Matteo Zanda

The trifluoroethylamine function as peptide bond replacement.

Peptides play a fundamental role in a number of physiological processes, and can be used as drugs in various therapeutic classes. However, a major drawback of peptides is represented by their low bioavailability, consequently they have to be injected or administered in the form of expensive formulations. For this reason, the design and synthesis of metabolically stable peptide analogues that can either mimic or block the bioactivity of natural peptides or enzymes is an important issue in bioorganic and medicinal chemistry research. The replacement of a scissile peptide bond represents a viable and popular approach in the rational design of peptidomimetics. Peptidomimetics find applications as drugs, in protein engineering and so on. This is evident from the wealth of therapeutically useful peptidomimetic leads incorporating any of the peptide bond surrogates that are currently available. Therefore, within the realm of peptide mimics, the replacement of amide bonds with appropriate functionalities is a classic approach in medicinal chemistry and drug discovery. Some peptide bond surrogates, such as the alkene ( CR=CH ) or fluoroalkene ( CF=CH ) functions, are purely geometric replacements preserving little or none of the capacity of the native peptide bond to undertake electrostatic interactions or hydrogen-bonding with the receptor. Other amide replacements are known which retain the geometry of the amide bond or maintain the hydrogen bond-accepting properties of the amide, such as the ketomethylene ( COCH2 ) or depsipeptide ( CO2 ) functions. However, there are a few functional groups, which are capable of preserving the hydrogen bond-donating properties of the amide. Among them, one can mention sulfonamides ( SO2 NH ), anilines, secondary alcohols, hydrazines, and certain heterocycles. How to minimize the basicity of an NH donor, so that a NH2 + moiety is not formed at physiological pH, is the main issue for identifying a truly effective NH amide replacement. In fact, ammonium ions are poorly tolerated deep in the active site of a protein where binding interactions cannot compensate for the energetic cost of desolvation. This is a serious drawback of popular peptide bond surrogates, such as the methyleneamino ( CH2 NH-) function. Currently, a powerful new strategy is emerging for replacing the peptide bond with a very effective surrogate: the stereogenic trifluoroethylamine function. Indeed, a trifluoroethyl group can replace the carbonyl of an amide and generate a metabolically stable, poorly basic amine that maintains the excellent hydrogen bond of an amide. This strategy was first proposed by our research group, and was used to replace both a glycine amide bond and a malonamide of a partially modified retro (PMR) peptide. The main properties featured by the trifluoroethylamino group are: 1) very low NH basicity, 2) a CHACHTUNGTRENNUNG(CF3)NHCH backbone angle close to 1208, 3) a C CF3 bond substantially isopolar with the C=O, and 4) structural analogy with the tetrahedral proteolytic transition state. Furthermore, the sp hybridization of all the atoms forming the stereogenic trifluoroethylamine moiety is expected to allow a better orientation of the atoms in the receptors’ active sites, thus optimizing the energetically favorable interactions (hydrogen-bonds, van der Waals, hydrophobic, etc.). With this in mind, in 2000 we published the first examples of peptidomimetic structures incorporating a trifluoroethylamine unit replacing the retropeptide bond. In that first work, we presented a number of PMR and partially modified retro-inverso (PMRI) peptides (Figure 1) in

Chiral sulfoxide controlled asymmetric additions to CN double bond. An efficient approach to stereochemically defined α-fluoroalkyl amino compounds

Abstract This paper presents a full account of studies into the asymmetric addition reactions between α-lithium derivatives of enantiomerically pure methyl and benzyl p-tolyl sulfoxides and the N-(p-methoxyphenyl)aldimines, bearing trifluoromethyl, pentafluoroethyl and ω-hydrotetrafluoroethyl groups, to afford the corresponding α-fluoroalkyl β-sulfinylamines, synthetically versatile precursors of a series of enantiomerically pure biomedicinally important α-fluoroalkylalkylamines and α-fluoroalkyl-β-hydroxyalkylamines. The addition reactions were found to proceed under mild conditions allowing for convenient preparation of the corresponding α-fluoroalkyl β-sulfinylamines in excellent yields and good enantiomeric purity. The stereochemical outcomes of these reactions were shown to be subject to kinetic control, that is in sharp contrast to the corresponding reactions of fluorine-free imines. The absolute configurations of the addition products suggest that the fluoroalkyl group on starting imines plays a role of enantiodirecting, sterically larger substituent causing realization of an unusual for this type of reactions transition states.

Synthesis of optically pure (R)- and (S)-α-trifluoromethyl-alanine

Abstract (+)-(R)- and (−)-(S)-3,3,3-trifluoro-2-methyl-alanine (1) were synthesized from (+)-(R)-methyl-p-tolyl-sulphoxide (5) and N-alkoxycarbonylimino derivatives 4 of methyl 3,3,3-trifluoropyruvate (3). The absolute configuration was determined by X-ray analyses of two synthetic intermediates (2S,RS)-6a and (2R,RS-6c.

Enantioselective reductions by chirally modified alumino- and borohydrides ☆

Abstract Fifty years after the first report on the reduction of carbonyl compounds using chiral LiAlH 4 -derived hydrides (Bothner-By, A. A. J. Am. Chem. Soc . 1951 , 73 , 846), the field of enantioselective aluminohydride and borohydride reagents modified by chiral additives is reviewed. The first section deals with the preparation, scope, limits, mechanism of action and synthetic applications of chiral aluminohydrides, classified according to the chemical nature of the stereogenic modifier. The second covers the field of chiral borohydrides, which have been further classified according to the boron sources, namely metal borohydrides (via reaction with chiral additives or in the presence of chiral catalysts), or chiral boranes (by reduction with alkyllithiums or metal hydrides).

Asymmetric synthesis of α-arylglycinols via additions of lithium methyl p-tolyl sulfoxide to N-(PMP)arylaldimines followed by “non oxidative” Pummerer reaction

Abstract The results presented in this paper demonstrate that the stereochemical outcome of the reversible additions of lithium (R)-methyl p-tolyl sulfoxide to N-arylidene-p-anisidines (N-PMP imines) is a function of a) the reaction conditions used and b) the electronic properties of the arylidene moiety on the starting imine. High kinetically controlled (2S,RS) diastereoselectivity (−70 °C) was achieved for additions of imines bearing relatively electron-rich N-arylidene groups, while an electron-deficient nature of this group was found to favor the opposite stereochemical outcome. On the other hand, the reactions run under thermodynamically controlled conditions (0 °C) afforded equimolar mixtures of the diastereomeric products regardless of the pattern of substitution on the starting imines. Enantiopure α-arylglycinols were readily synthesized by “non-oxidative” Pummerer rearrangement of diastereomerically pure β-aryl-β-N-(acyl)aminoalkyl sulfoxides, prepared from the corresponding N-PMP derivatives.

Synthesis and biological activity of β-fluoroalkyl β-amino alcohols

Abstract This paper reviews the synthesis of unnatural chiral β-fluoroalkyl β-amino alcohols, with an emphasis on their biological activity and pharmaceutical applications.

Replacement of Isobutyl by Trifluoromethyl in Pepstatin A Selectively Affects Inhibition of Aspartic Proteinases

Two bis‐trifluoromethyl pepstatin A analogues, carboxylic acid 1 and its methyl ester 2, have been synthesised in order to probe the properties and size of the trifluoromethyl (Tfm) group and compare it to the “bigger” isobutyl that is present in pepstatin A. The results demonstrate that Tfm can effectively replace the isobutyl chain as far as inhibitory activity against plasmepsin II (PMu2009II), an aspartic proteinase from Plasmodium falciparum, is concerned. On the other hand, replacement of isobutyl by Tfm selectively affected activity against other aspartic proteinases tested. Two lines of evidence led to these conclusions. Firstly, compounds 1 and 2 retained single‐digit nanomolar inhibitory activity against PMu2009II, but were markedly less active against PMu2009IV, cathepsin D and cathepsin E. Secondly, the X‐ray crystal structures of the three complexes of PMu2009II with 1, 2 and pepstatin A were obtained at 2.8, 2.4 and 1.7 Å resolution, respectively. High overall similarity among the three complexes indicated that the central Tfm was well accommodated in the lipophilic S1 pocket of PMu2009II, where it was involved in tight hydrophobic contacts. The interaction of PMu2009II with Phe111 appeared to be crucial. Comparison of the crystal structures presented here, with X‐ray structures or structural models of PMu2009IV and cathepsin D, allowed an interpretation of the inhibition profiles of pepstatin A and its Tfm variants against these three enzymes. Interactions of the P1 side chain with amino acids that point into the S1 pocket appear to be critical for inhibitory activity. In summary, Tfm can be used to replace an isobutyl group and can affect the selectivity profile of a compound. These findings have implications for the design of novel bioactive molecules and synthetic mimics of natural compounds.

Solution/solid-phase synthesis of partially modified retro-ψ[NHCH(CF3)]-peptidyl hydroxamates

Abstract The synthesis of a novel family of partially-modified (PM) retropeptidyl hydroxamates incorporating a [CH(CF 3 )CH 2 CO] unit as a surrogate of the conventional malonyl group, has been accomplished both in solution and in solid-phase. The key step is the Michael-type N -addition of free or polymer bound α-amino hydroxamates to 3-( E -enoyl)-1,3-oxazolidin-2-ones, which takes place very effectively, although with low stereocontrol. A number of tri- and tetra-peptidyl hydroxamates were obtained either in diastereomerically pure form (by solution-phase synthesis, after chromatographic purification), or as mixtures of two epimers in very good chemical purity (by solid-phase, after release from the resin), demonstrating that this method is suitable for preparing combinatorial libraries of PM retro- ψ [NHCH(CF 3 )]-peptidyl hydroxamates for screening as metalloprotease inhibitors.

Total synthesis of a pepstatin analog incorporating two trifluoromethyl hydroxymethylene isosteres (Tfm-GABOB) and evaluation of Tfm-GABOB containing peptides as inhibitors of HIV-1 protease and MMP-9

Abstract We describe the asymmetric total synthesis of a trifluoromethyl (Tfm) analogue of the aspartate protease inhibitor pepstatin incorporating two γ-Tfm-γ-amino-β-hydroxybutyric acid (γ-Tfm-GABOB) units instead of the natural statine units. The title compound as well as several Tfm-substituted precursors were tested as inhibitors of HIV-1 protease and Gelatinase B (MMP-9)

Dimerizable Redox-Sensitive Triazine-Based Cationic Lipids for in vitro Gene Delivery.

Introduction of a missing gene into the cell nucleus (transfection), followed by its expression by the natural machinery of the cell, is a very well-established strategy to produce proteins. This process can also be used therapeutically to produce proteins needed to heal a certain pathological condition (gene therapy). However, achievement of efficient transfection remains a challenging endeavor. A number of transfection methods have been developed, essentially based on the use of viruses, chemical reagents (for example, cationic lipids and polymers), or physical methods (mechanical stimulation, electroporation, magnetic field induced, etc.). All of these transfection strategies have advantages and drawbacks, but it is apparent that the use of chemical reagents is a very attractive option, because of their ready availability (many transfection reagents are commercial products), their versatility (they can be used to transfect different kinds of cells with genetic material having a wide range of dimensions), low toxicity for the operator (viruses can be pathogenic), and simple experimental use. The main drawback with chemicals as transfectants is connected with their generally low performance, both in terms of number of cells which are transfected and alive at the end of the process and in terms of duration of the transfection. For this reason, chemical transfection reagents must be effective and with limited cytotoxicity, but also cheap and readily prepared from inexpensive, nonexotic starting materials to be competitive and of potential practical use. With these premises, it is not surprising that calcium phosphate is still widely used to achieve transfection, particularly with “difficult” and resistant cells, in addition to popular “organic” reagents (which are generally cationic liposomes comprised of a cationic lipid and a neutral, helper lipid for example, cholesterol) such as Lipofectamine, DOTAP, and related compounds. Although a number of active ingredients for transfection have been recently described in the literature, few of them are truly innovative in terms of structure. In this paper we present a conceptually new family of cationic lipids for transfection featuring a triazine scaffold, which allows for an easy derivatization, with three functionally different amino side chains: 1) a linear C12–C16 chain (the lipophilic tail), 2) a 3-propylammonium chain which acts as polar head, 3) a redox-sensitive dimerizable 2-thioethyl chain (according to the so-called disulfide-linker strategy). The corresponding disulfide dimers have been synthesized and evaluated as well. The new triazine-based transfectants feature very simple preparation from inexpensive materials, and the triazine core allows for a smooth introduction of structural diversity by means of subsequent nucleophilic dechloroaminations of the starting trichlorotriazine by different amines. Most importantly, these triazine-based cationic lipids exhibit low cytotoxicity and high transfection efficiency on a variety of eukaryotic cells, even without any formulation with helper lipids. The lead thiol compound 4, having a C14 chain, was synthesized in multigram amounts as portrayed in Scheme 1.