An assessment of crucial structural contributors of HDAC6 inhibitors through fragment-based non-linear pattern recognition and molecular dynamics simulation approaches.

Amidst the Zn2+-dependant isoforms of the HDAC family, HDAC6 has emerged as a potential target associated with an array of diseases, especially cancer and neuronal disorders like Rett's Syndrome, Alzheimer's disease, Huntington's disease, etc. Also, despite the availability of a handful of HDAC inhibitors in the market, their non-selective nature has restricted their use in different disease conditions. In this situation, the development of selective and potent HDAC6 inhibitors will provide efficacious therapeutic agents to treat different diseases. In this context, this study has been carried out to evaluate the potential structural contributors of quinazoline-cap-containing HDAC6 inhibitors via machine learning (ML), conventional classification-dependant QSAR, and MD simulation-based binding mode of interaction analysis toward HDAC6 binding. This combined conventional and modern molecular modeling study has revealed the significance of the quinazoline moiety, substitutions present at the quinazoline cap group, as well as the importance of molecular property, number of hydrogen bond donor-acceptor functions, carbon-chlorine distance that significantly affects the HDAC6 binding of these inhibitors, subsequently affecting their potency . Interestingly, the study also revealed that the substitutions such as the chloroethyl group, and bulky quinazolinyl cap group can affect the binding of the cap function with the amino acid residues present in the loops proximal to the catalytic site of HDAC6. Such contributions of cap groups can lead to both stabilization and destabilization of the cap function after occupying the hydrophobic catalytic site by the aryl hydroxamate linker-ZBG functions.

Deep-Learning-Assisted Assessment of DNA Damage Based on Foci Images and Its Application in High-Content Screening of Lead Compounds.

DNA damage is one of major culprits in many complex diseases; thus, there is great interest in the discovery of novel lead compounds regulating DNA damage. However, there remain plenty of challenges to evaluate DNA damage through counting the amount of intranuclear foci. Herein, a deep-learning-based open-source pipeline, FociNet, was developed to automatically segment full-field fluorescent images and dissect DNA damage of each cell. We annotated 6000 single-nucleus images to train the classification ability of the proposed computational pipeline. Results showed that FociNet achieved satisfying performance in classifying a single cell into a normal, damaged, or nonsignaling (no fusion-protein expression) state and exhibited excellent compatibility in the assessment of DNA damage based on fluorescent foci images from various imaging platforms. Furthermore, FociNet was employed to analyze a data set of over 5000 foci images from a high-content screening of 315 natural compounds from traditional Chinese medicine. It was successfully applied to identify several novel active compounds including evodiamine, isoliquiritigenin, and herbacetin, which were found to reduce 53BP1 foci for the first time. Among them, isoliquiritigenin from Glycyrrhiza uralensis Fisch. exerts a significant effect on attenuating double strand breaks as indicated by the comet assay. In conclusion, this work provides an artificial intelligence tool to evaluate DNA damage on the basis of microscopy images as well as a potential strategy for high-content screening of active compounds.

1,2,4-Triazolo-quinazoline-thiones: Non-conventional synthetic approach, study of solvatochromism and antioxidant assessment.

A non-conventional methodology has been utilized for the synthesis of a series of 1,2,4-triazolo-quinazoline-thiones (2a-l). Here the reaction was carried out between 1,2,4-triazolo-quinazolinones (1a-l), in the presence of 1,4-dioxane. The mixture was irradiated under microwave (100W) for 7min to obtain targeted molecules (2a-l). All the synthesized molecules were confirmed by (1)H, (13)C NMR and HRMS. The solvatochromic property (absorption spectra) of compounds (2a-l) in solvents of different polarities was studied. The compounds (2a-l) were further subjected for their in vitro free radical screening using 2,2-diphenyl-1-picrylhydrazyl (DPPH) method and also screened for their in vitro anti-fungal property against Aspergillus flavus (A. flavus) and Aspergillus niger (A. niger). The results from free radical scavenging assay showed promising activity for compounds 2a, e-i, whereas compound 2d showed significant antioxidant activity when compared to ascorbic acid. In vitro anti-fungal study showed that the 1,2,4-triazolo-quinazoline-thiones (2a-l) had significant activity against A. flavus and A. niger compared with widely used antifungal agent Fluconazole.

Synthesis, biological evaluation, and physicochemical property assessment of 4-substituted 2-phenylaminoquinazolines as Mer tyrosine kinase inhibitors.

Current results identified 4-substituted 2-phenylaminoquinazoline compounds as novel Mer tyrosine kinase (Mer TK) inhibitors with a new scaffold. Twenty-one 2,4-disubstituted quinazolines (series 4-7) were designed, synthesized, and evaluated against Mer TK and a panel of human tumor cell lines aimed at exploring new Mer TK inhibitors as novel potential antitumor agents. A new lead, 4b, was discovered with a good balance between high potency (IC50 0.68µM) in the Mer TK assay and antiproliferative activity against MV4-11 (GI50 8.54µM), as well as other human tumor cell lines (GI50<20µM), and a desirable druglike property profile with low logP value (2.54) and high aqueous solubility (95.6µg/mL). Molecular modeling elucidated an expected binding mode of 4b with Mer TK and necessary interactions between them, thus supporting the hypothesis that Mer TK might be a biologic target of this kind of new active compound.

Rapid assessment of drug resistance of cancer cells to gefitinib and carboplatin using optical imaging.

The overall goal of this study was to evaluate optical molecular imaging approaches to determine the drug response of chemotherapy and molecular targeted agents in drug sensitive and drug resistant cell lines. The optical molecular imaging approaches selected in this study were based on changes in intracellular uptake and retention of choline and glucose molecules. The breast cancer cell lines were treated with a molecular targeted anti-EGFR therapy. The bladder cancer cell lines were treated with a conventional chemotherapy approach. Sensitivity of optical molecular imaging approach was also compared with conventional cell viability and cell growth inhibition assays. Results demonstrate that optical molecular imaging of changes in intracellular uptake of metabolites was effective in detecting drug susceptibility for both molecular targeted therapy in breast cancer cells and chemotherapy in bladder cancer cells. Between the selected metabolites for optical molecular imaging, changes in glucose metabolic activity showed higher sensitivity in discrimination between the drug sensitive and drug resistant cell lines. The results demonstrated that optical molecular imaging approaches more significantly sensitive as compared to the conventional cell viability and growth assays. Overall, the results demonstrate potential of optical molecular imaging of metabolic activity to improve sensitivity of in-vitro drug response assays.

A comparative study of binding affinities for 6,7-dimethoxy-4-pyrrolidylquinazolines as phosphodiesterase 10A inhibitors using the linear interaction energy method.

The linear interaction energy (LIE) method was used to estimate the free energies of binding for a set of 27 pyrrolidylquinazoline derivatives as phosphodiesterase 10A inhibitors. Twenty-six X-ray crystal structures of phosphodiesterase 10A and two sampling methods, minimization and Hybrid Monte Carlo, were used to assess the affinity models based on the linear interaction energies. The best model was obtained based on the parameters α=0.16 and ß=0.04, which represent non-polar and polar interactions, respectively, with a root mean square error (RMSE) of 0.42kcal/mol (R(2)=0.71) and 0.52kcal/mol (R(2)=0.86) for the training and test sets, respectively. In addition, the applicability domain of the model was investigated. After validation of the models, the best model was subsequently used in a virtual screening process, which resulted in a set of optimized compounds. The models developed in this study could be useful as filter for virtual screening and lead optimization processes for phosphodiesterase 10A drug developments.

Synthesis and assessment of 4-aminotetrahydroquinazoline derivatives as tick-borne encephalitis virus reproduction inhibitors.

Tick-borne encephalitis virus (TBEV) belonging to Flavivirus genus causes severe infection in humans. The search for therapeutically relevant compounds targeting TBEV requires the exploration of novel chemotypes. A versatile synthesis of previously unknown 4-aminopyrimidines and 4-aminopyrimidine N-oxides based on a fluorosubstituted heterocyclic core is described. A representative series of 4-aminotetrahydroquinazoline derivatives, containing aliphatic and aromatic substituents as well as the adamantane framework, was obtained and their activity against tick-borne encephalitis virus reproduction was studied. Nine compounds were found to inhibit TBEV entry into the host cells. A bulky hydrophobic adamantyl group was identified to be important for the antiviral activity. The developed synthetic route allowed an easy access to a consistent compound library for further structure-activity relationship studies.

Determination of raltitrexed in human plasma by high performance liquid chromatography-electrospray ionization-mass spectrometry.

A sensitive high performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) assay was developed to determine raltitrexed in human plasma. After addition of benazeprilat as the internal standard (IS), methanol was used to produce a protein-free extract. Chromatographic separation was achieved with a Zorbax SB-C18 column (Narrow-Bore 2.1 mmx150 mm, 5-microm) using a mobile phase of acetonitrile-water containing 0.1% formic acid and 2% methanol (21.9:78.1, v/v). Raltitrexed was determined with electrospray ionization-mass spectrometry. HPLC-ESI-MS was performed in the selected ion monitoring (SIM) mode using target ions at [M+H]+ m/z 459.1 for raltitrexed and [M+H]+ m/z 397.1 for IS. Calibration curves were linear over the range of 2.0-3000 ng/ml. The lower limit of quantification was 2.0 ng/ml. The intra- and inter-batch variability values were less than 6.7% and 10.3%, respectively. The mean plasma extraction recovery of raltitrexed was in the range of 85.2-91.1%. The method was successfully applied to determine the plasma concentrations of raltitrexed in eight Chinese colorectal cancer patients.

The centroidal algorithm in molecular similarity and diversity calculations on confidential datasets.

Chemical structure provides exhaustive description of a compound, but it is often proprietary and thus an impediment in the exchange of information. For example, structure disclosure is often needed for the selection of most similar or dissimilar compounds. Authors propose a centroidal algorithm based on structural fragments (screens) that can be efficiently used for the similarity and diversity selections without disclosing structures from the reference set. For an increased security purposes, authors recommend that such set contains at least some tens of structures. Analysis of reverse engineering feasibility showed that the problem difficulty grows with decrease of the screen's radius. The algorithm is illustrated with concrete calculations on known steroidal, quinoline, and quinazoline drugs. We also investigate a problem of scaffold identification in combinatorial library dataset. The results show that relatively small screens of radius equal to 2 bond lengths perform well in the similarity sorting, while radius 4 screens yield better results in diversity sorting. The software implementation of the algorithm taking SDF file with a reference set generates screens of various radii which are subsequently used for the similarity and diversity sorting of external SDFs. Since the reverse engineering of the reference set molecules from their screens has the same difficulty as the RSA asymmetric encryption algorithm, generated screens can be stored openly without further encryption. This approach ensures an end user transfers only a set of structural fragments and no other data. Like other algorithms of encryption, the centroid algorithm cannot give 100% guarantee of protecting a chemical structure from dataset, but probability of initial structure identification is very small-order of 10(-40) in typical cases.

Erlotinib OSI/Roche/Genentech.

Erlotinib (CP-358774, OSI-774, Tarceva), a quinazoline derivative, is an orally active epidermal growth factor receptor tyrosine kinase inhibitor under development jointly by Genentech, OSI (formerly Oncogene Science) and Roche, both as monotherapy and combination therapy for the potential treatment of solid tumors, including non-small-cell lung cancer (NSCLC) and pancreatic, breast, head and neck cancers [203487]. Development of the compound is most advanced for NSCLC and pancreatic cancer; in July 2001, phase III combination trials were initiated for NSCLC [416835]. In October 2001, phase III monotherapy trials in NSCLC and phase III combination trials in pancreatic cancer were also initiated [426704]. In Japan, the compound was in phase I studies in January 2002 [439189].

ZD-1839 (AstraZeneca).

AstraZeneca is developing ZD-1839, an inhibitor of epidermal growth factor receptor 1 (EGFR1) tyrosine kinase, for potential treatment of cancers which overexpress EGF receptors, including non-small cell lung cancer (NSCLC) and pancreatic cancer [196279], [270898]. Phase III studies had started by August 2000 [349551], [350295], [353050], [377656], with first results being expected at the 2001 meetings of the American Association for Cancer Research (AACR) and the American Society for Clinical Oncology (ASCO). The US FDA has issued ZD-1839 with Fast Track status [350295], [353050]. In September 2000, the company expected global NDA filing to take place at the end of 2001, with launch in the next four to five years [383469]. In January 1999, ABN Amro predicted sales of US $25 million in 2004 rising to $82 million in 2005 [316250]. In March 1999, Lehman Brothers predicted a 30% probability that the drug would reach worldwide markets and be launched onto the market in 2004 [336599]. In June 2000, Deutsche Bank predicted sales of US $8 million in 2002, rising to $100 million in 2003 [374500]. In September 2000, analysts Merrill Lynch predicted a launch in 2002 with sales estimated at UK 50 million pounds, rising to 360 million pounds in 2004, while in December 2000, the analysts predicted a filing date in the fourth quarter of 2001 [383742], [396280]. Also in December 2000, Lehman Brothers predicted a filing date late in 2001, and a possible Fast Track review. They also estimated peak sales of US $1 billion [394606].