Guang-Fu Yang

A review on recent developments of indole-containing antiviral agents.

Abstract Indole represents one of the most important privileged scaffolds in drug discovery. Indole derivatives have the unique property of mimicking the structure of peptides and to bind reversibly to enzymes, which provide tremendous opportunities to discover novel drugs with different modes of action. There are seven indole-containing commercial drugs in the Top-200 Best Selling Drugs by US Retail Sales in 2012. There are also an amazing number of approved indole-containing drugs in the market as well as compounds currently going through different clinical phases or registration statuses. This review focused on the recent development of indole derivatives as antiviral agents with the following objectives: 1) To present one of the most comprehensive listings of indole antiviral agents, drugs on market or compounds in clinical trials; 2) To focus on recent developments of indole compounds (including natural products) and their antiviral activities, summarize the structure property, hoping to inspire new and even more creative approaches; 3) To offer perspectives on how indole scaffolds as a privileged structure might be exploited in the future.

A Coumarin-Based Fluorescent Probe for Selective and Sensitive Detection of Thiophenols and Its Application

The development of probes for specific thiophenol detection is of great importance, due to the toxicity of thiophenols and their derivatives in the environment. In the present study, a novel fluorescent probe was rationally designed for detecting thiophenols via an intramolecular charge transfer mechanism. The developed probe selectively and sensitively distinguished thiophenols from aliphatic thiols. It displayed a large Stokes shift (145 nm) and >280-fold fluorescence enhancement. Moreover, the new probe not only displayed excellent cell permeability for the successful detection of thiophenol in HEK293 cells but also quantitatively measured thiophenols in water samples with good recovery (more than 90%), indicating that it has promising prospects for application for thiophenol sensing in environmental and biological sciences.

Synthesis and antitumor activity of novel dithiocarbamate substituted chromones

A series of chromone derivatives bearing diverse dithiocarbamate moieties were designed and synthesized via a three-component reaction protocol. Their in vitro antitumor activities were evaluated by MTT method against HCCLM-7, Hela, MDA-MB-435S, SW-480, Hep-2 and MCF-7. Two compounds (3-chloro-4-oxo-4H-chromen-2-yl)methyl piperidine-1-carbodithioate (Iq) and (6-chloro-4-oxo-4H-chromen-3-yl)methyl piperidine-1-carbodithioate (IIu), were identified as the most promising candidate due to their high potency and broad-spectrum. Further flow-activated cell sorting analysis revealed that compounds Iq and IIu arrest the cell cycle of SW-480 and MDA-MB-435s both in G(2)/M phase with dose-dependent effect and might display apoptosis-inducing effect on these tumor cell lines.

Subnanomolar Inhibitor of Cytochrome bc1 Complex Designed by Optimizing Interaction with Conformationally Flexible Residues

Cytochrome bc(1) complex (EC 1.10.2.2, bc(1)), an essential component of the cellular respiratory chain and the photosynthetic apparatus in photosynthetic bacteria, has been identified as a promising target for new drugs and agricultural fungicides. X-ray diffraction structures of the free bc(1) complex and its complexes with various inhibitors revealed that the phenyl group of Phe274 in the binding pocket exhibited significant conformational flexibility upon different inhibitors binding to optimize respective pi-pi interactions, whereas the side chains of other hydrophobic residues showed conformational stability. Therefore, in the present study, a strategy of optimizing the pi-pi interaction with conformationally flexible residues was proposed to design and discover new bc(1) inhibitors with a higher potency. Eight new compounds were designed and synthesized, among which compound 5c, with a K(i) value of 570 pM, was identified as the most promising drug or fungicide candidate, significantly more potent than the commercially available bc(1) inhibitors, including azoxystrobin (AZ), kresoxim-methyl (KM), and pyraclostrobin (PY). To our knowledge, this is the first bc(1) inhibitor discovered from structure-based design with a potency of subnanomolar K(i) value. For all of the compounds synthesized and assayed, the calculated binding free energies correlated reasonably well with the binding free energies derived from the experimental K(i) values, with a correlation coefficient of r(2) = 0.89. The further inhibitory kinetics studies revealed that 5c is a noncompetitive inhibitor with respect to substrate cytochrome c, but it is a competitive inhibitor with respect to substrate ubiquinol. Due to its subnanomolar K(i) potency and slow dissociation rate constant (k(-0) = 0.00358 s(-1)), 5c could be used as a specific probe for further elucidation of the mechanism of bc(1) function and as a new lead compound for future drug discovery.

Synthesis, fungicidal, and insecticidal activities of beta-Methoxyacrylate-containing N-acetyl pyrazoline derivatives.

1-Acetyl-3,-5-diarylpyrazolines have received considerable interests from the fields of medicinal and agricultural chemistry due to their broad spectrum of biological activities. To discover new lead compounds exhibiting both fungicidal and insecticidal activities, a series of pyrazoline derivatives were designed and synthesized by introducing the beta-methoxyacrylate pharmacophore into the scaffold of 1-acetyl-3,5-diarylpyrazoline. The fungicidal activities against Pseudoperoniospora cubensis, Sphaerotheca fuliginea, Botrytis cinerea, and Rhizoctonia solani and the insecticidal activities against Aphis medicagini, Nilaparvata legen, Mythima separata, and Tetranychus cinnabarnus were screened. The most potent compound 13, 1-aceto-3-[m-[o-(E-1-methoxycarboxyl-2-methoxy)-1-yl]benzyloxy]phenyl-5-(benzo-[1,3]-dioxolyl)-4,5-dihydro- pyrazoline, was identified. Its fungicidal IC(50) values against P. cubensis and S. fuliginea are 26.6 and 57.6 microg mL(-1), respectively, while its insecticidal LC(50) value against M. separata is 26.6 microg mL(-1). These results indicated that compound 13 could be used as a lead for further developing new pyrazoline type products exhibiting both fungicidal and insecticidal activities.

Development of Quantitative Structure-Activity Relationships and Its Application in Rational Drug Design

Over forty years have elapsed since Hansch and Fujita published their pioneering work of quantitative structure-activity relationships (QSAR). Following the introduction of Comparative Molecular Field Analysis (CoMFA) by Cramer in 1998, other three-dimensional QSAR methods have been developed. Currently, combination of classical QSAR and other computational techniques at three-dimensional level is of greatest interest and generally used in the process of modern drug discovery and design. During the last several decades, a number of different mythologies incorporating a range of molecular descriptors and different statistical regression ways have been proposed and successfully applied in developing of new drugs, thus QSAR method has been proven to be indispensable in not only the reliable prediction of specific properties of new compounds, but also the help to elucidate the possible molecular mechanism of the receptor-ligand interactions. Here, we review the recent developments in QSAR and their applications in rational drug design, focusing on the reasonable selection of novel molecular descriptors and the construction of predictive QSAR models by the help of advanced computational techniques.

Computational Discovery of Picomolar Qo Site Inhibitors of Cytochrome bc1 Complex

A critical challenge to the fragment-based drug discovery (FBDD) is its low-throughput nature due to the necessity of biophysical method-based fragment screening. Herein, a method of pharmacophore-linked fragment virtual screening (PFVS) was successfully developed. Its application yielded the first picomolar-range Q(o) site inhibitors of the cytochrome bc(1) complex, an important membrane protein for drug and fungicide discovery. Compared with the original hit compound 4 (K(i) = 881.80 nM, porcine bc(1)), the most potent compound 4f displayed 20 507-fold improved binding affinity (K(i) = 43.00 pM). Compound 4f was proved to be a noncompetitive inhibitor with respect to the substrate cytochrome c, but a competitive inhibitor with respect to the substrate ubiquinol. Additionally, we determined the crystal structure of compound 4e (K(i) = 83.00 pM) bound to the chicken bc(1) at 2.70 Å resolution, providing a molecular basis for understanding its ultrapotency. To our knowledge, this study is the first application of the FBDD method in the discovery of picomolar inhibitors of a membrane protein. This work demonstrates that the novel PFVS approach is a high-throughput drug discovery method, independent of biophysical screening techniques.

Design, synthesis, and 3D-QSAR analysis of novel 1,3,4-oxadiazol-2(3H)-ones as protoporphyrinogen oxidase inhibitors.

Protoporphyrinogen oxidase (PPO, EC 1.3.3.4) has been identified as one of the most significant action targets for a large chemically diverse family of herbicides that exhibit some interesting characteristics, such as low use rate, low toxicity to mammals, and low environmental impact. As a continuation of research work on the development of new PPO inhibitors, some benzothiazole analogues of oxadiargyl, an important PPO-inhibiting commercial herbicide, were designed and synthesized by ring-closing of the substituents at the C-4 and C-5 positions. The bioassay results indicated that the series 8, 9, and 10 have good PPO inhibition activity with k(i) values ranging from 0.25 to 18.63 microM. Most interestingly, 9l, ethyl 2-((5-(5-tert-butyl-2-oxo-1,3,4-oxadiazol-2(3H)-yl)-6-fluorobenzothiazol-2-yl)sulfanyl) propanoate, was identified as the most promising candidate due to its high PPO inhibition effect (k(i) = 1.42 microM) and broad spectrum postemergence herbicidal activity at the concentration of 37.5 g of ai/ha.

Quantitative structure-activity relationship for cyclic imide derivatives of protoporphyrinogen oxidase inhibitors: a study of quantum chemical descriptors from density functional theory.

This study examined the applicability of various density functional theory (DFT)-based descriptors, such as energy gap (DeltaE) between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), weighted nucleophilic atomic frontier electron density (WNAFED, FNi), mean molecular polarizability (alpha), and net atomic charge (Qi), in quantitative structure-activity relationship (QSAR) studies on a class of important protoporphyrinogen oxidase (Protox) inhibitors including a series of cyclic imide derivatives with various heterocyclic rings and substituents. Our QSAR analysis using the quantum chemical descriptors calculated at the B3LYP/6-31G(d,p) level led to a useful explicit correlation relationship, i.e. pI50 = -5.7414 + 0.1424alpha - 0.0003alpha2 - 0.4546FNC* + 0.2974QN** (n=26, R2=0.87), showing that descriptors mean molecular polarizability, alpha, and WNAFED FNC* of a critical carbon atom and net atomic charge (Qi) in the molecules are most likely responsible for the in vitro biological activity of cyclic imides. It has been shown that the use of the DFT-based quantum chemical descriptors indeed led to a better QSAR equation than that obtained from the use of the corresponding descriptors calculated at a semiempirical PM3 level. The present work demonstrates that the DFT-based quantum chemical descriptors are potentially useful in the future QSAR studies for quantitatively predicting biological activity, and, therefore, the DFT-based QSAR approach could be expected to help facilitate the design of additional substituted cyclic imide derivatives of Protox inhibitors with the potentially higher biological activity.

Design, syntheses and 3D-QSAR studies of novel N-phenyl pyrrolidin-2-ones and N-phenyl-1H-pyrrol-2-ones as protoporphyrinogen oxidase inhibitors.

The characteristics of low application rates, good crop selectivity, low residue and environmental safety exhibited by Protoporphyrinogen oxidase (PPO, EC 1.3.3.4)-inhibiting herbicides have attracted a world-wide research interests. As continuation of our research work on the development of new PPO inhibitors, a series of mono-carbonyl analogues of cyclic imides, N-phenyl pyrrolidin-2-ones and N-phenyl-1H-pyrrol-2-ones, were designed and synthesized based on previously established DFT-QSAR results. The PPO inhibition activities of 29 newly synthesized compounds were tested and a predictive comparative molecular field analysis (CoMFA) model was established with the conventional correlation coefficient r(2)=0.980 and the cross-validated coefficient q(2)=0.518. According to the CoMFA model, the substituent effects on the PPO inhibition activity were explained reasonably. Further greenhouse assay showed that 2-(4-chloro-2-fluoro-5-propoxy-phenyl)-2,3,4,5,6,7-hexahydro-isoindol-1-one (C(6), k(i)=0.095μM) and 2-(5-allyloxy-4-chloro-2-fluorophenyl)-2,3,4,5,6,7-hexahydro-isoindol-1-one (C(7), k(i)=0.12μM) displayed excellent post-emergency herbicidal activity at the concentration of 150g.ai/ha against seven tested weeds. Due to their high PPO inhibition effect and broad spectrum herbicidal activity, these two compounds have the potential for further study on crop selectivity and field trial. These results confirmed once again that only one of the carbonyl groups of cyclic imides is essential to the PPO inhibition activity.