A Hexasaccharide Containing Rare 2‐O‐Sulfate‐Glucuronic Acid Residues Selectively Activates Heparin Cofactor II

Glycosaminoglycan (GAG) sequences that selectively target heparin cofactor II (HCII), a key serpin present in human plasma, remain unknown. Using a computational strategy on a library of 46 656 heparan sulfate hexasaccharides we identified a rare sequence consisting of consecutive glucuronic acid 2‐O ‐sulfate residues as selectively targeting HCII. This and four other unique hexasaccharides were chemically synthesized. The designed sequence was found to activate HCII ca. 250‐fold, while leaving aside antithrombin, a closely related serpin, essentially unactivated. This group of rare designed hexasaccharides will help understand HCII function. More importantly, our results show for the first time that rigorous use of computational techniques can lead to discovery of unique GAG sequences that can selectively target GAG‐binding protein(s), which may lead to chemical biology or drug discovery tools.     

A Strategy for Creating Organisms Dependent on Noncanonical Amino Acids

The use of noncanonical amino acids (ncAAs) to control the viability of an organism provides a strategy for the development of conditional “kill switches” for live vaccines or engineered human cells. We report an approach inspired by the posttranslational acetylation/deacetylation of lysine residues, in which a protein encoded by a gene with an in‐frame nonsense codon at an essential lysine can be expressed in its native state only upon genetic incorporation of N ‐ϵ ‐acetyl‐l ‐Lys (AcK), and subsequent enzymatic deacetylation in the host cell. We applied this strategy to two essential E. coli enzymes: the branched‐chain aminotransferase BCAT and the DNA replication initiator protein DnaA. We also devised a barnase‐based conditional suicide switch to further lower the escape frequency of the host cells. This strategy offers a number of attractive features for controlling host viability, including a single small‐molecule‐based kill switch, low escape frequency, and unaffected protein function.     

Molecular docking studies of selected tricyclic and quinone derivatives on trypanothione reductase of Leishmania infantum

Visceral leishmaniasis, most lethal form of Leishmaniasis, is caused by Leishmania infantum in the Old world. Current therapeutics for the disease is associated with a risk of high toxicity and development of drug resistant strains. Thiol‐redox metabolism involving trypanothione and trypanothione reductase, key for survival of Leishmania, is a validated target for rational drug design. Recently published structure of trypanothione reductase (TryR) from L. infantum, in oxidized and reduced form along with Sb(III), provides vital clues on active site of the enzyme. In continuation with our attempts to identify potent inhibitors of TryR, we have modeled binding modes of selected tricyclic compounds and quinone derivatives, using AutoDock4. Here, we report a unique binding mode for quinone derivatives and 9‐aminoacridine derivatives, at the FAD binding domain. A conserved hydrogen bonding pattern was observed in all these compounds with residues Thr335, Lys60, His461. With the fact that these residues aid in the orientation of FAD towards the active site forming the core of the FAD binding domain, designing selective and potent compounds that could replace FAD in vivo during the synthesis of Trypanothione reductase can be deployed as an effective strategy in designing new drugs towards Leishmaniasis. We also report the binding of Phenothiazine and 9‐aminoacridine derivatives at the Z site of the protein. The biological significance and possible mode of inhibition by quinone derivatives, which binds to FAD binding domain, along with other compounds are discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

A Stable Isotopic Pre-digestion Labeling Method for Protein Quantitative Analysis Using Matrix-assisted Laser Desorption/ionization Mass Spectrometry

As an extension of our previous work, here a strategy was demonstrated for protein identification and quantification analyses utilizing a combination of stable isotope chemical labeling with subsequent denaturation, enzymatic digestion and matrix assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS). Using [d₀]‐ and [d₆]‐4,6‐dimethoxy‐2‐(methylsulfonyl)pyrimidine ([d₀]‐/[d₆]‐DMMSP), stable isotopic labels were incorporated before digestion. The comparative samples were combined before labeling after digestion, thus biases resulting from differences in sample digestion were avoided and the higher accuracy of quantification could be attained. The labeling was spatial‐selective to particular residues of cysteine, lysine, and tyrosine before denaturation, which could lead to a better universality of the strategy for cysteine‐free proteins. In addition, some lysine residues were blocked after labeling, the partly destroyed recognition sites could simplify the trypsin hydrolysates and hence facilitate the MS complexity. Together, our one‐step labeling strategy combined several desirable properties such as spatial‐selective labeling, reliability of quantitative results, simplification of analysis of complex systems and direct analysis with minimum sample handling. Our results demonstrate the usefulness of the method for analyzing lysozyme in egg white. The method was expected to provide a new powerful tool for comparative proteome research.     

Freezing the Dynamic Gap for Selectivity: Motion‐Based Design of Inhibitors of the Shikimate Kinase Enzyme

Shikimate kinase (SK), the fifth enzyme of the aromatic amino acid biosynthesis, is a recognized target for antibiotic drug discovery. The potential of the distinct dynamic apolar gap, which isolates the natural substrate from the solvent environment for catalysis, and the motion of Mycobacterium tuberculosis and Helicobacter pylori SK enzymes, which was observed by molecular dynamics simulations, was explored for inhibition selectivity. The results of the biochemical and computational studies reveal that the incorporation of bulky groups at position C5 of 5‐aminoshikimic acid and the natural substrate enhances the selectivity for the H. pylori enzyme due to key motion differences in the shikimic acid binding domain (mainly helix α5). These studies show that the less‐exploited motion‐based design approach not only is an alternative strategy for the development of competitive inhibitors, but could also be a way to achieve selectivity against a particular enzyme among its homologues.     

A Cyclized Helix‐Loop‐Helix Peptide as a Molecular Scaffold for the Design of Inhibitors of Intracellular Protein–Protein Interactions by Epitope and Arginine Grafting

The design of inhibitors of intracellular protein–protein interactions (PPIs) remains a challenge in chemical biology and drug discovery. We propose a cyclized helix‐loop‐helix (cHLH) peptide as a scaffold for generating cell‐permeable PPI inhibitors through bifunctional grafting: epitope grafting to provide binding activity, and arginine grafting to endow cell‐permeability. To inhibit p53–HDM2 interactions, the p53 epitope was grafted onto the C‐terminal helix and six Arg residues were grafted onto another helix. The designed peptide cHLHp53‐R showed high inhibitory activity for this interaction, and computational analysis suggested a binding mode for HDM2. Confocal microscopy of cells treated with fluorescently labeled cHLHp53‐R revealed cell membrane penetration and cytosolic localization. The peptide inhibited the growth of HCT116 and LnCap cancer cells. This strategy of bifunctional grafting onto a well‐structured peptide scaffold could facilitate the generation of inhibitors for intracellular PPIs.     

An Apoptosis‐Inducing Peptidic Heptad That Efficiently Clusters Death Receptor 5

Multivalent ligands of death receptors hold particular promise as tumor cell‐specific therapeutic agents because they induce an apoptotic cascade in cancerous cells. Herein, we present a modular approach to generate death receptor 5 (DR5) binding constructs comprising multiple copies of DR5 targeting peptide (DR5TP) covalently bound to biomolecular scaffolds of peptidic nature. This strategy allows for efficient oligomerization of synthetic DR5TP‐derived peptides in different spatial orientations using a set of enzyme‐promoted conjugations or recombinant production. Heptameric constructs based on a short (60–75 residues) scaffold of a C‐terminal oligomerization domain of human C4b binding protein showed remarkable proapoptotic activity (EC₅₀=3 nm ) when DR5TP was ligated to its carboxy terminus. Our data support the notion that inter‐ligand distance, relative spatial orientation and copy number of receptor‐binding modules are key prerequisites for receptor activation and cell killing.     

Proximity-induced amino-yne reaction for selective MDM4 conjugation via propargylated sulfonium

Whilst most bioorthogonal reactions focus on targeting binding-site cysteine residues, proximity-induced reactivity effect ensures that reaction also occurs at nucleophilic lysine residues. We report one example here that the propargylated-sulfonium center undergoes a nucleophilic reaction with lysine residue via proximity-induced conjugation. This propargylated-sulfonium tethered peptide resulting from a facile propargylation of thiolethers, enables amino-yne reaction at the selected lysine on MDM4 protein. This strategy represents a viable approach of lysine-targeted covalent inhibition in proximity.     

A Trimodal Closomer Drug‐Delivery System Tailored with Tracing and Targeting Capabilities

The construction and application of a unique monodisperse closomer drug‐delivery system (CDDS) integrating three different functionalities onto an icosahedral closo‐dodecaborane [B₁₂]^2? scaffold is described. Eleven B‐OH vertices of [closo‐B₁₂(OH)₁₂]^2? were used to attach eleven copies of the anticancer drug chlorambucil and the targeting vector glucosamine through a bifurcating lysine linker. The remaining twelfth vertex was used to attach a fluorescent imaging probe. The presence of multiple glucosamine units offered a monodisperse and highly water‐soluble CDDS with a high payload of therapeutic cargo. This array enhanced the penetration of the drug into cancer cells by exploiting the overexpression of GLUT‐1 receptors present on cancer cells. About 15‐fold enhancement in cytotoxicity was observed for CDDS‐1 against Jurkat cells, compared to CDDS‐2, which lacks the GLUT‐1 targeting glucosamine. A cytotoxicity comparison of CDDS‐1 against colorectal RKO cells and its GLUT‐1 knock‐out version confirmed that GLUT‐1 mediates endocytosis. Using fluorescent markers both CDDS‐1 and ‐2 were traced to the mitochondria, a novel target for alkylating agents.     

Poly(L‐lysine)‐Induced Aggregation of Single‐Strand Oligo‐DNA‐Modified Gold Nanoparticles

Single‐strand oligo‐DNA‐modified Au nanoparticles (AuNPs) undergo aggregation in the presence of poly(L ‐lysine) (PLL), which is attributed to the interactions between the oligo‐DNA and PLL. These interactions between the oligo‐DNA and PLL were identified to be electrostatic when the lysine residues of PLL were positively charged and to be hydrogen bonding when the residues were deprotonated. The aggregation was promoted with an increase in the pH value at a pH level lower than the pK_a value of PLL (pK_a≈10.0) due to the gradual deprotonation of the lysine residues and thus suppressed electrostatic interactions between the positively charged lysine residues of PLL and the negatively charged backbone phosphate groups of the oligo‐DNA. At pH levels higher than the pK_a value of PLL, the aggregation was identified to be dominated by the hydrogen bonds between the bases of the oligo‐DNA and the deprotonated lysine residues of PLL. This study prompts the possibility that the spectral, and thus color, change of AuNPs upon aggregation can be used as a probe to follow the interactions between oligo‐DNA and polypeptides.     

Targeting programmed cell death 4 (PDCD4) with biogenic compounds in ARDS by Gaussian process‐based QSAR virtual screening

The programmed cell death 4 (PDCD4) has recently been recognized as a new and attractive target of acute respiratory distress syndrome. Here, we attempted to discover new and potent PDCD4 mediator ligands from biogenic compounds using a synthetic strategy of statistical virtual screening and experimental affinity assay. In the procedure, a Gaussian process‐based quantitative structure‐activity relationship regression predictor was developed and validated statistically based on a curated panel of structure‐based protein‐ligand affinity data. The predictor was integrated with pharmacokinetics analysis, chemical redundancy reduction, and flexible molecular docking to perform high‐throughput virtual screening against a distinct library of chemically diverse, drug‐like biogenic compounds. Consequently, 6 hits with top scores were selected, and their binding affinities to the recumbent protein of human PDCD4 were identified, 3 out of which were determined to have high or moderate affinity with K_d at micromolar level. Structural analysis of protein‐ligand complexes revealed that hydrophobic interactions and van der Waals contacts are the primary chemical forces to stabilize the complex architecture of PDCD4 with these mediator ligands, while few hydrogen bonds, salt bridges, and/or π‐π stacking at the complex interfaces confer selectivity and specificity for the protein‐ligand recognition. It is suggested that the statistical Gaussian process‐based quantitative structure‐activity relationship screening strategy can be successfully applied to rational discovery of biologically active compounds. The newly identified molecular entities targeting PDCD4 are considered as promising lead scaffolds to develop novel chemical therapeutics for acute respiratory distress syndrome.     

Affinity capillary electrophoresis for the determination of binding affinities for low molecular weight heparins and antithrombin‐III

The anticoagulant properties of heparin stem in part from high‐affinity binding to antithrombin‐III (AT‐III) inducing a 300‐fold increase in its inhibitory activity against the coagulation protease factor Xa. The minimal structural requirements for AT‐III binding are contained in the rare heparin pentasaccharide sequence containing a 3,6‐O‐sulfated N‐sulfoglucosamine residue. ACE is used in this work to measure the relative AT‐III binding affinities of the low molecular weight heparins (LWMHs) dalteparin, enoxaparin, and tinzaparin and the synthetic pentasaccharide drug fondaparinux (Arixtra). Determination of the AT‐III binding affinities of the LWMHs is complicated by their inherent structural heterogeneity and polydispersity. The fractional composition of 3‐O‐sulfo‐N‐sulfoglucosamine residues was determined for each drug substance using 2D NMR and used in the interpretation of the ACE results.     

Three‐Component Synthesis of Spiro[indoline‐3,4′‐pyrazolo[3,4‐b]pyridines] under Microwave Irradiation

A domino three‐component strategy with high efficiency for the synthesis of spiro[indoline‐3,4′‐pyrazolo[3,4‐b ]pyridines] from easily available isatins, pyrazol‐5‐amines and β‐ketonitriles under microwave heating. During reaction process, HOAc plays dual roles as reaction media as well as a Brønsted acid‐promoter. Flexible structural modification, broad functional group compatibility and mild reaction conditions make this strategy a useful and attractive process of library generation for drug discovery.     

Addressing the Glycine‐Rich Loop of Protein Kinases by a Multi‐Facetted Interaction Network: Inhibition of PKA and a PKB Mimic

Protein kinases continue to be hot targets in drug discovery research, as they are involved in many essential cellular processes and their deregulation can lead to a variety of diseases. A series of 32 enantiomerically pure inhibitors was synthesized and tested towards protein kinase A (PKA) and protein kinase B mimic PKAB3 (PKA triple mutant). The ligands bind to the hinge region, ribose pocket, and glycine‐rich loop at the ATP site. Biological assays showed high potency against PKA, with K_i values in the low nanomolar range. The investigation demonstrates the significance of targeting the often neglected glycine‐rich loop for gaining high binding potency. X‐ray co‐crystal structures revealed a multi‐facetted network of ligand–loop interactions for the tightest binders, involving orthogonal dipolar contacts, sulfur and other dispersive contacts, amide–π stacking, and H‐bonding to organofluorine, besides efficient water replacement. The network was analyzed in a computational approach.     

Identification of modification sites on human serum albumin and human hemoglobin adducts with houttuynin using liquid chromatography coupled with mass spectrometry

Houttuynin, a β‐keto aldehyde compound, is the major active ingredient in herba houttuyniae injection. The injection was once used as an anti‐inflammatory drug associated with occasional serious hypersensitivity reactions in the clinic, which were proposed to be related to the formation of protein adducts. N^α‐Boc‐lysine, FEEM and IVTNTT were used as model amino acids or peptides containing one nucleophilic residue to investigate adduct types by liquid chromatography coupled with ion trap mass spectrometry (LC/MSⁿ) and high‐resolution quadrupole time‐of‐flight mass spectrometry (Q‐TOF MS). These adducts were respectively characterized as Schiff bases formed by 1:1 reaction of houttuynin with lysine or N‐terminal residue and pyridinium adducts by 2:1 reaction. LC/MSⁿ analysis of trypsin digests of HSA/Hb incubations with houttuynin revealed that houttuynin‐modified HSA adducts were formed mainly at N‐terminal amino acid and lysine residues, specifically at Lys‐212, Lys‐414 and Lys‐525 for Schiff base adducts, and at Lys‐414 and Lys‐432 for pyridinium adducts, and houttuynin adducted more readily with N‐terminal valine of the α‐ and β‐chains in Hb and lysine amine (Lys‐62) of the β‐chain for Schiff base adducts. The results showed the direct modification of houttuynin to HSA/Hb in vitro, which was speculated to be responsible for the adverse reactions induced by houttuyniae injection. Copyright © 2012 John Wiley & Sons, Ltd.     

Site‐Selective,Late‐Stage C−H 18F‐Fluorination on Unprotected Peptides for Positron Emission Tomography Imaging

Peptides are often ideal ligands for diagnostic molecular imaging due to their ease of synthesis and tuneable targeting properties. However, labelling unmodified peptides with ¹⁸F for positron emission tomography (PET) imaging presents a number of challenges. Here we show the combination of photoactivated sodium decatungstate and [¹⁸F]‐N‐fluorobenzenesulfonimide effects site‐selective ¹⁸F‐fluorination at the branched position in leucine residues in unprotected and unaltered peptides. This streamlined process provides a means to directly convert native peptides into PET imaging agents under mild aqueous conditions, enabling rapid discovery and development of peptide‐based molecular imaging tools.     

Site‐Selective,Late‐Stage C−H 18F‐Fluorination on Unprotected Peptides for Positron Emission Tomography Imaging

Peptides are often ideal ligands for diagnostic molecular imaging due to their ease of synthesis and tuneable targeting properties. However, labelling unmodified peptides with ¹⁸F for positron emission tomography (PET) imaging presents a number of challenges. Here we show the combination of photoactivated sodium decatungstate and [¹⁸F]‐N‐fluorobenzenesulfonimide effects site‐selective ¹⁸F‐fluorination at the branched position in leucine residues in unprotected and unaltered peptides. This streamlined process provides a means to directly convert native peptides into PET imaging agents under mild aqueous conditions, enabling rapid discovery and development of peptide‐based molecular imaging tools.     

New techniques and strategies in drug discovery

Great success has been witnessed in last decades, some new techniques and strategies have been widely used in drug discovery. In this roadmap, several representative techniques and strategies are highlighted to show recent advances in this filed. (A) A DOX protocol has been developed for accurate protein-ligand binding structure prediction, in which first principle method was used to rank the binding poses. Validation against crystal structures have found that DOX prediction achieved an impressive success rate of 99%, indicating significant improvement over molecular docking method. (B) Virtual target profiling is a compound-centric strategy enabling a parallel implementation of interrogating compounds against various targets in a single screen, which has been used in hit/lead identification, drug repositioning, and mechanism-of-action studies. Current and emerging methods for virtual target profiling are briefly summarized herein. (C) Research on targeted autophagy to treat diseases has received encouraging progress. However, due to the complexity of autophagy and disease, experimental and in silico methods should be performed synergistically for the entire process. This part focuses on in silico methods in autophagy research to promote their use in medicinal research. (D) Histone deacetylases (HDACs) play important roles in various biological functions through the deacetylation of lysine residues. Recent studies demonstrated that HDACs, which possess low deacetylase activities, exhibited more efficient defatty-acylase activities. Here, we review the defatty-acylase activity of HDACs and describe examples for the design of isoform selective HDAC inhibitor. (E) The FDA approval of three kinase allosteric inhibitors and some others entering clinical study has spurred considerable interests in this targeted drug discovery area. (F) Recent advances are reviewed in structure-based design of novel antiviral agents to combat drug resistance. (G) Since nitric oxide (NO) exerts anticancer activity depending on its concentration, optimal levels of NO in cancer cells is desirable. In this minireview, we briefly describe recent advances in the research of NO-based anticancer agents by our group and present some opinions on the future development of these agents. (H) The field of photoactivation strategies have been extensively developed for controlling chemical and biological processes with light. This review will summarize and provide insight into recent research advances in the understanding of photoactivatable molecules including photoactivatable caged prodrugs and photoswitchable molecules.     

A Genetically Encoded,Phage‐Displayed Cyclic‐Peptide Library

Superior to linear peptides in biological activities, cyclic peptides are considered to have great potential as therapeutic agents. To identify cyclic‐peptide ligands for therapeutic targets, phage‐displayed peptide libraries in which cyclization is achieved by the covalent conjugation of cysteines have been widely used. To resolve drawbacks related to cysteine conjugation, we have invented a phage‐display technique in which its displayed peptides are cyclized through a proximity‐driven Michael addition reaction between a cysteine and an amber‐codon‐encoded N^?‐acryloyl‐lysine (AcrK). Using a randomized 6‐mer library in which peptides were cyclized at two ends through a cysteine–AcrK linker, we demonstrated the successful selection of potent ligands for TEV protease and HDAC8. All selected cyclic peptide ligands showed 4‐ to 6‐fold stronger affinity to their protein targets than their linear counterparts. We believe this approach will find broad applications in drug discovery.     

Clickable functionalization of liposomes with the gH625 peptide from Herpes simplex virus type I for intracellular drug delivery

Liposomes externally modified with the nineteen residues gH625 peptide, previously identified as a membrane‐perturbing domain in the gH glycoprotein of Herpes simplex virus type I, have been prepared in order to improve the intracellular uptake of an encapsulated drug. An easy and versatile synthetic strategy, based on click chemistry, has been used to bind, in a controlled way, several copies of the hydrophobic gH625 peptide on the external surface of 1,2‐dioleoyl‐sn‐glycero‐3‐phosphocholine (DOPG)‐based liposomes. Electron paramagnetic resonance studies, on liposomes derivatized with gH625 peptides, which are modified with the 2,2,6,6‐tetramethylpiperidine‐1‐oxyl‐4‐amino‐4‐carboxylic acid (TOAC) spin label in several peptide positions, confirm the positioning of the coupled peptides on the liposome external surface, whereas dynamic light scattering measurements indicate an increase of the diameter of the liposomes of approximately 30 % after peptide introduction. Liposomes have been loaded with the cytotoxic drug doxorubicin and their ability to penetrate inside cells has been evaluated by confocal microscopy experiments. Results suggest that liposomes functionalized with gH625 may act as promising intracellular targeting carriers for efficient delivery of drugs, such as chemotherapeutic agents, into tumor cells.