Calculated and Experimental Low-Energy Conformations of Cyclic Urea HIV Protease Inhibitors

1,3-Diazepine: A privileged scaffold in medicinal chemistry

Privileged structures have been widely used as effective templates for drug discovery. While benzo-1,4-diazepine constitutes the first historical example of such a structure, the 1,3 analogue is just as rich in terms of applications in medicinal chemistry. The 1,3-diazepine moiety is present in numerous biological active compounds including natural products, and is used to design compounds displaying a large range of biological activities. It is present in the clinically used anticancer compound pentostatin, in several recent FDA approved β-lactamase inhibitors (e.g., avibactam) and also in coformycin, a natural product known as a ring-expanded purine analogue displaying antiviral and anticancer activities. Several other 1,3-diazepine containing compounds have entered into clinical trials. This heterocyclic structure has been and is still widely used in medicinal chemistry to design enzyme inhibitors, GPCR ligands, and so forth. This review endeavours to highlight the main use of the 1,3-diazepine scaffold and its derivatives, and their applications in medicinal chemistry, drug design, and therapy. We will focus more particularly on the development of enzyme inhibitors incorporating this scaffold, with a strong emphasis on the molecular interactions involved in the inhibition mechanism.

Rh-Catalyzed C-H activation/intramolecular condensation for the construction of benzo[f]pyrazolo[1,5-a][1,3]diazepines

A novel and mild Rh(iii)-catalyzed C-H activation/intramolecular condensation of 1-aryl-1H-pyrazol-5-amines with cyclic 2-diazo-1,3-diketones was developed, giving access to various important benzo[f]pyrazolo[1,5-a][1,3]diazepine scaffolds through sequential C-C/C-N bond formation in a one-pot procedure under additive- and oxidant-free conditions. Furthermore, 3-([1,1'-biphenyl]-2-ylamino)-2-ethoxycyclohex-2-enones can be obtained in good yields by constructing C-O and C-N bonds through 1,1'-insertion, dehydration, and isomerization processes.

Synthesis of Tetracyclic 2,3-Dihydro-1,3-diazepines from a Dinitrodibenzothiophene Derivative

Triply fused 1,3-diazepine derivatives have been obtained by acidic reduction of rotationally locked and sterically hindered nitro groups in the presence of an aldehyde or ketone. The nitro groups are sited on adjacent rings of a dicyanodibenzothiophene-5,5-dioxide, which also displays fully reversible two-electron-accepting behavior. The synthesis, crystallographically determined molecular structures, and aspects of the electronic properties of these new molecules are presented.

Synthesis and anticonvulsant activity of amino acid-derived sulfamides

Sulfamides are promising functions for the design of new antiepileptic drugs ( Bioorg. Med. Chem. 2007, 15, 1556-1567; 5604-5614 ). Following previous research in this line, a set of amino acid-derived sulfamides has been designed, synthesized, and tested as new anticonvulsant compounds. The experimental data confirmed the ability of some of the structures to suppress the convulsions originated by the electrical seizure (MES test) at low doses (100 mg/kg).

Greener and expeditious synthesis of bioactive heterocycles using microwave irradiation

The utilization of green chemistry techniques is dramatically reducing chemical waste and reaction times as has recently been proven in several organic syntheses and chemical transformations. To illustrate these advantages in the synthesis of bioactive heterocycles, we have studied various environmentally benign protocols that involve greener alternatives. Microwave (MW) irradiation of neat reactants catalyzed by the surfaces of recyclable mineral supports, such as alumina, silica, clay, or their "doped" versions, enables the rapid one-pot assembly of heterocyclic compounds, such as flavonoids, related benzopyrans, and quinolone derivatives. The strategy to assemble oxygen and nitrogen heterocycles from in situ generated reactive intermediates via enamines or using hypervalent iodine reagents is described. Examples of multicomponent reactions that can be adapted for rapid parallel synthesis include solventless synthesis of dihydropyrimidine-2(1H)-ones (Biginelli reaction), imidazo[1,2-a]annulated pyridines, pyrazines, and pyrimidines (Ugi reaction). The relative advantages of greener pathways, which use MW irradiation and eco-friendly aqueous reaction medium, for the synthesis of various heterocycles, such as N-aryl azacycloalkanes, isoindoles, 1,3-dioxane, 1,3,4-oxadiazole, 1,3,4-thiadiazole, pyrazole, and diazepines, are also summarized.

Design, Synthesis, and Computational Studies of Inhibitors of Bcl-XL

One of the primary objectives in the design of protein inhibitors is to shape the three-dimensional structures of small molecules to be complementary to the binding site of a target protein. In the course of our efforts to discover potent inhibitors of Bcl-2 family proteins, we found a unique folded conformation adopted by tethered aromatic groups in the ligand that significantly enhanced binding affinity to Bcl-XL. This finding led us to design compounds that were biased by nonbonding interactions present in a urea tether to adopt this bioactive, folded motif. To characterize the key interactions that induce the desired conformational bias, a series of substituted N,N'-diarylureas were prepared and analyzed using X-ray crystallography and quantum mechanical calculations. Stabilizing pi-stacking interactions and destabilizing steric interactions were predicted to work in concert in two of the substitution patterns to promote the bioactive conformation as a global energy minimum and result in a high target binding affinity. Conversely, intramolecular hydrogen bonding present in the third substitution motif promotes a less active, extended conformer as the energetically favored geometry. These findings were corroborated when the inhibition constant of binding to Bcl-XL was determined for fully elaborated analogues bearing these structural motifs. Finally, we obtained the NMR solution structure of the disubstituted N,N'-diarylurea bound to Bcl-XL demonstrating the folded conformation of the urea motif engaged in extensive pi-interactions with the protein.

Conformational Analysis and Rotational Barriers of Alkyl- and Phenyl-Substituted Urea Derivatives

Potential energy surfaces (PES) for rotation about the N-C(sp(3)) or N-C(aryl) bond and energies of stationary points on PES for rotation about the C(sp(2))-N bond are reported for methylurea, ethylurea, isopropylurea, tert-butylurea, and phenylurea, using the B3LYP/DZVP2 and MP2/aug-cc-pVDZ methods. The analysis of alkylureas reveals cis and (less stable) trans isomers that adopt anti geometries, whereas syn geometries do not correspond to stationary points. In contrast, the analysis of phenylurea reveals that the lowest energy form at the MP2 level is a trans isomer in a syn geometry. The fully optimized geometries are in good agreement with crystal structure data, and PESs are consistent with the experimental dihedral angle distribution. Rotation about the C(sp(2))-N bond in alkylureas and phenylurea is slightly more hindered (8.6-9.4 kcal/mol) than the analogous motion in the unsubstituted molecule (8.2 kcal/mol). At the MP2 level of theory, the maximum barriers to rotation for the methyl, ethyl, isopropyl, tert-butyl, and phenyl groups are predicted to be 0.9, 6.2, 6.0, 4.6, and 2.4 kcal/mol, respectively. The results are used to benchmark the performance of the MMFF94 force field. Systematic discrepancies between MMFF94 and MP2 results were improved by modification of several torsional parameters.

Comparing the conformational behavior of a series of diastereomeric cyclic urea HIV-1 inhibitors using the low mode:monte carlo conformational search method

The conformational flexibility of a series of diastereomeric cyclic urea HIV-1 protease inhibitors has been examined using the Low Mode:Monte Carlo conformational search method. Force fields were validated by a comparison of the energetic ordering of the minimum energy structures on the AMBER/GBSA(water), OPLSAA/GBSA(water) and HF/6-311G/SCRF(water) surfaces. The energetic ordering of the minima on the OPLSAA /GBSA(water) surface was in better agreement with the quantum calculations than the ordering on the AMBER/GBSA(water) surface. An ensemble of low energy structures was generated using OPLSAA/GBSA(water) and used to compare the molecular shape and flexibility of each diastereomer to the experimentally determined binding affinities and crystal structures of closely related systems. The results indicate that diastereomeric solution-phase energetic stability, conformational rigidity and ability to adopt a chair conformation correlate strongly with experimental binding affinities. Rigid body docking suggests that all of the diastereomers adopt solution-phase conformations suitable for alignment with the HIV-1 protease; however, these results indicate that the binding affinities are dependent upon subtle differences in the P1/P1' and P2/P2' substituent orientations.

1H-1,3-Diazepines, 5H-1,3-diazepines, 1,3-diazepinones, and 2,4-diazabicyclo[3.2.0]heptenes,

Tetrazolo[1,5-a]pyridines/2-azidopyridines 1 undergo photochemical nitrogen elimination and ring expansion to 1,3-diazacyclohepta-1,2,4,6-tetraenes 3, which react with alcohols to afford 2-alkoxy-1H-1,3-diazepines 4 (5), with secondary amines to 2-dialkylamino-5H-1,3-diazepines 16, sometimes via isolable 2-dialkylamino-1H-1,3-diazepines 15, and with water to 1,3-diazepin-2-ones 19. The latter are also obtained by elimination of isobutene or propene from 2-tert-butoxy- or 2-isopropoxy-1H-1,3-diazepines 4 or 5. 1,3-Diazepin-2-one 22B and 1,3-diazepin-4-one 24 were obtained from hydrolysis of the corresponding 4-chlorodiazepines. Diazepinones 19 undergo photochemical ring closure to diazabicycloheptenones 25 in high yields. The 2-alkoxy-1H-1,3-diazepines 4 and 5 interconvert by rapid proton exchange between positions N1 and N3. The free energies of activation for the proton exchange were measured by the Forsén-Hoffman method as DeltaG([double dagger])298= 16.2 +/- 0.6 kcal mol(-1) as an average for 4a-c in CD2Cl2, acetone-d6, and methanol-d4, and 14.1 +/- 0.6 kcal mol(-1) for in 4c acetone/D2O. The structures of 2-methoxy-5,6-bis(trifluoromethyl)-1H-1,3-diazepine 4k, 1,2-dihydro-4-diethylamino-5H-1,3-diazepin-2-one 22bB, and diazabicycloheptanone were 26 determined by X-ray crystallography. The former represents the first reported X-ray crystal structure of any monocyclic N-unsubstituted 1H-azepine.

Synthesis of seven-membered ring diazepin-2-ones via palladium-catalyzed highly regioselective cyclization of 2-vinylpyrrolidines with aryl isocyanates

The first palladium-catalyzed ring-expansion reaction of 2-vinylpyrrolidines with aryl isocyanates to form seven-membered ring heterocycles is described. This regioselective reaction requires 5 mol % of Pd(2)(dba)(3).CHCl(3) and 10 mol % of dppp at 40-60 degrees C in THF and results in the formation of 1,3-diazepin-2-ones in good isolated yields. When Pd(OAc)(2) and PPh(3) were utilized in the reaction, an intramolecular hydrogen migration occurs resulting in the formation of conjugated diene derivatives of urea.

Catalytic oxidative carbonylation of primary and secondary diamines to cyclic ureas. Optimization and substituent studies

W(CO)(6)-catalyzed oxidative carbonylation of 1,3-propanediamine to the corresponding urea has been examined under a variety of conditions. Following optimization, the Thorpe-Ingold effect on ring closure was studied using 2,2-dialkyl-1,3-propanediamines. For the 2,2-dimethyl- and 2,2-dibutyl-1,3-propanediamines, the yields were increased significantly as compared to that of the unsubstituted case. The eight-membered cyclic urea 5-butyl-5-ethyl-1,3-diazepan-2-one (5f) was formed in 38% yield, while only trace amounts of the cyclic urea were produced from the parent 1,5-pentanediamine. In a study of secondary diamines, yields from the carbonylation of N,N'-dialkyl-2,2-dimethyl-1,3-propanediamines were lower than those obtained from the primary diamines. The main byproducts from secondary diamines were tetrahydropyrimidine derivatives formed from a competitive reaction of the substrate with the oxidant and base.

H-bonding additives act like Lewis acid catalysts

[reaction: see text] A combination of NMR, IR, and ab initio techniques reveals the striking structural similarities of an exemplary H-bonded complex of an N-acyloxazolidinone with an N,N'-disubstituted electron-poor thiourea and the corresponding Lewis acid complex. Although the H-bond association constant is lower than for the Lewis acid adduct, Diels-Alder reactions are accelerated and stereochemically altered in a fashion similar to weak Lewis acids.

Synthesis and comparative molecular field analysis (CoMFA) of symmetric and nonsymmetric cyclic sulfamide HIV-1 protease inhibitors

We have previously reported on the unexpected flipped conformation in the cyclic sulfamide class of inhibitors. An attempt to induce a symmetric binding conformation by introducing P2/P2' substituents foreseen to bind preferentially in the S2/S2' subsite was unsuccessful. On the basis of the flipped conformation we anticipated that nonsymmetric sulfamide inhibitors, with P2/P2' side chains modified individually for the S1' and S2 subsites, should be more potent than the corresponding symmetric analogues. To test this hypothesis, a set of 18 cyclic sulfamide inhibitors (11 nonsymmetric and 7 symmetric) with different P2/P2' substituents was prepared and evaluated in an enzyme assay. To rationalize the structure-activity relationship (SAR) and enable the alignment of the nonsymmetric inhibitors, i.e., which of the P2/P2' substituents of the nonsymmetric inhibitors interact with which subsite, a CoMFA study was performed. The CoMFA model, constructed from the 18 inhibitors in this study along with seven inhibitors from previous work by our group, has successfully been used to rationalize the SAR of the cyclic sulfamide inhibitors. Furthermore, from the information presented herein, the SAR of the cyclic sulfamide class of inhibitors seems to differ from the SAR of the related cyclic urea inhibitors reported by DuPont and DuPont-Merck.

The synthesis of sterically demanding amino acid-derived cyclic phosphonamides

The preparation and utilization of C(2)-symmetric 1,4-diamines in the synthesis of amino acid-derived cyclic phosphonamides 1-3 are described. The 1,4-diamines are synthesized via three methods: (i) amino acid/fumaryl chloride coupling followed by amide reduction, (ii) amino acid/1,4-diamine coupling followed by amide reduction, and (iii) a template-supported ring-closing metathesis/hydrolysis sequence. The pseudo C(2)-symmetric cyclic phosphonamides 1-3 are prepared by condensation of the C(2)-symmetric 1,4-diamines to P(III) centers, followed by oxidation.

7-Azabicycloheptane carboxylic acid: a proline replacement in a boroarginine thrombin inhibitor

[formula: see text] The synthesis of thrombin inhibitor 3, which incorporates conformationally constrained 7-azabicycloheptane carboxylic acid (1) as a proline replacement, is described. The inhibition constant (Ki(thrombin) = 2.9 nM) indicates that 1 is a reasonable replacement of proline in the formation of a beta-turn tripeptide mimetic.