Pharmacophoric fragment

During the last decade we have been carrying out a systematic study of the reactions of nitroarenes with N-alkyl azomethine ylides. A fundamentally new approach has been advanced for the synthesis of polycyclic heterosystems bearing important pharmacophoric fragments, such as pyrrolidines, pyrrolines, and pyrroles. 

Anthracene-derived aminophosphonates are of particular interest due to the fact that the DNA-intercalating anthracene ring is the main pharmacophoric fragment of some cytostatic drugs [60], Also, anthracene-derived aminophosphonates can find applications in analytical biochemistry [61] due to the fluorescent properties of the anthracene moiety [62],... 

The search for structural fragments (substructures) is very important in medicinal chemistry, QSAR, spectroscopy, and many other fields in the process of perception of pharmacophore, chromophore, or other -phores. 

Each of the pharmacophore queries consisted of one donor, one acceptor and one of the two hydrophobic points indicated in Figure 1.16. The directionality of hydrogen bonds was inferred from the X-ray structure and reasonably loose tolerances of 1.5 A were used for donor-acceptor distances and 2-2.5 A to the hydrophobe were chosen to allow for the flexibility seen across kinase structures and to maximise the diversity amongst the identified fragments. Four pharmacophore queries were completed and the results were combined. The chosen fragments were further filtered by molecular weight (between 150 and 250), 51og P (between 2.5 and —2.5) and the presence of... 

Keywords VS, Virtual Screening, Lead discovery, lead, HTS, Pharmacophore-Based, Structure-Based, Fragment-based, Ligand-based, Docking, Scoring, hybrid workflows, VS strategy, Benchmarking VS... 

Methods that deduce a pharmacophore, an arrangement in 3D space of features that contribute or detract from binding and look for its presence in the database that is searched. This method places emphasis on features like hydrogen bond donors, hydrogen bond acceptors, acidic or basic units and hydrophobic fragments and opens the possibility of identifying unexpected scaffolds with required features (pharmacophore-based VS or PHBVS). 

The Surflex-Sim method operates significantly differently [104]. Each of the molecules is surrounded by a set of observer points that characterizes the local character of the surface and potential interactions. Two similar molecules will have a common subset of comparable observer points. A optimal alignment occurs when the differences in pharmacophore character and molecular surface inferred from the observer points are minimized between two molecules. To speed up the algorithm, large molecules can be fragmented into parts which are then compared, and then tested for consistency. This feature also makes the method capable of identifying alignments when one molecule is much smaller than the other. 

In many respects the fragment approach is ideally suited to projects which have X-ray crystal structures available. The fragments are small and relatively weak binders, but they often only possess one pharmacophoric element that binds to a specific feature on the target. If this interaction is identified by X-ray structure determination, then project teams can propose specific plans which maintain that critical interaction, and ideally optimize binding through other vectors in their fragments. 

In fact, the majority of the radiolabel was recovered in the small C-terminal fragment containing TM-6 and TM-7. It delivered biochemical evidence that the aryloxyalkyl side-chain of salmeterol was positioned in that region and represented a secondary binding site, while the pharmacophore portion of the compound bound to the expected catechol site. 

As illustrated in the next section, the use of biological fingerprints, such as from a BioPrint profile, provides a way to characterize, differentiate and cluster compounds that is more relevant in terms ofthe biological activity of the compounds. The data also show that different in silico descriptors based on the chemical structure can produce quite different results. Thus, the selection of the in silico descriptor to be used, which can range from structural fragments (e.g. MACCS keys), through structural motifs (Daylight keys) to pharmacophore/shape keys (based on both the 2D structure via connectivity and from actual 3D conformations), is very important and some form of validation for the problem at hand should be performed. 

It is well known that the identification of the pharmacophoric moiety (i.e. the essential atoms and molecular fragments of the bioactive compound, which selectively recognize the receptor eliciting the observed specific pharmacological effect) constitutes an important aspect of drug design procedures and SAR studies [84—86]. 

In this template, the lead compound fragment and the two pharmacophoric groups are separated by wildcard designations that denote where chemical variability can occur. 

Ji, H.T., Stanton, B.Z., Igarashi, J., Li, H.Y., Martasek, P., Roman, L.J., Poulos, T.L., Silverman, R.B. Minimal pharmacophoric elements and fragment hopping, an approach directed at molecular diversity and isozyme selectivity. Design of selective neuronal nitric oxide synthase inhibitors. J. Am. Chem. Soc. 2008, 130, 3900-14. 

A wide variety of features have been used in bit vectors, including molecular fragments, 3-D potential pharmacophores, atom pairs, 2-D pharmacophores, topological torsions, and variety of topological indices. 

Structural Fragments of a Drug Molecule Pharmacophore, Toxicophore, Metabophore... 

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