Channel‐forming,self‐assembling,bishelical amphiphilic peptides: design,synthesis and crystal structure of Py(Aibn)2, n = 2, 3, 4

Abstract: The design, synthesis, characterization and self‐assembling properties of a new class of amphiphilic peptides, constructed from a bifunctional polar core attached to totally hydrophobic arms, are presented. The first series of this class, represented by the general structure Py(Aib_n)₂ (Py = 2,6‐pyridine dicarbonyl unit; Aib = α, α′‐dimethyl glycine; n = 1–4), is prepared in a single step by the condensation of commercially available 2,6‐pyridine dicarbonyl dichloride with the methyl ester of homo oligoAib peptide (Aib_n‐OMe) in the presence of triethyl amine. ¹H NMR VT and ROESY studies indicated the presence of a common structural feature of 2‐fold symmetry and an NH…N hydrogen bond for all the members. Whereas the Aib3 segment in Py(Aib3)₂ showed only the onset of a 3₁₀‐helical structure, the presence of a well‐formed 3₁₀‐helix in both Aib4 arms of Py(Aib4)₂ was evident in the ¹H NMR of the bispeptide. X‐ray crystallographic studies have shown that in the solid state, whereas Py(Aib2)₂ molecules organize into a sheet‐like structure and Py(Aib3)₂ molecules form a double‐stranded string assembly, the tetra Aib bispeptide, Py(Aib4)₂, is organized to form a tetrameric assembly which in turn extends into a continuous channel‐like structure. The channel is totally hydrophobic in the interior and can selectively encapsulate lipophilic ester (CH₃COOR, R = C₂H₅, C₅H₁₁) molecules, as shown by the crystal structures of the encapsulating channel. The crystal structure parameters are: 1b , Py(Aib2)₂, C₂₅H₃₇N₅O₈, sp. gr. P2₁2₁2₁, a = 9.170(1) Å, b = 16.215(2) Å, c = 20.091(3) Å, R = 4.80; 1c , Py(Aib3)₂, C₃₃H₅₁N₇O₁₀·H₂O, sp. gr. P, a = 11.040(1) Å, b = 12.367(1) Å, c = 16.959(1) Å, α = 102.41°, β = 97.29°, γ = 110.83°, R₁ = 6.94; 1 da, Py(Aib4)₂?et ac, C₄₁H₆₅N₉O₁₂?1.5H₂O·C₄H₈O₂, sp. gr. P, a = 16.064(4) Å, b = 16.156 Å, c = 21.655(5) Å, α = 90.14(1)°, β = 101.38(2)°, γ = 97.07(1)°, Z = 4, R₁ = 9.03; 1db, Py(Aib4)₂?amylac,C₄₁H₆₅N₉O₁₂?H₂O ·C₇H₁₄O₂, P2₁/c, a = 16.890(1) Å, b = 17.523(1) Å, c = 20.411(1) Å, β = 98.18 °, Z = 4, R = 11.1 (with disorder).     

The crystal and molecular structure of bromhexine·HCl

The crystals of bromhexine-HCl, C₁₄H₂₁ N₂Br₂Cl, are orthorhombic, space group Pca2₁ with a=14.598(2)Å, b=12.461(3)Å, c=9.186(1)Å and Z=4. Intensity data for 967 reflections (Fobs>6σ(F)) were collected on a Rigaku-Denki automatic fourcircle diffractometer. The structure was solved by the Patterson and Fourier methods. Refinements were carried out to the final R value of 0.082. The cyclo-hexane ring has a normal chair form and the benzene ring is planar. There are three independent hydrogen bonds in the structure. One is an intermolecular hydrogen bond (N-H…Cl^?) and the others are intramolecular hydrogen bonds (N-H…Br, N⁺-H…Cl^?). Apart from the hydrogen bonding system the molecules are held together in the crystal by van der Waals force.     

Serine-containing 10-membered cyclodepsipeptides

As a part of a Research program aimed at studying synthesis and conformation of small ring peptides, the cyclization of diastereoisomeric N-phenylacetyl-seryl-propyl-proline tripeptides has been examined. Two 10- membered peptide lactones, and , have been isolated by treating the corresponding linear p-nitrophenyl esters with DBU in dry benzene. In these two compounds the serine lactone fragment (a common structural feature of several bioactive cyclodepsipeptides) is inserted into a highly strained small ring system. The conformation in the crystal of 5a and 5b has been studied by X-ray analysis. Both the 10-membered rings of 5a and 5b adopt an overall cis-cis-trans conformation in which the lactone junction is trans. The deviations from planarity of the peptide units vary from Δω= 30° for the DSer—Pro bond in 5b to Ao= 5-6° for the DSer-PrO bond in 5a and PrO—DPrO bond in 5b . The skeletal atoms of 5b , containing the PrO-DPrO sequence, are related by a pseudo-symmetry mirror plane passing through the Pro carbonyl and the opposite DSer C^βH₂ group. In both the molecules the exocyclic amide bond adopts an extended conformation with respect to the DSer-Pro ring junction; this arrangement gives rise to a C₅-type ring structure which is well evidenced in the case of 5a .     

Binding site analysis of CCR2 through in silico methodologies: docking, CoMFA, and CoMSIA

Chemokine receptor (CCR2) is a G protein‐coupled receptor that contains seven transmembrane domains. CCR2 is targeted for diseases like arthritis, multiple sclerosis, vascular disease, obesity and type 2 diabetes. Herein, we report on a binding site analysis of CCR2 through docking and three‐dimensional quantitative structure–activity relationship (3D‐QSAR). The docking study was performed with modeled receptor (CCR2) using β2‐andrenergic receptor structure as a template. Comparative molecular field analysis (CoMFA)‐ and comparative molecular similarity indices analysis (CoMSIA)‐based 3D‐QSAR models were developed using two different schemes: ligand‐based (CoMFA; q² = 0.820, r² = 0.966, = 0.854 and CoMSIA; q² = 0.762, r² = 0.846, = 0.684) and receptor‐guided (CoMFA; q² = 0.753, r² = 0.962, = 0.786, CoMSIA; q² = 0.750, r² = 0.800, = 0.797) methods. 3D‐QSAR analysis revealed the contribution of electrostatic and hydrogen bond donor parameters to the inhibitory activity. Contour maps suggested that bulky substitutions on the para position of R¹ substituted phenyl ring, electronegative and donor substitutions on meta (5′) and ortho (2′) position of R² substituted phenyl ring were favorable for activity. The results correlate well with previous results and newly report additional residues that may be crucial in CCR2 antagonism.     

Polymethylene spacer linked bis(A1a) peptides form modified β:-sheet structures

The adipoyl- and suberoyl-linked bis(Ala) peptides have an extended backbone between the two C^alpha; atoms in each molecule. They self-assemble, through intermolecular hydrogen bonds and stacking of parallel strands, into highly ordered modified β-sheet-like structures. Crystal data for adipoyl bis(A1a)diester are as follows: C₁₄H₂₄N₂)O₆, monoclinic space group P2₁, a = 4.900(1), b = 29.093(10), c = 6.021(2) Å, β= 104.20(2)?, R = 0.053 for 1100 data >3σ(F); for suberoyl bis(A1a)diester: C₁₆H₂₈N₂O₆, monoclinic space group P2¹, a = 4.887(2), b = 32.650(9), c = 6.004(2) Å; β= 103.79(3), R = 0.070 for 1065 data > 3σ.     

Crystal structure and conformation of a highly constrained linear tetrapeptide Boc-Leu-dehydro Phe-Ala-Leu-OCH3

The conformation of a tetrapeptide containing a dehydro amino acid, Δ^zPhe, in its sequence has been determined in the crystalline state using X-ray crystallographic techniques. The tetrapeptide, Boc-Leu-Δ^zPhe-Ala-Leu-OCH₃, crystallizes in the orthorhombic space group P2₁2₁2₁ with four molecules in a unit cell of dimensions a = 11.655(1) Å, b = 15.698(6) Å and c = 18.651(3) Å V = 3414.9 Å and Dcalc =1.12 g/cm ^?3. The asymmetric unit contains one tetrapeptide molecule, C₃₀H₄₆N₄O₇, a total of 41 nonhydrogen atoms. The structure was determined using the direct methods program SHELXS86 and refined to an R-factor of 0.049 for 3347 reflections (13.0(I). The linear tetrapeptide in the crystal exhibits a double bend of the Type III-I, with Leu¹ (<φ=?54.1°, Ψ=?34.5°) and Δ^zPhe² (φ=?59.9°, Ψ=?17.1°) as the corner residues of Type III turn and Δ^zPhe² (φ=?59.9°, Ψ=?17.1°) and Ala³ (φ=?80.4°, Ψ= 0.5°) residues occupying the corners of Type I turn, with Δ^zPhe as the common residue in the double bend. The turn structures are further stabilized by two intramolecular 4→1 type hydrogen bonds.     

Guanidinium-carboxylate interaction: methylguanidinium formate

The crystal structure of methylguanidinium formate is presented as a model for arginine - carboxylate interactions. The crystals are orthorhombic, P2₁2₁2₁, with a =6.963(2), b = 7.110(2), c = 11.873(3)Å. The structure was solved by direct methods and refined by block-diagonal least squares to R = 0.078 and R_w = 0.080. Ion pairs are formed by hydrogen bonds between the amino and CH³ NH- imino groups and the formate ion. Additional hydrogen bonding results in the formation of a three-dimensional network. Comparisons are made with similar compounds.     

Conformation and hydrogen bonding of N-formylpeptides: crystal and molecular structure of N-formyl-l-alanyl-l-aspartic acid†

Crystals of N-formyl-l -alanyl-l -aspartic acid (C₈H₁₁N₂O₆) grown from aqueous methanol solution are orthorhombic, space group, P2₁2₁2₁ with cell parameters at 294 K of a = 13.619(2), b = 8.567(2), c = 9.583(3)Å, V = 1118.1ų, M.W. = 232.2, Z = 4, D_m= 1.38g/cm³ and D_x= 1.378g/cm³. The crystal structure was solved by the application of direct methods and refined to an R value of 0.075 for 1244 reflections with I ≥ 3σ collected on a CAD-4 diffractometer. The structure contains two short inter-molecular hydrogen bonds: (i) between the C-terminal carboxyl OH and the N-acyl oxygen (2.624(3)Å), a characteristic feature found in many N-acyl peptides and (ii) between the aspartic carboxyl OH and the peptide oxygen OP1 (2.623(3)Å). The peptide is nonplanar (ω= 165.5(6)°). The molecule takes up a folded conformation in contrast to N-formyl peptides which form extended β-sheets; the values of ø₁, Ψ₁, ø₂, Ψ¹₂, and Ψ²₂ are, respectively –65.7(6), 152.0(5), –107.2(5), 30.9(5), and –150.3(6). The aspartic acid side chain conformation is g^? with χ¹= 73.1(5). The formyl group, as expected, is transplanar [OF-CF-N1-CA1 = -4.0(8)°]. The presence of the short O–H … O hydrogen bond emerges as a structural feature common to this peptide and several other N-formyl peptides. There are no C-H … O hydrogen bonds in this structure.     

Structure and conformation of peptides involving prolyl residue

The dipeptide, L-prolyl-L-leucine monohydrate (C₁₁ H₂₀ N₂ O₃· H₂O, molecular weight, 246.3) crystallizes in the monoclinic space group P2_1/, with cell constants: a = 6.492(2)Å b = 5.417(8)Å c = 20.491(5)Å, β= 96.59(2)°, Z = 2, Do = 1.15g/cm³, and Dc = 1.142g/cm³. The structure was solved by SHELX-86 and refined by full matrix least squares methods to a final R-factor of 0.081 for 660 unique reflections (I > 2σ (I)) measured on an Enraf Nonius CAD-4 diffractometer (CuK_x, λ= 1.5418 4AR, T = 293 K). The peptide linkage exists in the trans conformation. The pyrrolidine ring exists in the envelope conformation. The values of the sidechain torsion angles are: ψ₁= -59.3(13)°, ψ₂₁= -63.1(16)° and ψ₂₂= 174.8(15)° for leucine (C-terminal). The crystal structure is stabilised by a three-dimensional network of N—H… O, O—H… O, and C—H…O hydrogen bonds.     

Crystal and molecular structure of BN 52021, a PAF-acether antagonist. Comparison with the conformation of Kadsurenone and related compounds

BN52021 (Ginkgolide B) monohydrate C₂₀H₂₄O₁₀ · H₂O crystallizes in the triclinic space group P1 with two independent molecules in the unit cell of which parameters are a = 7.627(2), b = 11.514(3), c = 12.941(3)Å, α = 97.05(2), β = 90.27(2) and γ = 108.71(2)°, V = 1067.06ų. Calculated density D_x = 1.320g.cm⁻³. The crystal structure was solved by Patterson methods starting from dreiding model data. The final reliability index R = 0.099 for 3848 observed reflections collected with a four-circle diffractometer. Anti-PAF activities of Kadsurenone, Kadsurin-A, Kadsurin-B and Piperenone, molecular structure of MIRANDIN-A, related compounds and BN52021 suggest that a distance O-O of about 6.6Å observed in Kadsurenone and in BN52021 could be favourable to anti-PAF activity.     

Parallel and antiparallel aggregation of α-helices

An apolar helical decapeptide with different end groups, Boc- or Ac-, crystallizes in a completely parallel fashion for the Boc-analog and in an antiparallel fashion for the Ac-analog. In both crystals, the packing motif consists of rows of parallel molecules. In the Boc-crystals, adjacent rows assemble with the helix axes pointed in the same direction. In the Ac-crystals, adjacent rows assemble with the helix axes pointed in opposite directions. The conformations of the molecules in both crystals are quite similar, predominantly α-helical, except for the tryptophanyl side chain where χ¹? 60° in the Boc- analog and ? 180° in the Ac-analog. As a result, there is one lateral hydrogen bond between helices, N(lε)…O(7), in the Ac-analog. The structures do not provide a ready rationalization of packing preference in terms of side-chain interactions and do not support a major role for helix dipole interactions in determining helix orientation in crystals. The crystal parameters are as follow. Boc-analog: C₃H₇,N₁₁O₁₃ C₃H₇OH, space group P1 with a = 10.250(3) Å, b = 12.451(4) Å, c = 15.077(6) Å, x= 96.55(3)°, β= 92.31(3)°, y= 106.37(3)°, Z = 1, R = 5.5% for 5581 data (|F| > 3.0a(F)), resolution 0.89 Å. Ac-analog: C₅₇,H₉₁,N₁₁,O₁₂, space group P2₁, with a = 9.965(1) Å, b = 19.707(3) Å, c = 16.648(3) Å, β= 94.08(1), Z = 2, R = 7.2% for 2530 data (|F| > 3.0σ(F)), resolution 1.00 Å.     

Conformational features responsible for the binding of cyclic analogues of enkephalin to opioid receptors

Models of μ- and δ-receptor-bound backbone conformations of enkephalin cyclic analogues containing Phe⁴ were determined by comparing geometrical similarity among the previously found low-energy, backbone structures of -enkephalinamide, -enkephalinamide, -enkephalin and -enkephalin. The present μ-receptor-bound conformation resembles a β-I bend in the peptide backbone centred on the Gly³-Phe⁴ region. Two slightly different models were found for the δ-receptor-bound conformation; both of them are more extended than the μ-receptor-bound conformation and include a γ-turn (or a γ-like turn) on the Gly³ residue. Energetically favourable rotamers of Tyr and Phc side chains were also determined for the μ- and δ-conformations. The present models of μ- and δ-conformations share geometrical similarity with the low-energy structures of Leu-enkephalin and the analogue.     

Cystine peptides Antiparallel β-sheet conformation of the cyclic biscystine pep tide [Boc-Cys-Ala-Cys-NHCH3]2

The crystal structure analysis of the cyclic biscystine peptide [Boc-Cys¹-Ala²-Cys³-NHCH₃]₂ with two disulfide bridges confirms the antiparallel β-sheet conformation for the molecule as proposed for the conformation in solution. The molecule has exact twofold rotation symmetry. The 22-membered ring contains two transannular NH ? OC hydrogen bonds and two additional NH ? OC bonds are formed at both ends of the molecule between the terminal (CH₃)₃COCO and NHCH₃ groups. The antiparallel peptide strands are distorted from a regularly pleated sheet, caused mainly by the L-Ala residue in which φ=– 155° and ψ= 162°. In the disulfide bridge C^α (1)-C^β (1)-S(1)-(3′)-C^β(3′)-C^α(3′), S—S = 2.030 Å, angles C^β SS = 107° and 105°, and the torsional angles are –49, –104, +99, –81, –61°, respectively. The biscystine peptide crystallizes in space group C2 with a = 14.555(2) Å, b = 10.854(2) Å, c = 16.512(2)Å, and β= 101.34(1) with one-half formula unit of C₃₀H₅₂N₈O₁₀S₄· 2(CH₃)₂SO per asymmetric unit. Least-squares refinement of 1375 reflections observed with |F| > 3σ(F) yielded an R factor of 7.2%.     

Synthesis and crystal structures of Boc-L-Asn-L-Pro-OBzl·CH3OH and dehydration side product,Boc-β-cyano-L-alanine-L-Pro-OBzl

Boc-L-Asn-L-Pro-OBzl:C₂₁H₂₉O₆N₃·CH³OH, M_r= 419.48 + CH₃OH, monoclinic, P2₁, a= 10.049(1), b= 10.399(2), c= 11.702(1)Åβ= 92.50(1)°, V = 1221.7(3)ų, d_x= 1.14g cm^-3, Z = 2, CuKα (λ= 1.54178 Å), F(000) = 484 (with solvent), 23°, unique reflections (I > 3σ(I)) = 1745, R = 0.043, R_w= 0.062, S = 1.66. Boc-β-cyano-L-alanine-L-Pro-OBzl: C₂₁H₂₇O₅N₃, M_r= 401.46, orthorhombic, P2₁2₁2₁, a= 15.741(3), b= 21.060(3), c= 6.496(3)ÅV= 2153(1)ų, d_x= 1.24g·cm^-3, Z = 4, CuKα (λ= 1.54178 Å), F(000) = 856, 23°, unique reflections (I > 3σ(I)) = 1573, R = 0.055, R_w= 0.078, S = 1.86. The tert.-butyloxycarbonyl (Boc) protected dipeptide benzyl ester (OBzl), BOC-L-Asn-L-Pro-OBzl, prepared from a mixed anhydride reaction using isobutylchloroformate, BOC-L-asparagine, and HCI·L-proline-OBzl, crystallized with one methanol per asymmetric unit in an extended conformation with the Asn-Pro peptide bond trans. Intermolecular hydrogen bonding occurs between the methanol and the Asn side chain and between the peptide backbone and the Asn side chain. A minor impurity due to the dehydration of the Asn side chain to a β-CNaia crystallized with a similar extended conformation and a single intermolecular hydrogen bond.     

Cis/trans conformational equilibrium across the N‐methylphenylalanine2‐ N‐methylphenylalanine3 peptide bond of arginine vasopressin analogs

Abstract: Two cyclic analogs of vasopressin, ‐Pro‐Arg‐Gly‐NH₂ ( 1 ) and ‐Pro‐Arg‐Gly‐NH₂ ( 2 ) were synthesized by the solid phase method. Their structure was determined in aqueous solution by two‐dimensional NMR techniques and simulated annealing algorithm from an extended template in X‐PLOR. The total chemical shift correlation spectroscopy and rotating‐frame Overhauser enhancement spectroscopy of the peptides displayed four distinct sets of residual proton resonances. This suggests that both analogs adopt four families of conformations in H₂O/D₂O (9 : 1) (one major and three minor species). In further analysis only signals of major species (M) and of one minor species (m₁) were considered. The major species of both peptides include a trans peptide bond between the first and second residue, and a cis form between the second and third residue. In the minor species, all peptide bonds were found to exist in trans geometry.     

Monoclinic polymorph of Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe(anhydrous)

The structures of two crystal forms of Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe have been determined. The triclinic form (PI, Z= l) from DMSO/H₂O crystallizes as a dihydrate (Karle, Sukumar & Balaram (1986) Proc. Natl. Acad. Sci. USA 83, 9284-9288). The monoclinic form (P2¹, Z = 2) crystallized from dioxane is anhydrous. The conformation of the peptide is essentially the same in both crystal systems, but small changes in conformational angles are associated with a shift of the helix from a predominantly α-type to a predominantly 3₁₀-type. The r.m.s. deviation of 33 atoms in the backbone and Cβ positions of residues 2-8 is only 0.29 Å between molecules in the two polymorphs. In both space groups, the helical molecules pack in a parallel fashion, rather than antiparallel. The only intermolecular hydrogen bonding is head-to-tail between helices. There are no lateral hydrogen bonds. In the P2₁ cell, a = 9.422(2)Å, b = 36.392(11)Å, c = 10.548(2)Å, β= 111.31(2)° and V = 3369.3ų For 2 molecules of C⁶⁰H⁹⁷N¹¹O¹⁰ per cell.     

Unusual intramolecular hydrogen bonding in cycloamanide A,cyclic (LPro-LVal-LPhe-LPhe-LAla-Gly)

The naturally occurring cyclic hexapeptide, cycloamanide A, has only one intramolecular hydrogen bond. It is a 4 ← 1 type that encompasses the LPhe-LAla sequence in which the experimentally determined ø, ← values are + 54d?, – 118d? and – 88d?, – 4d?, respectively. Even though the chirality is L, L, the ø, ← values are characteristic for a D, L β-bend, Type II°. The conformation of the molecule was established by a crystal structure determination using X-ray diffraction analysis. Cycloamanide A (C₃₃H₄₂N₆O₆←. 4H₂O) crystallizes in space group P2₁2₁2₁ with cell parameters a = 13.307(2) Å, b = 24.820(4) Å and c = 11.231(1) Å.     

Crystal structure and conformation of glycyl-glycyl-sarcosine

Crystals of the tripeptide, glycyl-glycyl-sarcosine (C₇H₁₃N₃O₄) from aqueous methanol are orthorhombic, space group Pbcn with cell parameters at 294 K of a = 8.279(1), b = 9.229(4), c = 24.447(5) Å, V = 1868.0 ų, M.W. = 203.2, and Z = 8. The crystal structure was solved and refined using CAD-4 data (1171 reflections ≥ 3σ) to a final R-value of 0.053. The first peptide linkage is trans and planar whereas the second peptide link between Gly and sarcosine is cis and appreciably non-planar (w = 7.4°). The peptide backbone has an extended conformation at the N-terminal part but adopts a polyglycine-II type of conformation at the C-terminal part. The backbone torsion angles are: Ψ₁, =? 173.9, w₁=? 177.8, (φ, Ψ₂) = (-178.8, -170.8), w₂= 7.4, (φ₃, Ψ₃) = (-81.6, 165.6°).     

Peptide crystal growth via vapor diffusion

The structure of a dihydrated form of glycyl-L-tyrosyl-L-alanine (GYA) has been determined as part of a series of peptide structural investigations and development of microscale vapor diffusion experiments for peptide crystal growth. Crystals were grown by the hanging-drop method against sodium acetate. The tripeptide is a zwitterion in the crystal, adopting an extended conformation through glycine, a nearly perpendicular bend attyrosine and a reverse turn for the C-terminal carboxylate. Principal backbone torsion angles are ψ₁ 175(1)°, ω₂ 173(1)°, φ₂ -119(1)°, ψ₂ 120(1)°, ω₃3 172(1)°, φ₃ -73(1)°,ψ₃₁ -9(1)°, ψ₃₂ 171(1)°. The tyrosyl side chain adopts an unusual orientation (χ^1/2= -86(1)°). The relationship of the GYA.2H₂O structure to GYA sequences in proteins is examined, particularly as regards its helix-forming potential. Crystal data: C₁₄H₁₉N₃O₄.2H₂O, Mr = 345.36, orthorhombic, P2₁2₁2₁, a = 4.810 (4), b= 11.400(7), c = 30.162(23)Å, V=1653.8(24)Å^?3, Z = 4, Dx= 1.387 Mgm^?3, λ(CuK_α^?)= 1.540 Åμ= 9.053 mm^?1, F(000) = 736, T = 199K, R = 0.041 for 1458 observations with I ≥ 3σ(I).