Similar,or dissimilar,that is the question. How different are methods for comparison of compounds similarity?

Comparison of compounds similarity is one of the main strategies of virtual screening protocols. Both similarity and dissimilarity concepts are of great importance during the search for new active compounds. Similarity is important due to the assumption that underlies the process of searching for new drug candidates: structurally similar compounds should induce similar biological response. On the other hand, we are also interested in dissimilarity, as we usually aim to find structurally novel ligands. In the study, we compared several approaches of evaluating compound similarity. Various representations and metrics were applied and we indicated the rate of variation of the results that can occur when shifting from one strategy to another. We compared both general similarity of datasets using different approaches, as well as examined the changes in the set of nearest neighbors when changing one compound representation into another, and the influence of representation/metric settings on the clustering outcome. We hope that the study will be of great help during the preparation of virtual screening experiments, stressing the need for careful selection of the way, the compound similarity is assessed. The differences in the results that can be obtained via the application of particular strategy can significantly influence the outcome of comparison studies; therefore, its settings should be carefully selected beforerunning the comparison.     

Discovery of novel selective serotonin reuptake inhibitors through development of a protein-based pharmacophore

The serotonin transporter (SERT), a member of the neurotransmitter sodium symporter (NSS) family, is responsible for the reuptake of serotonin from the synaptic cleft to maintain neurotransmitter homeostasis. SERT is established as an important target in the treatment of anxiety and depression. Because a high-resolution crystal structure is not available, a computational model of SERT was built based upon the X-ray coordinates of the leucine transporter LeuT, a bacterial NSS homologue. The model was used to develop the first SERT structure-based pharmacophore. Virtual screening (VS) of a small molecule structural library using the generated SERT computational model yielded candidate ligands of diverse scaffolds. Pharmacological analysis of the VS hits identified two SERT-selective compounds, potential lead compounds for further SERT-related medication development.     

Throughput and efficiency of a mass spectrometry-based screening assay for protein—Ligand binding detection

An H/D exchange- and MALDI mass spectrometry-based screening assay was applied to search for novel ligands that bind to cyclophilin A, a potential therapeutic and diagnostic target in lung cancer. The assay is based on stability of unpurified proteins from rates of H/D exchange (SUPREX), which exploits the H/D exchange properties of amide protons to measure the increase in a protein's thermodynamic stability upon ligand binding in solution. The current study evaluates the throughput and efficiency with which 880 potential ligands from the Prestwick Chemical Library (Illkirch, France) could be screened for binding to cyclophilin A. Screening was performed at a rate of 3 min/ligand using a conventional MALDI mass spectrometer. False positive and false negative rates, based on a set of control data, were as low as 0% and 9%, respectively. Based on the 880-member library screening, a false positive rate of 0% was observed when a two-tier selection strategy was implemented. Although novel ligands for cyclophilin A were not discovered, cyclosporin A, a known ligand to CypA and a blind control in the library, was identified as a hit. We also describe a new strategy to eliminate some of the complications related to back exchange that can arise in screening applications of SUPREX.     

A knowledge-based weighting approach to ligand-based virtual screening

On the basis of the recently introduced reduced graph concept of ErG (extending reduced graphs), a straightforward weighting approach to include additional (e.g., structural or SAR) knowledge into similarity searching procedures for virtual screening (wErG) is proposed. This simple procedure is exemplified with three data sets, for which interaction patterns available from X-ray structures of native or peptidomimetic ligands with their target protein are used to significantly improve retrieval rates of known actives from the MDL Drug Report database. The results are compared to those of other virtual screening techniques such as Daylight fingerprints, FTrees, UNITY, and various FlexX docking protocols. Here, it is shown that wErG exhibits a very good and stable performance independent of the target structure. On the basis of this (and the fact that ErG retrieves structurally more dissimilar compounds due to its potential to perform scaffold-hopping), the combination of wErG and FlexX is successfully explored. Overall, wErG is not only an easily applicable weighting procedure that efficiently identifies actives in large data sets but it is also straightforward to understand for both medicinal and computational chemists and can, therefore, be driven by several aspects of project-related knowledge (e.g., X-ray, NMR, SAR, and site-directed mutagenesis) in a very early stage of the hit identification process.     

A three-hybrid approach to scanning the proteome for targets of small molecule kinase inhibitors

In this study, we explored the application of a yeast three-hybrid (Y3H)-based compound/protein display system to scanning the proteome for targets of kinase inhibitors. Various known cyclin-dependent kinase (CDK) inhibitors, including purine and indenopyrazole analogs, were displayed in the form of methotrexate-based hybrid ligands and deployed in cDNA library or yeast cell array-based screening formats. For all inhibitors, known cell cycle CDKs as well as novel candidate CDK-like and/or CDK-unrelated kinase targets could be identified, many of which were independently confirmed using secondary enzyme assays and affinity chromatography. The Y3H system described here may prove generally useful in the discovery of candidate drug targets.     

Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4

Combinatorial synthesis and large scale screening methods are being used increasingly in drug discovery, particularly for finding novel lead compounds. Although these "random" methods sample larger areas of chemical space than traditional synthetic approaches, only a relatively small percentage of all possible compounds are practically accessible. It is therefore helpful to select regions of chemical space that have greater likelihood of yielding useful leads. When three-dimensional structural data are available for the target molecule this can be achieved by applying structure-based computational design methods to focus the combinatorial library. This is advantageous over the standard usage of computational methods to design a small number of specific novel ligands, because here computation is employed as part of the combinatorial design process and so is required only to determine a propensity for binding of certain chemical moieties in regions of the target molecule. This paper describes the application of the Multiple Copy Simultaneous Search (MCSS) method, an active site mapping and de novo structure-based design tool, to design a focused combinatorial library for the class II MHC protein HLA-DR4. Methods for the synthesizing and screening the computationally designed library are presented; evidence is provided to show that binding was achieved. Although the structure of the protein-ligand complex could not be determined, experimental results including cross-exclusion of a known HLA-DR4 peptide ligand (HA) by a compound from the library. Computational model building suggest that at least one of the ligands designed and identified by the methods described binds in a mode similar to that of native peptides.     

PhAST: pharmacophore alignment search tool

We present a ligand-based virtual screening technique (PhAST) for rapid hit and lead structure searching in large compound databases. Molecules are represented as strings encoding the distribution of pharmacophoric features on the molecular graph. In contrast to other text-based methods using SMILES strings, we introduce a new form of text representation that describes the pharmacophore of molecules. This string representation opens the opportunity for revealing functional similarity between molecules by sequence alignment techniques in analogy to homology searching in protein or nucleic acid sequence databases. We favorably compared PhAST with other current ligand-based virtual screening methods in a retrospective analysis using the BEDROC metric. In a prospective application, PhAST identified two novel inhibitors of 5-lipoxygenase product formation with minimal experimental effort. This outcome demonstrates the applicability of PhAST to drug discovery projects and provides an innovative concept of sequence-based compound screening with substantial scaffold hopping potential.     

Nanopharmacological Force Sensing to Reveal Allosteric Coupling in Transporter Binding Sites

Controversy regarding the number and function of ligand binding sites in neurotransmitter/sodium symporters arose from conflicting data in crystal structures and molecular pharmacology. Here, we have designed novel tools for atomic force microscopy that directly measure the interaction forces between the serotonin transporter (SERT) and the S‐ and R‐enantiomers of citalopram on the single molecule level. This approach is based on force spectroscopy, which allows for the extraction of dynamic information under physiological conditions thus inaccessible via X‐ray crystallography. Two distinct populations of characteristic binding strengths of citalopram to SERT were revealed in Na⁺‐containing buffer. In contrast, in Li⁺‐containing buffer, SERT showed only low force interactions. Conversely, the vestibular mutant SERT‐G402H merely displayed the high force population. These observations provide physical evidence for the existence of two binding sites in SERT when accessed in a physiological context. Competition experiments revealed that these two sites are allosterically coupled and exert reciprocal modulation.     

Discovery of novel triple targeting G‑quadruplex and topoisomerase 1/2 ligands from natural products evodiamine and rutaecarpine

Inspired by the indolopyridoquinazoline scaffold of natural products evodiamine and rutaecarpine, novel triple G4 and Top1/2 ligands were rationally designed and synthesized. Systematic structure-activity relationship (SAR) studies led to the discovery of compound 15g, which effectively induced and stabilized G4 and inhibited Top1/2 with potent antitumor activity. Compound 15g represents a valuable chemical tool or lead compound for antitumor drug discovery. This proof-of-concept study also validated the feasibility of using planar natural products scaffold as templates to design new G4 ligands.     

Synthesis, structure and heterogeneous catalytic activities of Cu-containing polymeric compounds: anion effect and comparison of homogeneous vs. heterogeneous catalytic activity

The structures of new polymeric compounds containing Cu(II) ions and btp (2,6-bis(N'-1,2,4-triazolyl)pyridine) ligands have been determined. The btp ligands bridge Cu(II) ions to form double zigzag chains, [Cu(ClO4)2(btp)2] 3 with perchlorate anions, and form single zigzag chains, [Cu(btp)(H2O)4](SO4).2H2O 4 with sulfate anions. The polymeric compound 3 was found to effectively catalyze the epoxide ring-opening reaction with methanol, while polymeric compound 4 was almost inactive with epoxides under the same conditions. The polymeric compound 3 showed an efficient catalytic activity and regioselective reactivity in the ring opening of epoxides and allowed reuse without a significant loss of activity through three runs with epoxides.     

Unexpected ligand substitutions in the cluster core {Re6Se8}: synthesis and structure of the novel cluster compound Cs11(H3O)[Re6Se4(O)4Cl6]3.4H2O

The compound Cs11(H3O)[Re6Se4(O)4Cl6]3.4H2O containing a novel cluster core {Re6Se4(O)4} with ordered ligands, where the 4 positions of one face of a Se4(O)4 cube are occupied exclusively by Se atoms and 4 O atoms lie in the opposite face was synthesized via the interaction of solid Re6Se8Br2 with molten KOH.     

亲和色谱中配基的筛选与应用

亲和配基的选择与筛选是发展新的亲和色谱填料或构建一个新的亲和色谱体系所必须解决的首要问题。该文结合作者所在实验室的工作,对配基的选择、筛选与应用方面的一些进展进行了简要评述。作者所在实验室针对特定蛋白质和多肽的多肽亲和配基的筛选,开展了反义肽简并性的研究,发展了基于反义肽的组合化学筛选新方法。与常规的组合合成法相比,该方法简单、快捷、有效,极大地减小了合成和筛选的工作量,降低了筛选后亲和组分结构鉴定的难度。所建立的筛选策略已应用于流感病毒、严重急性呼吸道综合征(SARS)病毒亲和抑制剂的筛选和用于人β-干扰素测定的石英晶体微天平（QCM）生物传感器的构建,均取得了有意义的结果。     

Hydrothermal synthesis, structures, and physical properties of four new flexible multicarboxylate ligands-based compounds

Four new compounds of partially or wholly deprotonated 5,5'-(1,4-phenylenebis(methylene))bis(oxy)diisophthalic acid (H4L1) and 5,5'-(1,3-phenylenebis(methylene))bis(oxy)diisophthalic acid (H4L2), namely {[Co(L1)0.5] x (H2O)2}n (1), {[Mn(L1)0.5] x (H2O)2}n (2), {[Cu(H2L1)](mu2-bipy)}n (bipy = 4, 4'-bipyridyl) (3), and {[Zn2(L2)] x H2O}n (4) were synthesized in the presence or absence of auxiliary bipy ligand. Their structures have been determined by single-crystal X-ray diffraction analysis and further characterized by elemental analysis, IR spectra, and thermogravimetric analysis. Compounds 1 and 2 are isostructural and possess three-dimensional (3D) networks. In compound 3, multicarboxylate ligands and bipy ligands link Cu centers to generate a two-dimensional (2D) sheet structure which is further connected by intermolecular hydrogen bonds to form a 3D supramolecular structure. In compound 4, the Zn centers are connected by L2(4-) anions to generate a 3D framework. Magnetic susceptibility measurements indicate that compounds 1 and 2 exhibit antiferromagnetic coupling between adjacent Co(II) ions and Mn(II) ions. The photoluminescent properties of the free 4L1 and H4L2 ligands and compound 4 have been studied in the solid state at room temperature. Both ligands and compound 4 exhibit strong violet emissions. Compared with the fluorescent emission of the ligand, the emission of 4 is red-shifted and enhanced.     

Water substitution on iron centers: from 0D to 1D sandwich type polyoxotungstates

Four novel polyoxotungstates have been synthesized by reaction of the sandwich type compound [Fe (III) 4(H 2O) 10(B-beta-SbW 9O 33) 2] (6-) (noted Fe 4(H 2O) 10Sb 2W 18) with ethylenediamine (en) and/or oxalate (ox) ligands under various conditions. The one-dimensional (1D) compound [enH 2] 3[Fe (III) 4(H 2O) 8(SbW 9O 33) 2].20H 2O ( 1) is isolated at 130 degrees C and results from the elimination of two water molecules and the condensation of the polyoxotungstate precursor. The reaction of Fe 4(H 2O) 10Sb 2W 18 with oxalate ligands affords the molecular complex Na 14[Fe (III) 4(ox) 4(H 2O) 2(SbW 9O 33) 2].60H 2O ( 2) where two organic ligands substitute four water molecules, while the same reaction in the presence of en molecules at 130 degrees C leads to the formation of the functionalized 1D chain [enH 2] 7[Fe (III) 4(ox) 4(SbW 9O 33) 2].14H 2O ( 3) with protonated ethylenediamine counterions. Finally, at 160 degrees C a rearrangement of the Fe 4(H 2O) 10Sb 2W 18 polyoxotungstate is observed, and the sandwich type compound [enH 2] 5[Fe (II) 2Fe (II) 2(enH) 2(Fe (III)W 9O 34) 2].24H 2O ( 4) crystallizes. In 4, the heteroelement is a Fe (III) ion, and the water molecules on the two outer Fe (II) centers are bound to pendant monoprotonated en ligands. The four compounds have been characterized by IR spectroscopy, thermogravimetric analysis, and single crystal X-ray diffraction. A detailed study of the magnetic properties of the mixed-valent hexanuclear iron complex in 4 shows evidence of an S = 5 ground-state because of spin frustration effects. A quantification of the electronic parameters characterizing the ground state ( D = +1.12 cm (-1), E/ D = 0.15) confirms that polyoxotungstate ligands induce large magnetic anisotropy.     

Synthesis and <Emphasis Type="Italic">in vitro</Emphasis> evaluation of new diphenyl ether derivatives as serotonin transporter ligands

For the development of new ligands as potential imaging agents for the serotonin transporter (SERT), a series of diphenyl ether derivatives have been synthesized, characterized, and evaluated for their in vitro binding affinities to the SERT. Among the above compounds, 2-(2-((dimethylamino)methyl)-4-fluorophenoxy)-5-bromobenzenamine (15) and 2-(2-((dimethylamino)methyl)-4-fluorophenoxy)-5-iodobenzene amine (16) show high binding affinities for the SERT with K _i values of 0.28 and 0.20 nmol·L⁻¹, respectively. They can be further labeled with carbon-11, fluorine-18, iodine-123 or bromine-76, and evaluated as useful imaging agents for the SERT. Moreover, the study of the structure-activity relationship (SAR) provides some useful information for the future design of new ligands. Supported by the National Natural Science Foundation of China (Grant No. 20471011)     

Hidden active information in a random compound library: extraction using a pseudo-structure-activity relationship model

We propose a hypothesis that "a model of active compound can be provided by integrating information of compounds high-ranked by docking simulation of a random compound library". In our hypothesis, the inclusion of true active compounds in the high-ranked compound is not necessary. We regard the high-ranked compounds as being pseudo-active compounds. As a method to embody our hypothesis, we introduce a pseudo-structure-activity relationship (PSAR) model. Although the PSAR model is the same as a quantitative structure activity relationship (QSAR) model, in terms of statistical methodology, the implications of the training data are different. Known active compounds (ligands) are used as training data in the QSAR model, whereas the pseudo-active compounds are used in the PSAR model. In this study, Random Forest was used as a machine-learning algorithm. From tests for four functionally different targets, estrogen receptor antagonist (ER), thymidine kinase (TK), thrombin, and acetylcholine esterase (AChE), using five scoring functions, we obtained three conclusions: (1) the PSAR models significantly gave higher percentages of known ligands found than random sampling, and these results are sufficient to support our hypothesis; (2) the PSAR models gave higher percentages of known ligands found than normal scoring by scoring function, and these results demonstrate the practical usefulness of the PSAR model; and (3) the PSAR model can assess compounds failed in the docking simulation. Note that PSAR and QSAR models are used in different situations; the advantage of the PSAR model emerges when no ligand is available as training data or when one wants to find novel types of ligands, whereas the QSAR model is effective for finding compounds similar to known ligands when the ligands are already known.     

A novel peptide-based encoding system for "one-bead one-compound" peptidomimetic and small molecule combinatorial libraries

The "one-bead one-compound" (OBOC) combinatorial library method is highly efficient, especially when used with well-established on-bead binding or functional assays. Literally, millions of compounds can be screened concurrently within 1 to 2 days. However, structure determination of peptidomimetic and small molecule compounds on one single bead is not trivial. A novel, highly efficient, and robust peptide-based encoding system has been developed for OBOC peptidomimetic and small molecule combinatorial libraries. In this system, topologically segregated bifunctional beads, which are made by a simple biphasic solvent strategy, are employed for the preparation and screening of an OBOC combinatorial peptidomimetic and small molecule libraries. Testing molecules are on the outer layer, and the coding tags in the interior of the bead do not interfere with screening. The coding tag is a peptide containing a large number of unnatural alpha-amino acids derived from different building blocks used for generating the peptidomimetic or small molecule. By coupling common building blocks simultaneously to the scaffold of the testing compound and to the side chains of the alpha-amino acids on the coding peptide, extra synthetic steps are eliminated and the amount of undesirable side products is minimized. Positive bead decoding is easy and straightforward as there is no need for cleavage and retrieval of the coding tag, and positive beads can be sequenced directly with Edman degradation. To demonstrate the efficiency and simplicity of our encoding system, an encoded 158 400-member model peptidomimetic library has been generated and screened for ligands that bind to streptavidin. Potent and novel ligands with clear motifs have been identified.     

CCR4 expressing cells cultured adherently on a capillary wall and formaldehyde fixed as the stationary phase for ligand screening by ACE

We have developed an on‐line screening method for CC chemokine receptor 4 (CCR4) ligands, in which the whole cells expressed with CCR4 were cultured adherently and immobilized on the inner wall of the capillary as the stationary phase for the first time. Moreover, in this method it is unnecessary to isolate and purify the target receptors from cell membranes. Therefore, it is possible to almost completely preserve the native conformation of the target receptors. The binding activities of the immobilized CCR4 did not change. A known antagonist of CCR4, compound A, was employed to validate the bioactivity of the cell layer and stability of this method. The intraday, interday, and batch‐to‐batch reproducibilities were investigated (RSD ≤ 13.9%). Nonlinear chromatography was used to calculate the binding constant between the compound A and CCR4 (6.4 × 10⁴/M, RSD = 4.96%). Using this method, the qualitative and quantitative characterizations of 23 computer‐aided drug design compounds were achieved and the kinetic parameters (K, k_a, k_d, and k′) were obtained by nonlinear chromatography. Three active compounds were screened out, which also showed activity in chemotaxis inhibition assay. The experimental results show that this method is simple, sensitive, and efficient for drug screening. Moreover, it offered a novel way to detect the nonspecific interactions between ligands and cell membrane.     

Three New Zn(Ⅱ)/Cd(Ⅱ) Coordination Polymers Constructed with 2-Mercaptonicotinic Acid and 1,2-Di(4-pyridyl)ethylene: Syntheses and Structure Analysis

Three new Zn(Ⅱ)/Cd(Ⅱ) coordination polymers based on 2-mercaptonicotinic acid (H2mna) with 1,2-di(4-pyridyl)ethylene (dpe) introduced as a bridging ligand have been synthesized via hydrothermal method and structurally characterized by single-crystal X-ray diffraction as well as elemental analysis and IR. As reported in this paper, [Zn2(dpe)0.5(mna)2] (1) can be classified as a two-dimensional layer structure in which the 1D chain composed of Zn(Ⅱ) and mna ligands is bridged by dpe ligands, while the complex named [Zn4(dpe)4(mna)4] (2) is a tetra-nuclear cluster compound. These two compounds are further extended to three-dimensional structures by hydrogen bonds along with C-H…π and π…π interactions. Compound 3 with general formular [Cd2(dpe)0.5(mna)2]·H2O belongs to a three-dimensional porous structure in which the 2D metal layers formed by the coordination of Cd(Ⅱ) and mna ligands are connected with the bridging of dpe ligands.     

Cyclopropane-based stereochemical diversity-oriented conformational restriction strategy: histamine H3 and/or H4 receptor ligands with the 2,3-methanobutane backbone

The stereochemical diversity-oriented conformational restriction strategy can be an efficient method for developing specific ligands for drug target proteins. To develop potent histamine H(3) and/or H(4) receptor ligands, a series of conformationally restricted analogs of histamine with a chiral trans- or cis-4-amino-2,3-methano-1-(1H-imidazol-4-yl)butane structure was designed based on this strategy. These stereochemically diverse compounds were synthesized from previously developed versatile chiral cyclopropane units. Among these analogs, a trans-cyclopropane-type compound, (2S,3R)-4-(4-chlorobenzylamino)-2,3-methano-1-(1H-imidazol-4-yl)butane (5b), has remarkable antagonistic activity to both the H(3) (K(i) = 4.4 nM) and H(4) (K(i) = 5.5 nM) receptors, and a cis-cyclopropane-type compound, (2R,3R)-4-amino-2,3-methano-1-(1H-imidazol-4-yl)butane (6a), is a potent and selective H(3) receptor partial agonist (K(i) = 5.4 nM). Although (2S,3R)-4-amino-2,3-methano-1-(1H-imidazol-4-yl)butane (5a) does not have a hydrophobic group which the usual H(3) receptor antagonists have, it was found to be a potent H(3) receptor antagonist (K(i) = 20.1 nM). Thus, a variety of compounds with different pharmacological properties depending on the cyclopropane backbones and also on the side-chain functional groups were identified. In addition to the previously used 1,2-methanobutane backbone, the 2,3-methanobutane backbone also worked effectively as a cyclopropane-based conformational restriction structure. Therefore, the combination of these two cyclopropane backbones increases the stereochemical and three-dimensional diversity of compounds in this strategy, which can provide a variety of useful compounds with different pharmacological properties.