An integrated approach to knowledge-driven structure-based virtual screening

In many practical applications of structure-based virtual screening (VS) ligands are already known. This circumstance requires that the obtained hits need to satisfy initial made expectations i.e., they have to fulfill a predefined binding pattern and/or lie within a predefined physico-chemical property range. Based on the RApid Index-based Screening Engine (RAISE) approach, we introduce cRAISE—a user-controllable structure-based VS method. It efficiently realizes pharmacophore-guided protein-ligand docking to assess the library content but thereby concentrates only on molecules that have a chance to fulfill the given binding pattern. In order to focus only on hits satisfying given molecular properties, library profiles can be utilized to simultaneously filter compounds. cRAISE was evaluated on a range of strict to rather relaxed hypotheses with respect to its capability to guide binding-mode predictions and VS runs. The results reveal insights into a guided VS process. If a pharmacophore model is chosen appropriately, a binding mode below 2 Å is successfully reproduced for 85 % of well-prepared structures, enrichment is increased up to median AUC of 73 %, and the selectivity of the screening process is significantly enhanced leading up to seven times accelerated runtimes. In general, cRAISE supports a versatile structure-based VS approach allowing to assess hypotheses about putative ligands on a large scale.     

A structure-based design approach to advance the allyltyrosine-based series of HIV integrase inhibitors

As of mid-2017, only one structure of the human immunodeficiency virus (HIV) integrase core domain co-crystallised with an active site inhibitor was reported. In this structure (1QS4), integrase is complexed with a diketo-acid based strand-transfer inhibitor (INSTI). This structure has been a preferred platform for the structure-based design of INSTIs despite concerns relating to structural irregularities arising from crystallographic packing effects. A survey of the current pool of 297 reported integrase catalytic core structures indicated that the anatomy of the active site in the complex structure 1QS4 exhibits subtle variations relative to all other structures examined. Consequently, the 1QS4 structure was employed for docking studies. From the docking of twenty-seven allyltyrosine analogues, a 3-point inhibitor binding motif required for activity was established and successfully utilised in the development of a tripeptide displaying an EC₅₀ value of 10 ± 5 μM in HIV infected human T-cells. Additional docking of “in-house” compound libraries unearthed a methyl ester based nitrile derivative displaying an IC₅₀ value of 0.5 μM in a combined 3′-processing and strand-transfer assay.     

A new approach to fluorinated 4(3H)-quinazolinones

A new approach for the synthesis of fluorinated 1H-quinazolin-4-ones and 4-substituted quinazolines has been developed. 6-Fluoro-1H-quinazolin-4-ones were obtained by intramolecular cyclization of fluorine-containing S-ethyl N-benzoylisothioureas. Nucleophilic substitution reactions at positions 2 and 7, as well as alkylation at 1-position of quinazolinones were investigated. In addition, the synthesis of fluorine-containing 4-aminoquinazolines was carried out.     

A new approach to the synthesis of ethyl (4E)-alkenoates

A new approach to the preparation of ethyl (4E)-alkenoates was developed on the basis of Fe-catalyzed cross-coupling of ethyl (4E)-5-chloropent-4-enoate with the Grignard reagents. The starting ethyl (4E)-5-chloropent-4-enoate was obtained by alkylation of malonic ester of (E)-1,3-dichloropropene followed by decarbethoxylation.     

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.     

A new approach to (±)-apovincamine

(±)-Apovincamine ($\text{2}$) is synthesized by dehydration of the β-hydroxyrster ($\text{7}$) obtained by alkylation of the aldehyde ($\text{6}$) with metal chloroacetate     

A convenient approach to the total synthesis of (±) 4-demethoxydaunomycinone

A convenient and most practical approach to the synthesis of (±) 4-demethoxydaunomycinone starting from 2-methylhydroquinone is described.     

A thermodynamic approach to understanding liquid crystal selectivity in gas chromatography

Summary The thermodynamics of four new liquid crystals were investigated in order to understand their selectivity as stationary phases in gas chromatography. In this case study, liquid crystals with a benzoyloxy azobenzene mesogenic core substituted with heptyloxy (C7) and/or dioxyethylene ether (DOE) groups, were used. The chromatographic separations of linalool and citronellal, and of xylene, tetraethylbenzene and cresol isomers, which were achieved with the liquid crystal stationary phases, have been related to the dissolution thermodynamics of the solutes. The results gave us an insight into the mechanism of the molecular recognition involved in the separation processes.     

A novel approach to 4-benzylisoouinolines

The reaction of quinone methides with 3.4-dihydroisoquinoline or isoquinoline leads to benzylisoquinoline derivatives. NMR and ms investigations as well as chemical degradation prove that benzylation takes place at C-4 of the isoquinoline nucleus. Spectroscopic data are given for all new compounds.     

A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase

We report a new structure-based strategy for the identification of novel inhibitors. This approach has been applied to Bacillus stearothermophilus alanine racemase (AlaR), an enzyme implicated in the biosynthesis of the bacterial cell wall. The enzyme catalyzes the racemization of l- and d-alanine using pyridoxal 5-phosphate (PLP) as a cofactor. The restriction of AlaR to bacteria and some fungi and the absolute requirement for d-alanine in peptidoglycan biosynthesis make alanine racemase a suitable target for drug design. Unfortunately, known inhibitors of alanine racemase are not specific and inhibit the activity of other PLP-dependent enzymes, leading to neurological and other side effects.This article describes the development of a receptor-based pharmacophore model for AlaR, taking into account receptor flexibility (i.e. a `dynamic' pharmacophore model). In order to accomplish this, molecular dynamics (MD) simulations were performed on the full AlaR dimer from Bacillus stearothermophilus (PDB entry, 1sft) with a d-alanine molecule in one active site and the non-covalent inhibitor, propionate, in the second active site of this homodimer. The basic strategy followed in this study was to utilize conformations of the protein obtained during MD simulations to generate a dynamic pharmacophore model using the property mapping capability of the LigBuilder program. Compounds from the Available Chemicals Directory that fit the pharmacophore model were identified and have been submitted for experimental testing.The approach described here can be used as a valuable tool for the design of novel inhibitors of other biomolecular targets.     

Hot-spots-guided receptor-based pharmacophores (HS-Pharm): a knowledge-based approach to identify ligand-anchoring atoms in protein cavities and prioritize structure-based pharmacophores

The design of biologically active compounds from ligand-free protein structures using a structure-based approach is still a major challenge. In this paper, we present a fast knowledge-based approach (HS-Pharm) that allows the prioritization of cavity atoms that should be targeted for ligand binding, by training machine learning algorithms with atom-based fingerprints of known ligand-binding pockets. The knowledge of hot spots for ligand binding is here used for focusing structure-based pharmacophore models. Three targets of pharmacological interest (neuraminidase, beta2 adrenergic receptor, and cyclooxygenase-2) were used to test the evaluated methodology, and the derived structure-based pharmacophores were used in retrospective virtual screening studies. The current study shows that structure-based pharmacophore screening is a powerful technique for the fast identification of potential hits in a chemical library, and that it is a valid alternative to virtual screening by molecular docking.     

A new approach to the facile synthesis of 2-substituted-quinazolin-4(3H)-ones

A new approach to the facile synthesis of 2-substituted-quinazolin-4(3H)-ones and its derivatives using the condensation reaction of substituted 2-aminobenzamide and orthoesters is reported.     

A novel synthetic approach towards 2-guanidinomethyl-4(5)-sulfamoylimidazoles

A library of 2-guanidinomethyl-4(5)-sulfamoylimidazoles was synthesised in a convergent manner by introducing a sulfonyl chloride group via a trianion electrophilic sulfinylation of suitably protected 2-guanidinomethyl imidazoles.     

A minimalist approach to understanding the efficiency of mononuclear Zn(II) complexes as catalysts of cleavage of an RNA analog

Mononuclear complexes between Zn(2+) and the following four macrocycles were prepared: 1,4,7,10-tetraazacyclododecane (1), 1-oxa-4,7,10-triazacyclododecane (2), 1,5,9-triazacyclododecane (3) and 1-hydroxyethyl-1,4,7-triazacyclononane (4). The pH rate profiles of values of the observed second-order rate constant log (k(Zn))(app) for Zn(X)(OH(2))-catalyzed cleavage (X = 1, 2, 3 and 4) of 2-hydroxypropyl-4-nitrophenyl phosphate (HpPNP) show downward breaks centered at the pK(a) for ionization of the respective zinc bound water. At low pH, where the rate acceleration for the catalyzed reaction is largest, the stabilizing interaction between the catalyst and the bound transition state is 5.7, 7.4, 7.4 and 5.9 kcal mol(-1) for the reactions catalyzed by Zn(1)(OH(2)), Zn(2)(OH(2)), Zn(3)(OH(2)) and Zn(4)(OH(2)), respectively. The interactions between the metal cation and the macrocycle cause either a modest increase or reduction in transition state stabilization compared with 6.6 kcal mol(-1) stabilization for catalysis by Zn(OH(2))(6). The best Zn(II)-macrocycle catalysts are those for which the interactions between the metal ion and macrocycle are the weakest. Inhibition studies show that each of the four catalysts form complexes with phosphate and oxalate dianions with a much higher affinity than diethyl phosphate monoanion, consistent with stronger interaction of the catalysts with the transition state dianion compared with the substrate monoanion HpPNP. The pH-dependence of methyl phosphate inhibition of Zn(2) catalyzed cleavage of HpPNP shows that only the Zn(2)(OH(2)) species binds the inhibitor. This result is consistent with a mechanism that has Zn(2)(OH(2)) as the active catalytic species.     

Novel approach to structure-based pharmacophore search using computational geometry and shape matching techniques

Computationally efficient structure-based virtual screening methods have recently been reported that seek to find effective means to utilize experimental structure information without employing detailed molecular docking calculations. These tools can be coupled with efficient experimental screening technologies to improve the probability of identifying hits and leads for drug discovery research. Commercial software ROCS (rapid overlay of chemical structures) from Open Eye Scientific is such an example, which is a shape-based virtual screening method using the 3D structure of a ligand, typically from a bound X-ray costructure, as the query. We report here the development of a new structure-based pharmacophore search method (called Shape4) for virtual screening. This method adopts a variant of the ROCS shape technology and expands its use to work with an empty crystal structure. It employs a rigorous computational geometry method and a deterministic geometric casting algorithm to derive the negative image (i.e., pseudoligand) of a target binding site. Once the negative image (or pseudoligand) is generated, an efficient shape comparison algorithm in the commercial OE SHAPE Toolkit is adopted to compare and match small organic molecules with the shape of the pseudoligand. We report the detailed computational protocol and its computational validation using known biologically active compounds extracted from the WOMBAT database. Models derived for five selected targets were used to perform the virtual screening experiments to obtain the enrichment data for various virtual screening methods. It was found that our approach afforded similar or better enrichment ratios than other related methods, often with better diversity among the top ranking computational hits.     

A stereodivergent approach to substituted 4-hydroxypiperidines

A stereodivergent route toward both diastereomeric forms of functionalized 4-hydroxypiperidines has been successfully developed. This route involves biocatalytic generation of the enantiopure starting materials followed by functionalization via N-acyliminium ion-mediated CC-bond formation.     

A chemo-enzymatic approach to optically active 3-(4-methoxycarbonyl)phenyl-2-methyl-1-propanols

With a view to obtaining both enantiomers of 3-(4-methoxycarbonyl)phenyl-2-methyl-1-propanols, (R)-1 and (S)-1, from the respective racemate, (±)-1, the hydrolysis of its acetate, (±)-2, in the presence of porcine pancreatic lipase (PPL) has been studied. The optical puriry of (R)-1 and (S)-1 thus obtained was unsatisfactory (ee 22–27%), and could not be increased beyondee 33% by repeated enzymatic hydrolysis of the unconverted fraction of the acetate. In contrast with this, the biohydrogenation of 3-(4-methoxycarbonyl)phenyl-2-methyl-2-propen-1-ol (4) with fermentingSaccharomyces cerevisiae afforded (S)-1 of considerably higher optical purity (ee 41–90 %, depending on the strain). The stereochemical correlation of the products obtained in the two biochemical processes under study shows that the PPL-catalyzed hydrolysis of (±)-2 produces preferably (R)-1.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 761–766, April, 1995.The authors express their gratitude to the Russian Foundation for Basic Research for financial support (Grant No. 93-03-5893).