Benzofused hydroxamic acids: useful fragments for the preparation of histone deacetylase inhibitors. Part 2: 7-fluorobenzothiophenes and benzofurans.

In the search for a new class of histone deacetylase inhibitors, we prepared a series of very simple benzofused hydroxamic acids to find an anchoring fragment of minimal molecular weight: they showed very good ligand efficiencies. Following these findings, classical fragment growing work was performed to increase binding energy and selective cytotoxicity. In the second phase of the work, information from the SARs of the benzothiophene series and data available in literature, we explored the in vitro pharmacological properties of the 6-substituted-7-fluoro-benzothiophene hydroxamates and the 5-susbtituted-benzofuran hydroxamates.

Benzofused hydroxamic acids: useful fragments for the preparation of histone deacetylase inhibitors. Part 1: hit identification.

In the search for a new class of histone deacetylase inhibitors, we prepared a series of simple benzofused hydroxamic acids to find an anchoring fragment of minimal molecular weight. These initial hits, all belonging to the benzothiophene class, showed very good ligand efficiencies. Following these findings, a classical fragment growing approach was performed to increase binding affinity and cytotoxicity.

Fragment-based approach to drug lead discovery: overview and advances in various techniques.

In the last 20 years the advent of new technologies, such as high-throughput screening (HTS) and combinatorial chemistry, has produced new tools for the discovery of biologically active molecules. In the past decade, fragment-based drug discovery has emerged as a more rational and focused approach that concentrates on the quality, rather than the quantity, of hits and leads. The principles behind this strategy are different from those that represented the basis of conventional HTS. The starting point of this approach is always a small chemical entity (typically MW 150-200), a fragment, with low affinity for the selected target. Fragments should satisfy key features such as diversity, reduced structural complexity, aqueous solubility and availability. Because of their small size, they occupy a smaller region of chemical space if compared with classical HTS compounds; hence, fragment libraries provide a good diversity with a relatively low number of compounds. Classical biochemical assays are often not suitable to detect the low binding affinities involved, so some well known biophysical techniques, such as nuclear magnetic resonance and x-ray, have been opportunely modified in order to render them able to perform the task. When selecting fragments suitable for subsequent optimization, a useful parameter has been introduced, the ligand efficiency, which is defined as the free energy of binding divided by the non-hydrogen atom count. Once selected, a fragment must undergo a heavy elaboration to improve binding affinity, at the same time acquiring drug-like properties. There are two main ways to go on at this point. The most common one is the so-called 'fragment evolution', consisting of a stepwise and systematic addition of chemical functionalities to the starting fragment core, together with a continuous feedback for pharmacological and physicochemical properties. The second one, less common but with great potential, is 'fragment linking': when two or more fragment hits are found to bind in adjacent regions of the target protein, they can be linked through appropriate spacers to rapidly produce a single molecule with much higher binding affinity. Two representative case histories are described: Abbott's ABT 518, an MMP (matrix metalloproteinase) inhibitor, and Eli-Lilly's LY-517717, an inhibitor of factor Xa serine protease. In addition, a list of molecules claimed to be derived from fragment approach and currently undergoing clinical trials is presented.

Selective binding of L-glutamate derivative in aqueous solvents.

A chiral bisguanidinium macrocycle binds N-Boc-L-glutamate in a 1 : 1 stoichiometry with significant selectivity in competitive solvent (DMSO-H(2)O).

Fragment-based drug design: combining philosophy with technology.

Fragment-based drug design began more than ten years ago and has been steadily gaining in popularity. This review discusses how fragments have been used to choose druggable targets, and what parameters need to be evaluated if a fragment hit is to be considered a suitable ligand for development. Examples of fragment-based screening from the recent literature are reviewed to highlight the various approaches used, along with the possible application of additional techniques to fragment screening against immobilized targets. Finally, mention is made of two different areas, multi-target drug discovery and selective tumor cell targeting, where fragment-based approaches may play an important role in the future.

Trifluoroacetyl as an orthogonal protecting group for guanidines.

The trifluoroacetyl moiety has been used as a new protecting group for guanidine functionality. The protecting group is easily cleaved under mild basic conditions and is complementary to the Boc, Cbz, and Ddpe protecting groups. The protecting group can be applied to peptide synthesis in solution as well as on a solid phase as it is orthogonal to a Boc and Cbz strategy and semiorthogonal to an Fmoc strategy.

Binding of tetramethylammonium to polyether side-chained aromatic hosts. Evaluation of the binding contribution from ether oxygen donors.

A set of macrocyclic and open-chain aromatic ligands endowed with polyether side chains has been prepared to assess the contribution of ether oxygen donors to the binding of tetramethylammonium (TMA), a cation believed incapable of interacting with oxygen donors. The open-chain hosts consisted of an aromatic binding site and side chains possessing a variable number of ether oxygen donors; the macrocyclic ligands were based on the structure of a previously investigated host, the dimeric cyclophane 1,4-xylylene-1,4-phenylene diacetate (DXPDA), implemented with polyether-type side chains in the backbone. Association to tetramethylammonium picrate (TMAP) was measured in CDCl(3) at T = 296 K by (1)H NMR titrations. Results confirm that the main contribution to the binding of TMA comes from the cation-pi interaction established with the aromatic binding sites, but they unequivocally show that polyether chains participate with cooperative contributions, although of markedly smaller entity. Water is also bound, but the two guests interact with aromatic rings and oxygen donors in an essentially noncompetitive way. An improved procedure for the preparation of cyclophanic tetraester derivatives has been developed that conveniently recycles the oligomeric ester byproducts formed in the one-pot cyclization reaction. An alternative entry to benzylic diketones has also been provided that makes use of a low-order cyanocuprate reagent to prepare in fair yields a class of compounds otherwise uneasily accessible.

Binding of acetylcholine and tetramethylammonium to a cyclophane receptor: anion's contribution to the cation-pi interaction.

The interaction of the lipophilic cyclophane 1 with several acetylcholine (ACh) and tetramethylammonium (TMA) salts has been investigated in deuteriochloroform to ascertain the influence of the counterion on the cation-pi interaction. Reliable association constants have been measured for 17 salts of commonly used anions; corresponding binding free energies -DeltaG degrees ranged from over 8 kJ mol(-1) down to the limit of detection. The dramatic dependence of the binding energy on the anion showed that the latter takes part in the process with a passive and adverse contribution, which inhibits cation binding even to complete suppression in unfavorable cases. Thermodynamic parameters for the association of 1 with TMA picrate demonstrate that binding is enthalpic in origin, showing a substantial enthalpy gain (DeltaH degrees = -16.7 kJ mol(-1)) and an adverse entropic contribution (DeltaS degrees = -27.9 J mol(-1) K(-1)). A correlation has been found between the "goodness" of anions as binding partners and the solubility of their salts. Conversion of the anion into a more charge-dispersed species, for example, conversion of chloride into dialkyltrichlorostannate, improves cation binding substantially, indicating that charge dispersion is a main factor determining the influence of the anion on the cation-pi interaction. DFT computational studies show that the variation of the binding free energy of TMA with the counterion is closely accounted for by the electrostatic potential (EP) of the ion pair: guest binding appears to respond to the cation's charge density exposed to the receptor, which is determined by the anion's charge density through a polarization mechanism. A value of -DeltaG degrees = 38.6 kJ mol(-1) has been extrapolated for the free energy of binding of TMA to 1 in chloroform but in the absence of a counterion. The transmission of electrostatic effects from the ion pair to the cation-pi interaction demonstrates that host-guest association is governed by Coulombic attraction, as long as factors (steric, entropic, solvation, etc.) other than pure electrostatics are not prevalent.