs) and nanobodies, have recently shown promising results. Several Mabs and nanobodies were found to inhibit norovirus replication using a human intestinal enteroid (HIE) culture system and/or could block norovirus attachment to histo-blood group antigen (HBGA) co-factors. In our pursuit to develop a single broad-spectrum norovirus therapeutic, we continued our analysis and development of a cross-reactive and HBGA interfering nanobody (NB26). To improve NB26 binding capacity and therapeutic potential, we conjugated NB26 onto a human IgG Fc domain (Fc-NB26). We confirmed that Fc-NB26 cross-reacts with genetically diverse GII genotype capsid protruding (P) domains (GII.8, GII.14, GII.17, GII.24, GII.26, and GII.NA1) using a direct enzyme-linked immunosorbent assay. Furthermore, X-ray crystallography structures of these P domains and structures of other GII genotypes reveal that the NB26 binding site is largely conserved, validating its broad reactivity. We showed that Fc-NB26 has ~100-fold higher affinity toward the norovirus P domain compared to native NB26. We also found that both NB26 and Fc-NB26 neutralize human norovirus replication in the HIE culture system. Furthermore, the mode of inhibition confirmed that like NB26, Fc-NB26 caused norovirus particle disassembly and aggregation. Overall, these new findings demonstrate that structural modifications to nanobodies can improve their therapeutic potential.IMPORTANCEDeveloping vaccines and antivirals against norovirus remains a challenge, mainly due to the constant genetic and antigenic evolution. Moreover, re-infection with genetically related and/or antigenic variants is not uncommon. We further developed our leading norovirus nanobody (NB26) that indirectly interfered with norovirus binding to HBGAs, by converting NB26 into a dimeric Fc-linked Nanobody (Fc-NB26). We found that Fc-NB26 had improved binding affinity and neutralization capacity compared with native NB26. Using X-ray crystallography, we showed this nanobody engaged highly conserved capsid residues among genetically diverse noroviruses. Development of such broadly reactive potent therapeutic nanobodies delivered as a slow-releasing prophylactic could be of exceptional value for norovirus outbreaks, especially for the prevention or treatment of severe acute gastroenteritis in high-risk groups such as the young, elderly, and immunocompromised.

Structure-based mapping of the histone-binding pocket of KDM4D using functionalized tetrazole and pyridine core compounds

KDM4 histone demethylases became an exciting target for inhibitor development as the evidence linking them directly to tumorigenesis mounts. In this study, we set out to better understand the binding cavity using an X-ray crystallographic approach to provide a detailed landscape of possible interactions within the under-investigated region of KDM4. Our design strategy was based on utilizing known KDM binding motifs, such as nicotinic acid and tetrazolylhydrazides, as core motifs that we decided to enrich with flexible tails to map the distal histone binding site. The resulting X-ray structures of the novel compounds bound to KDM4D, a representative of the KDM4 family, revealed the interaction pattern with distal residues in the histone-binding site. The most prominent protein rearrangement detected upon ligand binding is the loop movement that blocks the accessibility to the histone binding site. Apart from providing new sites that potential inhibitors can target, the novel compounds may prove helpful in exploring the capacity of ligands to bind in sites distal to the cofactor-binding site of other KDMs or 2-oxoglutarate (2OG)-dependent oxygenases. The case study proves that combining a strong small binding motif with flexible tails to probe the binding pocket will facilitate lead discovery in classical drug-discovery campaigns, given the ease of accessing X-ray quality crystals.

Synthesis of a CCC-NHC pincer Mn complex: An earth abundant catalyst for synthesis of α-alkylated ketones, 2-oxindole derivatives via borrowing hydrogen and one-pot synthesis of quinolines

A CCC-NHC pincer Mn complex was prepared and was characterized by 1H and 13C NMR spectroscopy, mass spectroscopy, elemental analysis, and single crystal X-ray crystallography. Its catalytic activities were demonstrated through diverse chemical transformations including cross-coupling borrowing hydrogen reactions and dehydrogenative cyclization reactions, which resulted in the formation of both C–C and C–N bonds. These cascade reactions involved multiple processes, including dehydrogenation, condensation, and hydrogenation. Under optimized conditions, Mn catalyst affectively converted a broad substrate scope. The different reactions yielded saturated ketones (isolated yields, 42 %–92 %), 2-oxindole derivatives (isolated yields, 70 %–83 %), and quinoline derivatives (isolated yields, 70 %–89 %). These atom economical transformations produce only water molecules as by-products enhancing their environmental friendliness. The catalyst utilized earth-abundant Mn potentially reduce costs. Catalytic cycles were proposed for borrowing hydrogen and acceptorless dehydrogenative cyclization reactions based on control experiments. These included oxidation, aldol condensation, and hydrogenation reactions.

Functionalized olive wood shell stone as a new revalorized agri-food waste active in organocatalysis

Olive wood shell stone has been used as an effective matrix for silanization and further anchoring of an organic probe such as 3-(5-chloro-anthraquinonylamino)propanoic acid (1). Covalent fixation of the anthraquinoid molecule was achieved by a “grafting to” silanization process with 3-aminopropyltrimethoxysilane (APTMS) followed by an amidation procedure. Ligand 1 was routinely characterized by multinuclear magnetic resonance (1H, 13C and 15N) and X-ray diffraction crystallography, while the new agri-food revalorized organocatalyst material was characterized by a number of analytical techniques such as granulometry, elemental analysis, thermogravimetry, differential scanning calorimetry, X-ray photoelectron spectroscopy, FTIR (ATR and DRIFT), moisture content, Karl-Fisher, ζ-potential and optical and fluorescence microscopy. The new revalorized material was assayed in the heterogeneous organocatalytic cyanosilylation of carbonyls compounds under very mild conditions with excellent yields and high recyclability under both presence and absence of solvent. Kinetic studies were also performed in order to understand the water uptake implications of this new organocatalyst.

The Development of Organotin(IV) N-Ethyl-N-Benzyldithiocarbamate Complexes: A Study on Their Synthesis, Characterization, and Cytocidal Effects on A549 Cell Line.

Organotin(IV) complexes of dithiocarbamate are vital in medicinal chemistry, exhibiting potential in targeting cancer cells due to their unique properties that enhance targeted delivery. This study aimed to synthesize and characterize organotin(IV) N-ethyl-N-benzyldithiocarbamate complexes (ONBDCs) and evaluate their cytotoxicity against A549 cells, which are commonly used as a model for human lung cancer research. The two ONBDC derivatives - ONBDC 1 (dimethyltin(IV) N-ethyl-N-benzyldithiocarbamate) and ONBDC 2 (triphenyltin(IV) N-ethyl-N-benzyldithiocarbamate) - were synthesized via the reaction of tin(IV) chloride with N-ethylbenzylamine in the presence of carbon disulfide. A range of analytical techniques, including elemental analysis, IR spectroscopy, NMR spectroscopy, UV-Vis spectrometry, TGA/DTA analysis, and X-ray crystallography, was conducted to characterize these compounds comprehensively. The cytotoxic effects of ONBDCs against A549 cells were evaluated using MTT assay. Both compounds were synthesized and characterized successfully via elemental and spectroscopies analysis. MTT assay revealed that ONBDC 2 demonstrated remarkable cytotoxicity towards A549 cells, with an IC50 value of 0.52 μM. Additionally, ONBDC 2 displayed significantly higher cytotoxic activity against the A549 cell line when compared to the commercially available chemotherapeutic agent cisplatin (IC50: 32 μM). Thus, it was shown that ONBDC 2 could have important anticancer properties and should be further explored as a top contender for creating improved and specialized cancer treatments.

Crystal structure of the GluK1 ligand-binding domain with kainate and the full-spanning positive allosteric modulator BPAM538

Kainate receptors play an important role in the central nervous system by mediating postsynaptic excitatory neurotransmission and modulating the release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. To date, only three structures of the ligand-binding domain (LBD) of the kainate receptor subunit GluK1 in complex with positive allosteric modulators have been determined by X-ray crystallography, all belonging to class II modulators. Here, we report a high-resolution structure of GluK1-LBD in complex with kainate and BPAM538, which belongs to the full-spanning class III. One BPAM538 molecule binds at the GluK1 dimer interface, thereby occupying two allosteric binding sites simultaneously. BPAM538 stabilizes the active receptor conformation with only minor conformational changes being introduced to the receptor. Using a calcium-sensitive fluorescence-based assay, a 5-fold potentiation of the kainate response (100 μM) was observed in presence of 100 μM BPAM538 at GluK1(Q)b, whereas no potentiation was observed at GluK2(VCQ)a. Using electrophysiology recordings of outside-out patches excised from HEK293 cells, BPAM538 increased the peak response of GluK1(Q)b co-expressed with NETO2 to rapid application of 10 mM L-glutamate with 130 ± 20 %, and decreased desensitization determined as the steady-state/peak response ratio from 23 ± 2 % to 90 ± 4 %. Based on dose–response relationship experiments on GluK1(Q)b the EC50 of BPAM538 was estimated to be 57.5 ± 29.2 μM.

Hybrid silver(I) coumarin-carbene and coumarin-triphenylphosphine complexes: Towards more effective antimicrobial therapies

The rise of antimicrobial resistance and the resulting societal burden has highlighted the need for the development of novel therapeutics. Towards that end, a series of hybrid silver(I) coumarin-carbene and coumarin-triphenylphosphine complexes were synthesised and characterised by spectroscopic analysis including IR, 1H and 13C NMR spectroscopy, elemental analysis, and X-ray crystallography. Isolation of coumarin-carbene hybrid complexes was achieved using two methods, with isolation via firstly the in-situ generation of a free carbene under Schlenk conditions, followed by reaction with a coumarin silver(I) complex resulting in the formation of a hybrid complex with two silver ions forming a strong argentophilic Ag(I)–Ag(I) interaction. In this hybrid complex one silver(I) ion was bound to two coumarin carboxylate ligands with the other ion bound to two carbene ligands. Isolation via an ionic carbene route led to more complex aggregates but both types of complexes had good solubility and photostability as did the triphenylphosphine hybrid complexes. All the hybrid complexes showed therapeutic potential as antimicrobial agents against MRSA with the carbene hybrid complexes exhibiting an increased antimicrobial activity against both E. coli and MRSA when compared to the initial silver(I) complexes.

Characterization and structural identification of a novel alginate-specific carbohydrate-binding module (CBM): The founding member of a new CBM family

Alginate is a commercially important polysaccharide widely distributed in brown algae. Carbohydrate-binding modules (CBMs), a class of commonly used polysaccharide-binding proteins, have greatly facilitated the investigations of polysaccharides. Few alginate-binding CBMs have been hitherto reported and structurally characterized. Herein, an unknown domain from a potential PL6 family alginate lyase in the marine bacterium Vibrio breoganii was discovered and recombinantly expressed. The obtained protein, designated VbCBMxx, displayed the favorable specificity to alginate. The unique sequence and well-defined function of VbCBMxx reveal a new CBM family. Moreover, the structure of VbCBMxx was determined at a 1.5 Å resolution by the X-ray crystallography, which shows a typical β-sandwich fold comprised of two antiparallel β-sheets. Site-directed mutagenesis assays confirmed that positively charged polar residues are crucial for the ligand binding of VbCBMxx. The discovery of VbCBMxx enriches the toolbox of alginate-binding proteins, and the elucidation of critical residues would guide the future practical applications of VbCBMxx.

Structural, computational, docking and biological studies of a triaminopyrimidine caspase-1 inhibitor

In order to more fully characterize the binding properties and activities of a potent, low nanomolar IC50 (half maximal inhibitory concentration) inhibitor of caspase-1, CK-1–41, a series of experiments were designed to probe its structure and function. To accomplish this, larger quantities of the molecule were synthesized in an efficient manner using a microwave method, in only 30 min. The structure of the inhibitor was determined by X-ray crystallography in its neutral and protonated form yielding useful structural information. The protonation site in the X-ray structure was found to be the trialkylamine basic site, but nuclear magnetic resonance (NMR) H/D exchange experiments shows that protonation at the triaminopyrimidine sp2 C is also accessible in solution. Density Functional Theory (DFT) calculations were performed and supported the experimental H/D exchange results. Docking studies with several protonated forms of the inhibitor with caspase-1 revealed the compound binds favorably in an allosteric site, with the strongest binding from the protonated form where the proton is bound to the sp2 C. Due to the involvement of caspase-1 in inflammatory cancers, CK-1–41 was screened against a panel of cancer cell lines displaying modest activity against some of the cell lines tested. These studies further clarify the structure and biological function of the representative member of the triaminopyrimidine inhibitors of caspase-1.

Entrance channels to coproheme in coproporphyrin ferrochelatase probed by exogenous imidazole binding

Iron insertion into porphyrins is an essential step in heme biosynthesis. In the coproporphyrin-dependent pathway, specific to monoderm bacteria, this reaction is catalyzed by the monomeric enzyme coproporphyrin ferrochelatase. In addition to the mechanistic details of the metalation of the porphyrin, the identification of the substrate access channel for ferrous iron to the active site is important to fully understand this enzymatic system. In fact, whether the iron reaches the active site from the distal or the proximal porphyrin side is still under debate. In this study we have thoroughly addressed this question in Listeria monocytogenes coproporphyrin ferrochelatase by X-ray crystallography, steady-state and pre-steady-state imidazole ligand binding studies, together with a detailed spectroscopic characterization using resonance Raman and UV–vis absorption spectroscopies in solution. Analysis of the X-ray structures of coproporphyrin ferrochelatase-coproporphyrin III crystals soaked with ferrous iron shows that iron is present on both sides of the porphyrin. The kinetic and spectroscopic study of imidazole binding to coproporphyrin ferrochelatase‑iron coproporphyrin III clearly indicates the presence of two possible binding sites in this monomeric enzyme that influence each other, which is confirmed by the observed cooperativity at steady-state and a biphasic behavior in the pre-steady-state experiments. The current results are discussed in the context of the entire heme biosynthetic pathway and pave the way for future studies focusing on protein-protein interactions.

Appraising protein conformational changes by resampling time-resolved serial x-ray crystallography data.

With the development of serial crystallography at both x-ray free electron laser and synchrotron radiation sources, time-resolved x-ray crystallography is increasingly being applied to study conformational changes in macromolecules. A successful time-resolved serial crystallography study requires the growth of microcrystals, a mechanism for synchronized and homogeneous excitation of the reaction of interest within microcrystals, and tools for structural interpretation. Here, we utilize time-resolved serial femtosecond crystallography data collected from microcrystals of bacteriorhodopsin to compare results from partial occupancy structural refinement and refinement against extrapolated data. We illustrate the domain wherein the amplitude of refined conformational changes is inversely proportional to the activated state occupancy. We illustrate how resampling strategies allow coordinate uncertainty to be estimated and demonstrate that these two approaches to structural refinement agree within coordinate errors. We illustrate how singular value decomposition of a set of difference Fourier electron density maps calculated from resampled data can minimize phase bias in these maps, and we quantify residual densities for transient water molecules by analyzing difference Fourier and Polder omit maps from resampled data. We suggest that these tools may assist others in judging the confidence with which observed electron density differences may be interpreted as functionally important conformational changes.

Bromine/Sulfur-Substituted 9H-Carbazoles Produced by the Marine-Derived Streptomyces sp. OUCMDZ-5511 upon NaBr Exposure.

Ten undocumented carbazole derivatives (2-11) along with the reported analogue (1) were isolated from the mangrove-derived Streptomyces sp. OUCMDZ-5511, cultured with NaBr-supplemented liquid medium. Compounds 1-7 are brominated carbazoles, and 8, 10, and 11 feature an additional thiazole or 2,3-dihydro-1,4-oxathiine rings, respectively. Their structures were identified through spectroscopic techniques, computational chemistry, and X-ray crystallography. Notably, compounds 6 and 8 effectively inhibited immune cell migration, indicating anti-inflammatory activity in vivo, potentially via Myd88/Nf-κB pathways, as suggested for compound 6.

A neutron diffraction study of the hydrous borate inderborite, CaMg[B3O3(OH)5]2(H2O)4·2H2O

Abstract The crystal chemistry of inderborite, a B-rich mineral (B2O3 ~41 wt%) with ideal formula CaMg[B3O3(OH)5]2·6H2O or CaMg[B3O3(OH)5]2(H2O)4·2H2O from the Inder Deposit, Kazakhstan, was re-investigated by a multi-methodological approach (single-crystal X-ray and neutron diffraction, electron probe micro-analysis in wavelength-dispersive mode, laser ablation multi-collector inductively mass spectrometry). The experimental findings show that the real chemical formula of inderborite from the Inder Deposit is virtually identical to the ideal one: the fraction of potential isomorphic substituents is insignificant. Boron is, therefore, the only industrially relevant element occurring in this mineral. The in situ B isotope composition of the Inder inderborite shows enrichment in the heavy 11B isotope, giving a weighted mean δ11BNIST951 of +35.15 ± 0.49 ‰ (2σ, N = 6). Such a positive δ11B value falls within the range of values in which the source of boron is ascribable to marine reservoirs rather than to terrestrial ones. X-ray (at 293 K) and neutron (at 20 K) structure refinements confirm that the principal building block unit of the structure is a [B3O3(OH)5]2– ring, consisting of two BO2(OH)2 tetrahedra (B-ion in sp3 electronic configuration) and one planar-triangular BO2OH group (B-ion in sp2 electronic configuration). In the [B3O3(OH)5]2– ring, all the oxygen atoms that are not shared between two boron atoms are protonated. The building units share corners with the CaO2(OH)4(OH2)2 polyhedra and Mg(OH)4(OH2)2 octahedra, forming hetero-polyhedral sheets parallel to (100). Subsequent hetero-polyhedral sheets are mutually connected only by H-bonding interactions, even mediated by the zeolitic (“interstitial”) H2O molecules. Ten out of 11 independent oxygen sites in the structure of inderborite are involved in H-bonds as donors or acceptors, and this reflects the pervasive effect of the H-bonding network. The role played by the complex H-bond network is expected to be substantial on the stability of the crystalline edifice, having effects within the single hetero-polyhedral sheet, between subsequent sheets, and in the bonding with the interstitial zeolitic H2O molecules. Finally, the potential utilizations of inderborite, as a B-bearing mineral, are discussed.

Bitopic Ligands Support the Presence of a Metastable Binding Site at the β2 Adrenergic Receptor.

Metastable binding sites (MBS) have been observed in a multitude of molecular dynamics simulations and can be considered low affinity allosteric binding sites (ABS) that function as stepping stones as the ligand moves toward the orthosteric binding site (OBS). Herein, we show that MBS can be utilized as ABS in ligand design, resulting in ligands with improved binding kinetics. Four homobivalent bitopic ligands (1-4) were designed by molecular docking of (S)-alprenolol ((S)-ALP) in the cocrystal structure of the β2 adrenergic receptor (β2AR) bound to the antagonist ALP. Ligand 4 displayed a potency and affinity similar to (S)-ALP, but with a >4-fold increase in residence time. The proposed binding mode was confirmed by X-ray crystallography of ligand 4 in complex with the β2AR. This ligand design principle can find applications beyond the β2AR and G protein-coupled receptors (GPCRs) as a general approach for improving the pharmacological profile of orthosteric ligands by targeting the OBS and an MBS simultaneously.

Structural Study of an Electroactive Allyl Ester Thiophenoazomethine for PDMS Blending

A conjugated thiophene azomethine was prepared having pendant allyl esters. X-ray crystallography confirmed its structure and hydrogen bonding. The compound switched its absorption between 495 and 645 nm with electrochemical oxidation/neutralization and between 495 and 710 nm with chemical oxidation. The azomethine could be blended with PDMS for homogeneous elastomeric film preparation while maintaining its intrinsic color.

Designing Dual-State and Aggregation-Induced Emissive Luminogens from Lignocellulosic Biosourced Molecules.

Utilizing lignocellulosic biosourced platforms, we synthesized novel cyanostilbene (CS) derivatives featuring the 3,4-dimethoxyphenyl moiety. These derivatives were investigated for their emission properties in both solution and solid states. The two simple CS derivatives exhibit very weak luminescence in solution but significant luminescence in the solid state, indicating distinct Aggregation-Induced Emission (AIE) characteristic. Furthermore, combining these two CS units, without conjugation and with quasi perpendicular orientation, results in a Dual-State Emission (DSE) fluorophore showing luminescence both in solution and solid states. X-ray crystallography studies on the solid-state compounds reveal a structure-emission relationship, demonstrating that the colour emission correlates with the conformations adopted by the molecules in the solid state, which influence the type of stacking.

Discovery of a novel exceptionally potent and orally active Nur77 ligand NB1 with a distinct binding mode for cancer therapy

The orphan nuclear receptor Nur77 is emerging as an attractive target for cancer therapy, and activating Nur77's non-genotypic anticancer function has demonstrated strong therapeutic potential. However, few Nur77 site B ligands have been identified as excellent anticancer compounds. There are no co-crystal structures of effective anticancer agents at Nur77 site B, which greatly limits the development of novel Nur77 site B ligands. Moreover, the lack of pharmaceutical ligands restricts Nur77's therapeutic proof of concept. Herein, we developed a first-in-class Nur77 site B ligand (NB1) that significantly inhibited cancer cells by mediating the Nur77/Bcl-2-related apoptotic effect at mitochondria. The X-ray crystallography suggests that NB1 is bound to the Nur77 site B with a distinct binding mode. Importantly, NB1 showed favorable pharmacokinetic profiles and safety, as evidenced by its good oral bioavailability in rats and lack of mortality, bodyweight loss, and pathological damage at the 512.0 mg/kg dose in mice. Furthermore, oral administration of NB1 demonstrated remarkable in vivo anticancer efficacy in an MDA-MB-231 xenograft model. Together, our work discovers NB1 as a new generation Nur77 ligand that activates the Nur77/Bcl-2 apoptotic pathway with a safe and effective cancer therapeutic potency.

Aqueous anion binder for phenolate and nitro substituted phenolates through second-sphere coordination network

A series of four cobalt(III) complexes, [Co(Hbig)3]1.5Cl3.5(Ph).2H2O (1), [Co(Hbig)3] (PNP)3.H2O (2), [Co(Hbig)3](DNP)3.H2O (3) and [Co(Hbig)3](TNP)3·4H2O (4) have been synthesized by reacting [Co(Hbig)3]Cl3.H2O (Hbig: biguanide) with sodium phenolates (Ph: pheonlate, PNP: 4-nitrophenolate, DNP: 2,4-dinitrophenolate or TNP: 2,4,6-trinitrophenolate) in 1:3 molar ratio in aqueous medium. All the complexes were initially characterized by physiochemical and spectroscopic (UV–Visible, IR and NMR) studies. Anion binding affinity of complex cation for anions has been studies in aqueous medium using UV–Visible spectroscopic titrations and found log β values for anions. The single crystal X-ray structures of complex 3 and 4 were also determined and stacking of layers has been observed in both the structures. These stacking layers contains layers of [Co(Hbig)3]3+, nitro-phenolate (DNP or TNP) and water molecules along b-axis. These layers connected with one another by numerous intermolecular N-H…O hydrogen bonds leads to formation of second-sphere coordination network. Further, all the complexes and their respective reactants have been tested for antimicrobial activities against strain of Gram negative (P. aeruginosa, E. coli, K. pneumoniae, S. typhi), strain of Gram positive bacteria (B. subtilis, S. epidermidis) and antifungal against C. herbarum, A. alternata and F. oxysporum.

The Importance of Structured Water in HDAC8 for Correct Binding Pose Applied for Drug Design of Anticancer Molecules.

Validating the docking procedure and maintaining the structural water molecules at HDAC8 catalytic site. Molecular docking simulations play a significant role in Computer-Aided Drug Design, contributing to the development of new molecules. To ensure the reliability of these simulations, a validation process called "Re-docking" is employed, focusing on the binding mode of a ligand co-crystallized with the protein of interest. In this study, several molecular docking studies were conducted using five X-ray structures of HDAC8-ligand complexes from the PDB. Ligands initially complexed with HDAC8 were removed and re-docked onto the free protein, revealing a poor reproduction of the expected binding mode. In response to this, we observed that most HDAC8-ligand complexes contained one to two water molecules in the catalytic site, which were crucial for maintaining the cocrystallized ligand. These water molecules enhance the binding mode of the co-crystallized ligand by stabilizing the proteinligand complex through hydrogen bond interactions between ligand and water molecules. Notably, these interactions are lost if water molecules are removed, as is often done in classical docking methodologies. Considering this, molecular docking simulations were repeated, both with and without one or two conserved water molecules near Zn+2 in the catalytic cavity. Simulations indicated that replicating the native binding pose of co-crystallized ligands on free HDAC8 without these water molecules was challenging, showing greater coordinate displacements (RMSD) compared to those including conserved water molecules from crystals. The study highlighted the importance of conserved water molecules within the active site, as their presence significantly influenced the successful reproduction of the ligands' native binding modes. The results suggest an optimal molecular docking procedure for validating methods suitable for filtering new HDAC8 inhibitors for future experimental assays.

DNA binding/cleavage study of mixed ligand complexes of di-/triorganotin 4-fluoroanthranilates with 1,10-phenanthroline/benzimidazole: Synthesis, characterization, X-ray structures of [Bu2Sn(FA)2.phen], [Me3Sn(FA).bz], and DFT calculations

The mixed ligand complexes of di-/tri-organotin 4-fluoroanthranilates with 1,10-phenanthroline (phen), viz. [R2Sn(FA)2.phen] {R=Bu (1), Oct (2), Me (3)} and benzimidazole (bz), viz. [R3Sn(FA).bz] {R=Me (4), Ph (5)} have been synthesized and satisfactorily characterized by analytical and spectroscopic techniques, especially FT-IR, NMR (1H, 13C, and 119Sn NMR) spectroscopy and ESI-MS spectrometry. Single crystal-Xray diffraction measurements (Sc-XRD) confirmed a distorted pentagonal-bipyramidal geometry for complex (1), where one carboxylate group is monodentate, and the second (–COO) group behaves as a bidentate, while complex (4) affirms trigonal–bipyramidal geometry around the tin centre. The bond angles, especially ∠C–Sn–C obtained by optimizing complexes’ gaseous phase geometry showed significant conformity with the data obtained from Sc-XRD and NMR. The Kb (binding constant) and Ksv (Stern-Volmer quenching constant) values, ranging from 103 to 107, have been obtained through UV–visible absorption and fluorescence titrations with CT-DNA. These results strongly indicate partial minor groove binding/electrostatic interactions between the complex and CT-DNA, which has also been evidenced by circular dichroism studies. The studied complexes cleaved efficiently pBR322 plasmid DNA in NC (nicked circular form), SC (supercoiled form), and linear form.