Synthesis of Some New Fluorine Containing Thiadiazolotriazinones as Potential Antibacterial Agents

2,4-dichloro-5-fluorophenyl, 4-fluoro-3-(Phenoxy)phenyl, 4-fluorophen-yl groups are known pharmacophores and can be used in the synthesis of new biologically active molecules. Therefore, 4-amino-6-arylmethyl-3-mercapto-1,2,4-triazin5(4H)-ones 1 are condensed with 3-phenoxy-4-fluoro-benzoic acid, 2,4-dichloro-5-fluorobenzoic acid, and 4-fluorobenzoic acid 2 to give 7-substituted-3-arylmethyl-4H-1,3,4-thiadiazolo[2,3-c]-1,2,4-triazin-4-ones 3 . Phosphorous oxychloride was used as cyclizing agent. All the newly synthesized compounds 3a-l was screened for their antibacterial activities. Most of them showed promising activity in the range of 10 w g/mL concentrations.     

Simulated molecular evolution in a full combinatorial library

BACKGROUND: The Darwinian concept of 'survival of the fittest' has inspired the development of evolutionary optimization methods to find molecules with desired properties in iterative feedback cycles of synthesis and testing. These methods have recently been applied to the computer-guided heuristic selection of molecules that bind with high affinity to a given biological target. We describe the optimization behavior and performance of genetic algorithms (GAs) that select molecules from a combinatorial library of potential thrombin inhibitors in 'artificial molecular evolution' experiments, on the basis of biological screening results. RESULTS: A full combinatorial library of 15,360 members structurally biased towards the serine protease thrombin was synthesized, and all were tested for their ability to inhibit the protease activity of thrombin. Using the resulting large structure-activity landscape, we simulated the evolutionary selection of potent thrombin inhibitors from this library using GAs. Optimal parameter sets were found (encoding strategy, population size, mutation and cross-over rate) for this artificial molecular evolution. CONCLUSIONS: A GA-based evolutionary selection is a valuable combinatorial optimization strategy to discover compounds with desired properties without needing to synthesize and test all possible combinations (i.e. all molecules). GAs are especially powerful when dealing with very large combinatorial libraries for which synthesis and screening of all members is not possible and/or when only a small number of compounds compared with the library size can be synthesized or tested. The optimization gradient or 'learning' per individual increases when using smaller population sizes and decreases for higher mutation rates.     

High Throughput and High Speed Organic Synthesis in Drug Discovery: An Integration of Chemistry and Technology

Drug discovery is a complicated process that involves multiple synthetic chemistry tasks. Among them, lead generation and optimization is the core business in the discovery research. During the stage of lead generation, a large library of many thousands individual compounds will be screened against a biological target to identify a set of hits that showed desirable activity. Once a hit has been identified, analog synthesis and development of SAR around this hit and establishment of relationsh…     

Combinatorics of combinatorial chemistry

The hot topic among medicinal chemists today is a novel technique for chemical synthesis in drug research called combinatorial chemistry, where usually a core structure and some building‐block molecules are given and all combinatorially possible combinations are produced. The resulting set of compounds (called a library) can afterwards be systematically screened for a desired biological activity. In this paper we discuss the applications of the mathematical discipline of combinatorics to this process, especially an algorithm for the exhaustive and redundancy‐free generation of a combinatorial library as well as equations for the enumeration of library sizes. This revised version was published online in July 2006 with corrections to the Cover Date.     

A versatile synthetic approach to peptidyl privileged structures using a "safety-catch" linker

Peptidyl privileged structures have been widely used by many groups to discover biologically active molecules. In this context, privileged substructures are used as "hydrophobic anchors", to which peptide functionality is appended to gain specificity. Utilization of this concept has led to the discovery of many different active compounds at a wide range of biological receptors. A synthetic approach to these compounds has been developed on a "safety-catch" linker that allows rapid preparation of large libraries of these molecules. Importantly, amide bond formation/cleavage through treatment with amines is the final step; it is a linker strategy that allows significant diversification to be easily incorporated, and it only requires the inclusion of an amide bond. In addition, chemistry has been developed that permits the urea moiety to be inserted at the N-terminus of the peptide, allowing the same set of amines (either privileged substructures or amino acid analogues) to be used at both the N- and C-termini of the molecule. To show the robustness of this approach, a small library of peptidyl privileged structures were synthesized, illustrating that large combinatorial libraries can be synthesized using these technologies.     

Comparative molecular surface analysis (CoMSA) for virtual combinatorial library screening of styrylquinoline HIV-1 blocking agents

We used comparative molecular surface analysis to design molecules for the synthesis as part of the search for new HIV-1 integrase inhibitors. We analyzed the virtual combinatorial library (VCL) constituted from various moieties of styrylquinoline and styrylquinazoline inhibitors. Since imines can be applied in a strategy of dynamic combinatorial chemistry (DCC), we also tested similar compounds in which the -C=N- or -N=C- linker connected the heteroaromatic and aromatic moieties. We then used principal component analysis (PCA) or self-organizing maps (SOM), namely, the Kohonen neural networks to obtain a clustering plot analyzing the diversity of the VCL formed. Previously synthesized compounds of known activity, used as molecular probes, were projected onto this plot, which provided a set of promising virtual drugs. Moreover, we further modified the above mentioned VCL to include the single bond linker -C-N- or -N-C-. This allowed increasing compound stability but expanded also the diversity between the available molecular probes and virtual targets. The application of the CoMSA with SOM indicated important differences between such compounds and active molecular probes. We synthesized such compounds to verify the computational predictions.     

Synthesis of New Phenolic Derivatives of Quinazolin-4(3H)-One as Potential Antioxidant Agents—In Vitro Evaluation and Quantum Studies

Considering the important damage caused by the reactive oxygen (ROS) and nitrogen (RNS) species in the human organism, the need for new therapeutic agents, with superior efficacy to the known natural and synthetic antioxidants, is crucial. Quinazolin-4-ones are known for their wide range of biological activities, and phenolic compounds display an important antioxidant effect. Linking the two active pharmacophores may lead to an increase of the antioxidant activity. Therefore, we synthesized four series of new hybrid molecules bearing the quinazolin-4-one and phenol scaffolds. Their antioxidant potential was evaluated in vitro, considering different possible mechanisms of action: hydrogen atom transfer, ability to donate electrons and metal ions chelation. Theoretical quantum and thermodynamical calculations were also performed. Some compounds, especially the ortho diphenolic ones, exerted a stronger antioxidant effect than ascorbic acid and Trolox.     

Tetrazoles as carboxylic acid isosteres: chemistry and biology

Tetrazoles are often used as metabolism-resistant isosteric replacements for carboxylic acids in SAR-driven medicinal chemistry analogue syntheses. Tetrazoles have not been found in nature; with rare exceptions, these compounds do not exhibit appreciable biological activity, but they are at the same time resistant to biological degradation. This property makes it possible to use tetrazoles as isosteric substituents of various functional groups in the development of biologically active substances. The tetrazole motif has been used in various drug pharmacophores as a suitable replacement of carboxylic acid moiety and different methods have been used for the synthesis of tetrazoles using different reaction conditions. This review tries to give a vivid look on the different synthetic methods, using catalysts or different reagents for the synthesis of tetrazoles. The biological importance of tetrazoles has also been highlighted.     

Utility of β‐(4‐Chlorobenzoyl)acrylic Acid in Heterocyclic Synthesis

β‐(4‐Chlorobenzoyl)acrylic acid (1) proved to be a convenient precursor for the synthesis of a variety of heterocyclic systems through the reaction with compounds containing active methylene groups under Michael reaction conditions. Also, the reactivity of Michael adduct towards nitrogen nucleophiles was investigated to afford diazepine, indazole, isoxazole and quinazoline derivatives. Some of the synthesized compounds were screened for their biological activity.     

Biological mechanism profiling using an annotated compound library

We present a method for testing many biological mechanisms in cellular assays using an annotated library of 2036 small organic molecules. This annotated compound library represents a large-scale collection of compounds with diverse, experimentally confirmed biological mechanisms and effects. We found that this chemical library is (1) more structurally diverse than conventional, commercially available libraries, (2) enriched in active compounds in a tumor cell viability assay, and (3) capable of generating hypotheses regarding biological mechanisms underlying cellular processes. We elucidated biological mechanisms relevant to the antiproliferative activity of 85 compounds from this library that were selected using a high-throughput cell viability screen. We developed a novel automated scoring system for identifying statistically enriched mechanisms among such a subset of compounds. This scoring system can identify both previously known and potentially novel antiproliferative mechanisms.     

Ligand-based virtual screening by novelty detection with self-organizing maps

We describe a novel method for ligand-based virtual screening, based on utilizing Self-Organizing Maps (SOM) as a novelty detection device. Novelty detection (or one-class classification) refers to the attempt of identifying patterns that do not belong to the space covered by a given data set. In ligand-based virtual screening, chemical structures perceived as novel lie outside the known activity space and can therefore be discarded from further investigation. In this context, the concept of "novel structure" refers to a compound, which is unlikely to share the activity of the query structures. Compounds not perceived as "novel" are suspected to share the activity of the query structures. Nowadays, various databases contain active structures but access to compounds which have been found to be inactive in a biological assay is limited. This work addresses this problem via novelty detection, which does not require proven inactive compounds. The structures are described by spatial autocorrelation functions weighted by atomic physicochemical properties. Different methods for selecting a subset of targets from a larger set are discussed. A comparison with similarity search based on Daylight fingerprints followed by data fusion is presented. The two methods complement each other to a large extent. In a retrospective screening of the WOMBAT database novelty detection with SOM gave enrichment factors between 105 and 462-an improvement over the similarity search based on Daylight fingerprints between 25% and 100%, when the 100 top ranked structures were considered. Novelty detection with SOM is applicable (1) to improve the retrieval of potentially active compounds also in concert with other virtual screening methods; (2) as a library design tool for discarding a large number of compounds, which are unlikely to possess a given biological activity; and (3) for selecting a small number of potentially active compounds from a large data set.     

Combinatorial library of peptide isosters based on Diels-Alder reactions: identification of novel inhibitors against a recombinant cysteine protease from Leishmania mexicana

A combinatorial split-and-mix library of peptide isosters based on a Diels-Alder reaction was synthesized as a "one-bead-two-compounds" library and encoded by ladder synthesis for facile analysis by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. In the "one-bead-two-compounds" library approach, each bead contains a library member as a putative protease inhibitor along with a fluorescence-quenched substrate for the protease. When the library was screened with CPB2.8 DeltaCTE, a recombinant cysteine protease from L. mexicana, several beads containing compounds with inhibitory activity could be selected from the library and analyzed by MALDI-TOF MS for structure elucidation. Two types of inhibitors were revealed. One novel class of inhibitors had the bicyclic Diels-Alder product isosteric element incorporated internally in a peptide, while the other type was an N-terminal alpha,beta-unsaturated ketone Michael acceptor used as starting material for the Diels-Alder reaction. Selected hit sequences and constructed consensus sequences based on the observed frequencies of amino acids in different subsites were resynthesized and assayed in solution for inhibitor activity and were shown to have IC(50) values in the high nanomolar to low micromolar range.     

Active-site-directed 3D database searching: Pharmacophore extraction and validation of hits

Summary Two new computational tools, PRO_PHARMEX and PRO_SCOPE, for use in active-site-directed searching of 3D databases are described. PRO_PHARMEX is a flexible, graphics-based program facilitating the extraction of pharmacophores from the active site of a target macromolecule. These pharmacophores can then be used to search a variety of databases for novel lead compounds. Such searches can often generate many hits of varying quality. To aid the user in setting priorities for purchase, synthesis or testing, PRO_SCOPE can be used to dock molecules rapidly back into the active site and to assign them a score using an empirical scoring function correlated to the free energy of binding. To illustrate how these tools can add value to existing 3D database software, their use in the design of novel thrombin inhibitors is described.     

Evaluating chemical structure similarity as an indicator of cellular growth inhibition

Chemical variations of small compounds are commonly used to probe biological systems and potentially discover lead-like compounds with selective target activity. Molecular probes are either generated by synthesis or acquired through directed searches of commercially available compound libraries. The data generated when testing the probes in various biological systems constitutes a structure/activity analysis. The ability to detect variations and classify biological responses requires the analysis of a compound in multiple assays. While the concept of a structure/activity relationship is straightforward, its implementation can vary considerably depending on the biological system under study and the probe library selected for testing. The analysis presented here will focus on the accumulated compound library used to screen for growth inhibition across the National Cancer Institute's panel of 60 tumor cells. The considerable chemical and biological diversity inherent in these data offers an opportunity to establish a quantifiable connection between chemical structure and biological activity. We find that the connection between structure and biological response is not symmetric, with biological response better at predicting chemical structure than vice versa. Structurally and functionally similar compounds can have distinguishable biological responses reflecting different mechanisms of action.     

In‐Bead Screening of Hydroxamic Acids for the Identification of HDAC Inhibitors

A one bead–one compound screening format is presented. Following solid‐phase synthesis on a photolabile linker, library compounds were readily released and screened inside polymer beads. The release of screening compounds was readily controlled by varying photolysis time and light intensity. Dose‐response experiments were carried out to effectively distinguish high‐ and low‐affinity ligands. A library containing 55 800 compounds was synthesized and screened in a fluorometric assay, thereby identifying potent HDAC inhibitors with IC₅₀ values in the nanomolar range.     

Encoding method for OBOC small molecule libraries using a biphasic approach for ladder-synthesis of coding tags

In the "one-bead one-compound" (OBOC) combinatorial library method, each compound bead displays only one compound entity. Hundreds of thousands to millions of compound beads can be synthesized rapidly and screened simultaneously. Positive compound beads are then isolated for structural analysis. To fully exploit the power of OBOC combinatorial small molecule libraries, a robust and high throughput encoding method is needed to decode the positive compound beads. In this paper, we report on the development of a novel encoding strategy that combines the concepts of ladder-synthesis and chemical encoding on bilayer beads. In these encoded libraries, small molecule compounds are displayed on the bead surface, and cleavable coding tags consisting of a series of truncated molecules reside in the bead interior. Such a library can be easily constructed using the biphasic approach (J. Am. Chem. Soc.2002, 124, 7678) to topologically segregate the functionalities of the beads during library synthesis. The ladder members and coding tags are then released for MALDI-TOF-MS analysis. To simplify the interpretation of the mass spectra, we purposely add bromine into the cleavable linker so that the cleavage products generate a characteristic isotope fingerprint. The chemical structure of library compounds can be determined by analyzing the mass differences between adjacent peaks on the mass spectra. This encoding strategy also provides valuable information on the quality of the testing compound on the surface of the bead. To validate this methodology, a model OBOC small molecule library with 12,288 members was synthesized on TentaGel beads and screened against streptavidin. The chemical structures of the compound on each positive bead were unambiguously identified.