Identification of novel HDAC8 selective inhibitors through ligand and structure based studies: Exploiting the acetate release channel differences among class I isoforms

Histone deacetylases (HDACs) are key regulators of gene expression and have emerged as crucial therapeutic targets for cancer. Among the HDACs, inhibition of HDAC8 enzyme has been reported to be a novel strategy in the treatment of female-specific cancers. Most of the HDAC inhibitors discovered so far inhibit multiple HDAC isoforms causing toxicities in the clinic thus limiting their potential. Therefore, the discovery of isoform-selective HDAC8 inhibitors is highly desirable. In the present study, a combination of ligand and structure based drug design tools were utilized to build a statistically significant pharmacophore based 3D QSAR model with statistical parameters R²: 0.9964, and Q²: 0.7154, from a series of 31 known HDAC8 inhibitors. Top 1000 hits obtained from Virtual screening of Phase database were subjected to docking studies against HDAC8. Top 100 hits obtained were redocked into HDAC Class I (HDAC 1,2,3) and Class II isoforms (HDAC 4, 6) and rescored with XP Glide Score. Based on fitness score, XP glide score and interacting amino acid residues, five HDAC8 inhibitors (1–5) were selected for in vitro studies. The HDAC8 activity assay followed by enzyme kinetics clearly indicated Compounds 1, 2 and 3 to be potent HDAC8 selective inhibitors with IC₅₀ of 126 pM, 112 nM, and 442 nM respectively. These compounds were cytotoxic to HeLa cells where HDAC8 is overexpressed but not to normal cells, HEK293. Also, they were able to induce apoptosis by modulating Bax/Bcl2, cleavage of PARP and release of Cytochrome C. Molecular Dynamics simulations observed most favorable interaction patterns and presented a rationale for the activities of the identified compounds. Selectivity against HDAC8 was due to exploitation of the architectural difference in the acetate release channel among class I HDAC isoforms.     

Synthesis and biological evaluation of -n[4-(2-trans-[([2,6-diamino-4(3H)-oxopyrimidin-5-yl]methyl)thio]cyclobutyl)benzoyl] -l-glutamic acid a novel 5-thiapyrimidinone inhibitor of dihydrofolate reductase

The synthesis and biological evaluation of N-[4-(2-trans-[([2,6-diamino-4(3H)-oxopyrimidin-5-yl]methyl)thio]cyclobutyl)benzoyl]-L-glutamic acid (1) is reported. Compound 1 is a potent dihydrofolate reductase (DHFR) inhibitor (K_j = 12 nM) with excellent in vitro cell culture growth inhibition (L1210, IC₅₀ = 29 nM). Protection experiments showed that the cell growth inhibitory activity was due to DHFR inhibition. The key step in the synthesis was the coupling of a cyclobutylmethylthiol with the 5-bromo-2,6-diamino-4-oxopyrimidine ⁸.     

Design,synthesis and characterization of a series of 6-substituted-4-hydroxy-1-(2-substitutedthiazol-4-yl)quinolin-2(1H)-one derivatives and evaluation of their in vitro anticancer and antibacterial activity

The current research work deals with the design, synthesis and characterization of a series of 6-substituted-4-hydroxy-1-(2-substitutedthiazol-4-yl)quinolin-2(1H)-one derivatives [III(a-d)(1–3)] and evaluation of their in-vitro anticancer activity against MDA-MB (Breast cancer) and A549 (Lung cancer) cell lines based upon MTT assay and in-vitro antibacterial by the measurement of zone of inhibition and determining the Minimum Inhibitory Concentration (MIC). All the synthesized compounds were characterized by UV, IR, ¹H NMR and ¹³C NMR spectral data.Molecular docking studies of the title compounds were carried out using Molegro Virtual Docker (MVD-2013, 6.0) software. The synthesized compounds exhibited well conserved hydrogen bond interactions with one or more amino acid residues in the active pocket of EGFRK tyrosine kinase domain (PDB ID: 1m17) for docking study on anticancer activity and S. aureus DNA Gyrase domain complexed with a ciprofloxacin inhibitor (PDB ID: 2XCT) for antibacterial docking study. All synthesized derivatives were potent against A549 (Lung cancer) cell line as compared to MDA-MB (Breast cancer) cell line. Compound 2-(4-(4-hydroxy-6-methyl-2-oxoquinolin-1(2H)-yl)thiazol-2-yl)hydrazin-1-ium iodide (IIId-2) was found to be the most cytotoxic as compared to the other synthesized derivatives, with IC₅₀ values of 346.12 μg/mL against A549 (Lung cancer) cell line, however all synthesized derivatives were found to be a poor antibacterial agent when compared with standard ciprofloxacin.Thus, the synthesized derivatives possessed a potential to bind with some of the residues of the active site and can be further developed into potential pharmacological agents.     

Discriminations of active from inactive HDAC8 inhibitors Part II: Bayesian classification study to find molecular fingerprints

ABSTRACT

In continuation of our earlier work (Doi: 10.1080/07391102.2019.1661876), a statistically validated and robust Bayesian model was developed on a large diverse set of HDAC8 inhibitors. The training set comprised of 676 small molecules and 293 compounds were considered as test set molecules. The findings of this analysis will help to explore some major directions regarding the HDAC8 inhibitor designing approach. Acrylamide (G1-G3, G9), N-substituted 2-phenylimidazole (G4-G8, G9, G12-G13, G16-G19), benzimidazole (G10-G11), piperidine substituted pyrrole (G13-G14) groups, alkyl/aryl amide (G15) and aryloxy carboxamide (G20) fingerprints were found to play a crucial role in HDAC8 inhibitory activity whereas -CH-N=CH- (B1, B4-B6, B14) motif, benzamide (B2-B3, B9-B13, B16-B17) groups and heptazepine (B7-B8, B15, B18-B20) group were found to influence negatively the HDAC8 inhibitory activity. The importance of such fingerprints was further validated by the HDAC8 enzyme and related inhibitor interactions at the receptor level. These results are in close agreement with those of our previous work that validate each other. Moreover, this comparative learning may enrich future endeavours regarding the designing strategy of HDAC8 inhibitors.     

Serendipitous Discovery of a Potent Influenza Virus A Neuraminidase Inhibitor

We have previously reported a potent neuraminidase inhibitor that comprises a carbocyclic analogue of zanamivir in which the hydrophilic glycerol side chain is replaced by the hydrophobic 3‐pentyloxy group of oseltamivir. This hybrid inhibitor showed excellent inhibitory properties in the neuraminidase inhibition assay (K_i=0.46 nM ; K_{i (zanamivir)}=0.16 nM ) and in the viral replication inhibition assay in cell culture at 10^?8 M . As part of this lead optimization, we now report a novel spirolactam that shows comparable inhibitory activity in the cell culture assay to that of our lead compound at 10^?7 M . The compound was discovered serendipitously during the attempted synthesis of the isothiourea derivative of the original candidate. The X‐ray crystal structure of the spirolactam in complex with the N8 subtype neuraminidase offers insight into the mode of inhibition.     

Syntheses,Structures, and Polymorphism of β‐Diketonato Complexes – Co(thd)3

Oxidation of Co(thd)₂ dissolved in different solvents has been investigated in air and oxygen atmosphere. In oxygen atmosphere and at the boiling point of the solvents this treatment leads to oxidation of Co^II to Co^III, but also to degradation of some of the thd ligands and formation of a new mixed‐ligand complex. Three pure‐cultivated crystalline Co(thd)₃ phases are reported: 1 (room‐temperature phase), 2 (low‐temperature phase), and 3 (metastable phase) and in addition there exists an amorphous Co(thd)₃ phase ( 4 ) with approximate composition Co(thd)₃·xH(thd); x = 0.06. Reaction of metal(II) oxides (MO, M = Mn, Fe, and Co) with H(thd) under air or O₂ atmosphere is an easy direct route to M(thd)₃ complexes. Structure determinations are reported for Co(thd)₃ ( 1 – 3 ) based on single‐crystal X‐ray diffraction data. Modification 1 crystallizes in space group with a = b = 18.8100(10), c = 18.815(2) Å at 295 K; R(wR2) = 0.180, modification 2 in space group C2/c with a = 28.007(12), b = 18.482(8), c = 21.356(9) Å, β = 97.999(5)° at 100 K; R(wR2) =0.211, and modification 3 in space group Pnma with a = 19.2394(15), b = 18.8795(15), c = 10.7808(8) Å at 100 K; R(wR2) = 0.193. The molecular structures of 1 – 3 all comprise a central Co atom octahedrally co‐ordinated by the ketonato O atoms of three thd ligands. The transformation between modifications 1 and 2 is of a fully reversible second‐order character. Modifications 1 and 3 are, on the other hand, related by a quasi‐reversible cycle. Heat treatment (specifically sublimation) of 1 leads to 3 whereas re‐crystallization or prolonged storage at room temperature is required to regenerate 1 . Co(thd)₃ has sufficient thermal stability to permit sublimation without degradation. The various forms of Co(thd)₃ are all diamagnetic, viz. a confirmation of the Co^III valence state.     

Pharmacophore modelling,virtual screening and molecular docking studies on PLD1 inhibitors

Lipid metabolism plays a significant role in influenza virus replication and subsequent infection. The regulatory mechanism governing lipid metabolism and viral replication is not properly understood to date, but both Phospholipase D (PLD1 and PLD2) activities are stimulated in viral infection. In vitro studies indicate that chemical inhibition of PLD1 delays viral entry and reduction of viral loads. The current study reports a three-dimensional pharmacophore model based on 35 known PLD1 inhibitors. A sub-set of 25 compounds was selected as the training set and the remaining 10 compounds were kept in the test set. One hundred and twelve pharmacophore models were generated; a six-featured pharmacophore model (AADDHR.57) with survival score (2.69) produced a statistically significant three-dimensional quantitative structure–activity relationship model with r² = 0.97 (internal training set), r² = 0.71 (internal test set) and Q² = 0.64. The predictive power of the pharmacophore model was validated with an external test set (r² = 0.73) and a systematic virtual screening work-flow was employed showing an enrichment factor of 23.68 at the top 2% of the dataset (active and decoys). Finally, the model was used for screening of the filtered PubChem database to fetch molecules which can be proposed as potential PLD1 inhibitors for blocking influenza infection.     

How Does the Fluorination of the Linker Affect the Structural Chemistry of Trimesate-Based Metal-Organic Frameworks (MOFs)?

FMOFs, i.e. metal-organic frameworks with linkers with fluoro substituents, were supposed to show enhanced thermal and chemical stability as well as high gas affinity and hydrophobicity. However, at least for aromatic carboxylate ligands it was shown in a subsequent work that fluoro substituents weaken the C(phenyl)-COO^– bond and thus facilitate decarboxylation leading to a decreased chemical and thermal stability. Nonetheless, it was concluded that linker fluorination leads to a rich structural chemistry, as the torsion angle between the phenyl ring and the carboxylate group is significantly increased in these compounds. Here, we present the very first examples of four MOFs all based on Sr²⁺ cations and trimesate-based linkers with three different degrees of fluorination as well as the known non-fluorinated counterpart: [Sr(HL)(H₂O)] · n H₂O [ 1 : L = mF-BTC^3–, n = 0.5, P1 , Z = 2; 2 : L = dF-BTC^3–, n = 0.5, C2/c, Z = 8; 3 : L = pF-BTC^3–, n = 1.5, C2/c, Z = 8; 4 : L = BTC^3–, n = 0.5, P1 , Z = 2; BTC^3– ≡ 1,3,5-benzenetricarboxylate (trimesate); mF-BTC^3– ≡ monofluorinated trimesate, dF-BTC^3– ≡ difluorinated trimesate, pF-BTC^3– ≡ per-(tri-)fluorinated trimesate]. Whereas 1 and known 4 are found to crystallize in isotypic structures and 2 in a very similar structural arrangement [all CN(Sr²⁺) = 9], 3 with the highest degree of fluorination exhibits a completely different crystal structure [CN(Sr²⁺) = 8], which is already obvious from the different composition. It is shown that the torsion angles between the phenyl ring and the carboxylate groups play an important structure-directing role. DSC/TGA investigations confirm that with increasing fluorination the thermal stability is decreased. However, the release temperature of water, i.e. the affinity to water, increases with the number of fluoro substituents.     

Gold(I) bis(N‐heterocyclic carbene) complexes: Metabolic stability,in vitro inhibition,and genotoxicity

We report the profiling of the metabolic stability, normal cell inhibition, and genotoxicity of the two gold complexes [Au (ⁱPr₂‐bimy)₂]PF₆ ( 1 ) and [Au (Fpyr)(ⁱPr₂‐bimy)]PF₆ ( 2 ), which show strong apoptotic activities in lung cancer cells. Liver microsomal tests revealed that the compounds have a relatively high half‐life compared to midazolam and do not suffer rapid metabolism and in vitro clearance. The cytotoxic potential of these compounds were also relatively weak in normal cells, with higher IC₅₀ values compared to cancer cells, with a 2–60 times difference. The Ames test revealed that the compounds do not give rise to any mutations as well. Overall, the compounds showed stability in liver microsomes, specificity for cancer cells, and a lack of genotoxic potential.     

Structural designing,spectral and computational studies of bioactive Schiff's base ligand and its transition metal complexes

Transition metal complexes of Mn(II) and Ni(II) have been synthesized with novel bioactive Schiff's base ligand. Schiff's base ligand i.e. benzoylacetone‐bis(2‐amino‐4‐methylbenzothioazole) has been synthesized via condensation reaction between 2‐amino‐4‐methylbenzothioazole and benzoylacetone in 2:1 ratio, respectively. Synthesized ligand has been characterized using elemental analysis, infra‐red, ¹H–NMR and mass spectroscopy techniques. Characterization of complexes was based on magnetic moment, molar conductance, elemental analysis, electronic spectra, infra‐red and EPR spectroscopic techniques. Molar conductance data suggest that metal complexes are non‐electrolytic in nature. Therefore, these complexes are formulated as [M(L)X₂], where M = Mn(II), Ni(II), L = Schiff's base ligand, X = Cl^?, CH₃COO^?, NO₃^?. Data of characterization study suggest octahedral geometry for Mn(II) and Ni(II) complexes. Geometry of metal complexes was also optimized with the help of computational study i.e. molecular modelling. Computational study also suggests octahedral geometry for complexes. Free ligand as well as its all metal complexes have been screened against the growth of pathogenic bacteria (E.coli, S.aureus) and fungi (C.albicans, C.krusei, C.parapsilosis, C.tropicalis) to assess their inhibition potential. The inhibition data revealed that metal complexes exhibit higher inhibition potential against the growth of bacteria and fungi microorganisms than free ligand.     

Pharmacophore modelling and electronic feature analysis of hydroxamic acid derivatives,the HIV integrase inhibitors

Hydroxamic acid derivatives with metal ion binding properties were collected from the literature to generate a pharmacophore and 3D-QSAR model for HIV strand transfer inhibition. The derived pharmacophore model (AAAHRR) recognizes both metal ion binding site and hydrophobic group. The QSAR model generated using this hypothesis expressed statistical significance (r ² = 0.971 for the training set and q ² = 0.913 for the test set). The ability of this pharmacophore model to retrieve other metal ion binding inhibitors was examined by screening the ChemBank database (ligandinfo) incorporated with 10 known strand transfer inhibitors. The studied favourable and unfavourable contours of chemical features (H-bond donor, acceptor and hydrophobic sites) revealed the role of hydrophobic substitution at the fluorobenzene ring and cyclization of the metal ion binding hydroxamic acid in effective integrase inhibition. Analysis of the frontier orbitals, HOMO and LUMO revealed that the nucleophilic / electrophilic interactions depend on the significant overlapping observed at the azaindole and hydroxamic acid groups. In essence, the generated pharmacophore model is competent enough to disclose the essential site-specific interactions involved in the inhibition of HIV integrase, and hence can be used in virtual screening to identify novel scaffolds as leads with increased anti-viral potency.     

Ferromagnetic Ordering in the Layer‐Structured Pd(HS2O7)2

The reaction of (NO₂)(CF₃SO₃) and elemental palladium in oleum (65 % SO₃) leads to violet single crystals of Pd(HS₂O₇)₂ (monoclinic, P2₁/c, Z=2, a=927.80(9), b=682.58(7), c=920.84(9) pm, β=117.756(2)°, wR₂=0.0439). In the crystal structure, the Pd²⁺ ions show an uncommon octahedral coordination of six oxygen atoms belonging to six HS₂O₇^? ions. The linkage of [PdO₆] octahedra and the hydrogendisulfate anions leads to a layer structure, and the layers are held together by hydrogen bonds. The unusual coordination of the Pd²⁺ ions results in an electronic d⁸ high‐spin configuration, which leads to the paramagnetic behavior of the compound. Moreover, at low temperature, a ferromagnetic ordering was observed with a Curie temperature of 8 K.     

Silver(I)‐N‐heterocyclic carbene complexes of bis‐imidazol‐2‐ylidenes having different aromatic‐spacers: synthesis,crystal structure,and in vitro antimicrobial and anticancer studies

A series of Ag(I) complexes ( 6 , 7 , 8 , 9 ) derived from imidazol‐2‐ylidenes was synthesized by reacting Ag₂O with an o‐, m‐, p‐xylyl or 1,3,5‐triazine‐linked imidazolium salts ( 1 , 2 , 3 , 4 ) and then characterizing these using various spectro‐analytical techniques. Additionally, triazine‐linked bis‐imidazolium salt 5 was characterized using the single‐crystal X‐ray diffraction method. Complexes 6–9 were formed from the N‐heterocyclic carbene ligand precursors 1–3 as PF₆^‐ salts in good yields. Conversely, salt 5 does not form Ag(I) complex even under various reaction conditions. Using ampicillin as a standard, complexes 6–9 were tested against bacteria strains Escherichia coli and Staphylococcus aureus as Gram‐negative and Gram‐positive bacteria, respectively, showing potent antimicrobial activities against the tested bacteria even at minimum inhibition concentration and bacterial concentration levels. Furthermore, the potential anticancer activities of the reported complexes were evaluated against the human colorectal cancer (HCT 116) cell lines, using 5‐fluorouracil as a standard drug. The highest anticancer activities were observed for complex 8 with an IC₅₀ value of 3.4 μm , whereas the lowest was observed for complex 9 with an IC₅₀ value of 18.1 μm . Copyright © 2013 John Wiley & Sons, Ltd.     

Determination of initiation rate of copolymerization of acrylonitrile with p-bromophenyl acrylate carried out in N,N-dimethylformamide

Studies of the initiation rate of the copolymerization reaction of acrylonitrile with p-bromophenyl acrylate initiated by azobisisobutyronitrile in dimethylformamide at 60°C are reported. The inhibition method involved use of stable Banfield's radical (N-[1,1-dimethyl 3-(N-oxidophenylimine)butyl]-N-phenylaminyl oxide). In the case of acrylonitrile, a side reaction effect of the initiation with the stable radical was observed along with a retarding effect resulting from inhibition reaction products (2k_df) = 8.2 × 10^?4 min^?1. During the inhibited homopolymerization of p-bromophenyl acrylate a very strong side initiation reaction effect results from the Banfield radical; the inhibition reaction products do not influence the further course of the polymerization reaction. Side initiation effects of the Banfield radical (BR) increase with increasing concentration of p-bromophenyl acrylate. The overall contribution of the side initiation reaction changes for different comonomer mixtures; with their compositions the actual changes are nonadditive. The inhibition reaction products do not influence the further course of copolymerization. The initiation rate in monomer mixtures depends on their composition and may be described by the following relation:      

Arylquinolinecarboxamides: Synthesis,in vitro and in silico studies against Mycobacterium tuberculosis

A series of fourteen 6-substituted-2-(methoxyquinolin-3-yl) methyl)-N-(pyridin-3-ylmethyl) benzamides was prepared from commercially available anilines in five simple and convenient synthetic steps. The structures of all new products were confirmed by routine spectroscopic methods: IR, ¹H and ¹³C NMR, and HRMS (electrospray ionization). The resulting arylquinolinecarboxamides were subjected to biological screening assay for in vitro inhibitory activity against Mycobacterium tuberculosis (Mtb) H37Rv strain. Several compounds exhibited modest antitubercular activity with compounds 8–11 , 15 and 19 exhibiting MIC₉₀ values in the range of 32–85 μM. The antitubercular data suggested that inhibition of Mtb can be imparted by the introduction of a non-polar substituent on C-6 of the quinoline scaffold. Further, to understand the possible mode of action of the series, the reported compounds and bedaquiline were subjected to in silico docking studies against MtbATPase to determine their potential to interfere with the mycobacterial adenosine triphosphate (ATP) synthase. The results showed that these compounds have the potential to serve as antimycobacterial agents. In silico ADME pharmacokinetic prediction results showed the ability of these arylquinolinecarcboxamides to be absorbed, distributed, metabolized and excreted efficiently.     

Regulation of α‐Chymotrypsin Catalysis by Ferric Porphyrins and Cyclodextrins

Positively charged α‐chymotrypsin (ChT) formed a 1:1 complex with negatively charged 5,10,15,20‐tetrakis(4‐sulfonatophenyl)porphyrinato iron(III) (FeTPPS) in phosphate buffer at pH 7.4 through electrostatic interaction. In spite of the large binding constant (K=4.8×10⁵ M ^?1), FeTPPS could not completely inhibit the catalysis of ChT in the hydrolysis of the model substrate, N‐succinyl‐L ‐phenylalanine p‐nitroanilide (SPNA). The degree of inhibition (60 %) was saturated at 1.6 equivalents of FeTPPS, which indicates that covering of the active site of ChT by FeTPPS was insufficient. The enzymatic activity lowered by FeTPPS was entirely recovered for the freshly prepared sample when the porphyrin on the protein surface was detached by per‐O‐methylated β‐cyclodextrin (TMe‐β‐CD), which formed a stable 1:2 inclusion complex with FeTPPS (K₁=1.26×10⁶ M ^?1, K₂=6.3×10⁴ M ^?1). FeTPPS gradually induced irreversible denaturation of ChT, and the denatured ChT further lost its catalytic ability. No repairing effect of TMe‐β‐CD was observed with irreversibly denatured ChT. A new reversible inhibitor, 5,10,15,20‐tetrakis[4‐(3,5‐dicarboxyphenylmethoxy)phenyl]porphyrinato iron(III) (FeP8M), was then designed, and its inhibitory behavior was examined. FeP8M formed very stable 1:1 and 1:2 FeP8M/ChT complexes with ChT, the K₁ and K₂ values being 2.0×10⁸ and 1.0×10⁶ M ^?1, respectively. FeP8M effectively inhibited the ChT‐catalyzed hydrolysis of SPNA (maximum degree of inhibition=85 %), and the activity of ChT was recovered by per‐O‐methylated γ‐cyclodextrin. No irreversible denaturation of ChT occurred upon binding with FeP8M. The kinetic data support the observation that, for nonincubated samples, both inhibitors did not cause significant conformational change in ChT and inhibited the ChT activity by covering the active site of the enzyme.     

Molecular-orbital treatment of complex cations of magnesium and beryllium with acetonitrile

Semiempirical MO calculations of the self-consistent charge and configuration (SCCC ) method are reported for the acetonitrile–metal solvated species (CH₃CN)_xMⁿ⁺, where M = Be²⁺ and Mg²⁺. Comparison of the delocalization energies for various chemical structures x = 1, 2, 3, 4, 6 leads to an expectation of a tetrahedral structure for the Be²⁺ species and an octahedral structure for the Mg²⁺ species. The electronic nature of the donor–acceptor interaction is also discussed.     

Synthesis and Feasibility Evaluation of a new Trastuzumab Conjugate Integrated with Paclitaxel and 89Zr for Theranostic Application Against HER2-Expressing Breast Cancers

The preparation and in vitro evaluation of a theranostic conjugate composed of trastuzumab, paclitaxel (PTX), and deferoxamine (DFO)-chelated ⁸⁹Zr have been reported. These comounds have potential applications against HER2 receptor positive breast cancers. We conjugated DFO and PTX to trastuzumab by exploiting simple conjugation chemistry. The conjugate (DFO-trastuzumab-PTX) showed excellent radiolabeling efficiency with ⁸⁹Zr and the labeled conjugate had high in vitro stability in human serum. Furthermore, DFO-trastuzumab-PTX displayed comparable cytotoxicity with PTX and ⁸⁹Zr-DFO-trastuzumab-PTX exhibited HER2 receptor-mediated binding on HER2-positive MDA-MB-231 breast cancer cells. The results of our in vitro study indicate high potential of ⁸⁹Zr-DFO-trastuzumab-PTX to be utilized in the theranostic application against HER2-postive breast cancers.