Rapid and quantitative cyclization of multiple peptide loops onto synthetic scaffolds for structural mimicry of protein surfaces.
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Amino Acid Sequence↗
Biomedical subjects
Peter Timmerman
Publications and source records attributed to Peter Timmerman.
Mapping of a discontinuous and highly conformational binding site on follicle stimulating hormone subunit-beta (FSH-beta) using domain Scan and Matrix Scan technology.
This paper describes the application of two novel screening technologies, i.e. Domain Scan (24- and 30-mer peptides) and Matrix Scan (24-mer peptides) technology, in the mapping of a discontinuous epitope on FSH-beta for a series of 20 monoclonal antibodies. 11 out of 20 mAb's, mapping of which was not successful by conventional Pepscan technology (12-mer peptides), showed selective binding to peptide-constructs corresponding to the beta3-loop of FSH in the Domain and/or Matrix Scan. Systematic replacement analysis studies with peptide-construct 57VYETVRVPGCAC-SAc-ADSLYTYPVATQ81 revealed that for most mAb's the amino acids R62, A70, D71, and L73 form the core of the epitope. A Domain Scan performed in the C-O format showed highly selective binding for mAb's 1 and 2 with only three beta1-beta3 peptide-constructs covering the residues 60TVRVPGCAHHADSLY74 in combination with 10IAIEKEECRFAI21, while for mAb 10 binding was observed with peptide-constructs containing the C-terminal residues 97RGLGPSYCSFGEMKE114 in combination with the residues 10IAIEKEECRFAI21. A Matrix Scan of mAb 17 showed that peptides from four different regions on FSH (1st strand beta3-loop, alpha 1-loop, long alpha2-loop, det. loop) showed enhanced binding in combination with several 70ADSL73-containing peptides. BIACORE measurements with mAb's 1, 2, 13, and 17 using a set of 21 different peptide(-construct)s partially confirmed the Domain and Matrix Scan screening results. Only 24- and 33-mer peptides covering both the 1st and 2nd strand of the beta3-loop showed measurable binding. Cyclic beta3-loop peptide mimics were found to bind significantly stronger (Kd approximately 5 microM) than the lineair analogues, in agreement with the fact that the discontinuous epitope is part of a loop structure. Coupling of the lineair beta1-peptide 1oIAIEKEECRFAI21 to the linear beta3-peptide *52TFKELVYETVRVPGCAHHADSLYTYPVATQAH83# via disulfide bond formation showed a 2-3 fold increase in Kd, thus conforming participation of the beta 1-loop in antibody binding for these mAb's.
Amino Acid Sequence↗
Bioactive peptides based on diversity libraries, supramolecular chemistry and rational design: a new class of peptide drugs. Introduction.
A new class of pharmaceutical molecules--synthetic vaccines, synthetic diagnostics and peptide drugs--are emerging based on recent advances of peptide libraries, supramolecular chemistry and rational design. The molecules of this growing class have exciting potential, not met by classical drugs based on small molecules or recombinant proteins.
Combinatorial Chemistry Techniques↗
Heme-protein active site models via self-assembly in water.
[structure: see text] Water-soluble models of heme-protein active sites are obtained via the self-assembly of cationic porphyrins 1 and tetrasulfonato calix[4]arene 2 (K(1.2)() = 10(5) M(-)(1)). Selective binding of ligands either outside or inside the cavity of assemblies 1.2 via coordination to the zinc center has been observed. Small ligands such as 4-methylpyridine and 1-methylimidazole are encapsulated, while the bulkier caffeine is bound outside. Assemblies Co-1.2, in which the Zn porphyrin moiety has been replaced by a Co(II) porphyrin, can act as O(2) carriers.
Binding Sites↗
Complexation of phenolic guests by endo- and exo-hydrogen-bonded receptors.
This article describes the complexation of phenol derivatives by hydrogen-bonded receptors. These phenol receptors are formed by self-assembly of calix[4]arene dimelamine or tetramelamine derivatives with 5,5-diethylbarbiturate (DEB) or cyanurate derivatives (CYA). The double rosette assemblies 3(3).(DEB)6/(CYA)6 have their phenol-binding functionalities (ureido groups) at the top and at the bottom of the double rosette (exo-receptors). The tetrarosette assemblies 4(3).(DEB)12/(CYA)12 form a cavity with binding sites between the two double rosettes for guest encapsulation (endo-receptors). An intrinsic binding constant Ka of 202 M-1 and 286 M-1 for the binding of 4-nitrophenol to the ureido functionalized exo- and endo-receptors, respectively, was observed. For the exo-receptor a 1:6 stoichiometry was observed while for the endo-receptor 1:4 binding stoichiometry was determined by Job plot and MALDI-TOF MS. The important role that the hydroxy group's acidity plays in the complexation of 4-nitrophenol is clarified by binding studies with different phenol derivatives. The hydrogen-bonded receptors showed a much smaller response towards less acidic phenol derivatives.
Barbiturates↗
Self-assembled receptors that stereoselectively recognize a saccharide.
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Carbohydrate Metabolism↗
A novel type of hydrogen-bonded assemblies based on the melamine.cyanuric acid motif.
This paper reports the formation of novel hydrogen-bonded assemblies 1(3).CA obtained upon mixing cyanuric acid (CA) with melamine derivatives 1, in which two of the three possible H-bonding arrays have been blocked. The four components are held together by 9 hydrogen bonds and form a rigid planar structure in which a central CA (three ADA motifs: A = acceptor, D = donor) is hydrogen bonded to three peripheral melamine derivatives (DAD motif). Furthermore, the synthesis and assembly studies are described of hydrogen-bonded assemblies 2-4.CA, comprised of three melamine derivatives that are covalently connected, and CA. The overall thermodynamic stability of assemblies 2-4.CA is superior to 1(3).CA (I(Tm) = 9 vs 3.6). The presence of the 2.CA complex in chloroform was confirmed by (1)H NMR spectroscopy and MALDI-TOF mass spectrometry. Substitution of the trimelamines with chiral or fluorescent groups (R(3)) enabled the study of the assemblies by CD and fluorescence spectroscopy. Titration experiments revealed strongly enhanced stabilities even in the presence of polar solvents, such as THF and CH(3)OH. Depending on the polarity of the solvent, stacking between the planar assembly units was observed.
Journal Article↗
Growth of individual hydrogen-bonded nanostructures on gold monolayers.
The growth of individual nanometer-sized (3.4 +/- 1.4 nm) hydrogen bonded assemblies 1(2) x (DEB)6 on gold monolayers was achieved through an exchange reaction between single isolated calix[4]arene dimelamine 2 (1.1 +/- 0.2 nm) embedded in hexanethiol monolayers and double rosette hydrogen bonded assembly 1(3) x (DEB)6 in solution. The growth process was monitored by tapping mode atomic force microscopy (TM-AFM).
Journal Article↗
Recognition of caffeine in aqueous solutions.
Binding of caffeine in aqueous solutions has been achieved for the first time by using water-soluble, tetracationic peptide-porphyrin conjugates Zn-1 as the receptor molecules. The association constant for caffeine with receptor Zn-1 is in some cases as high as 6000 M(-1), only 5-6 times lower than the highest binding constant reported for an artificial caffeine receptor in low polarity aprotic solvents. The binding mechanism has been studied by a combination of experimental techniques such as UV-visible and NMR spectroscopy and microcalorimetry. Recognition of caffeine involves both stacking with the porphyrin ring and metal coordination. Subtle variations of the receptor structure affect the complexation. Receptors Zn-1 have also been investigated for the recognition of molecules structurally related to caffeine, for example, 1-methylimidazole. Selectivity towards oxopurine derivatives (caffeine and theophylline) have been found.
Caffeine↗
Enantioselective formation of a dynamic hydrogen-bonded assembly based on the chiral memory concept.
In this paper, we report the enantioselective formation of a dynamic noncovalent double rosette assembly 1a(3).(CYA)(6) composed of three 2-pyridylcalix[4]arene dimelamines (1a) and six butylcyanuric acid molecules (BuCYA). The six 2-pyridyl functionalities of the assembly interact stereoselectively with chiral dicarboxylic acids 3a-e via two-point hydrogen-bonding interactions. One of the two enantiomeric assemblies (P- or M-) 1a(3).(CYA)(6) is formed in excess as the result of the complexation of the chiral diacids, resulting in formation of optically active assemblies. The complexations with dibenzoly tartaric acids D-3a and L-3a (3 equivalent), respectively, leading to the formation of diastereomeric assemblies (P)-1a(3).(BuCYA)(6).(D-3a)(3) and (M)-1a(3).(BuCYA)(6).(L-3a)(3) with 90% diastereomeric excess. The diastereomeric excess in (M)-1a(3).(BuCYA)(6).(L-3a)(3) is "memorized" when L-3a is removed by precipitation with ethlylenediamine (EDA). The assembly (M)-1a(3).(BuCYA)(6) is still optically active (90% enantiomeric excess), although none of its individual components are chiral. (M)-1a(3).(BuCYA)(6) has a high kinetic stability toward racemization (E(a) = 119 kJ mol(-)(1), half-life of (M)-1a(3).(BuCYA)(6) is ca. 1 week at 20 degrees C).
Journal Article↗
Kinetic stabilities of double, tetra-, and hexarosette hydrogen-bonded assemblies.
A study of the kinetic stabilities of hydrogen-bonded double, tetra-, and hexarosette assemblies, comprising 36, 72, and 108 hydrogen bonds, respectively, is described. The kinetic stabilities are measured using both chiral amplification and racemization experiments. The chiral amplification studies show that solvent polarity and temperature strongly affect the kinetic stabilities of these hydrogen-bonded assemblies. For example, the activation energy for the dissociation of a tetramelamine from a tetrarosette assembly, a process that involves the breakage of 24 hydrogen bonds, was determined at 98.7 +/- 16.6 kJ mol(-1) in chloroform and 172.8 +/- 11.3 kJ mol(-1) in benzene. Moreover, racemization studies with enantiomerically enriched assemblies reveal a strong dependence of the kinetic stability on the number and strength of the hydrogen bonds involved in assembly formation. The half-lives for double, tetra-, and hexarosette assemblies were found to be 8.4 min, 5.5 h, and 150 h in chloroform at 50 degrees C, respectively. For higher generations of these types of assemblies, the kinetic stabilities become so high that they can no longer measured in a direct manner.
Journal Article↗
Molecular "chaperones" guide the spontaneous formation of a 15-component hydrogen-bonded assembly.
Chaperones are small molecules that assist in the folding of naturally occurring peptides. There are no examples of small molecules acting as chaperones in the self-assembly of synthetic noncovalent assemblies. In this communication we describe an unprecedented example of the "chaperone effect" in the noncovalent synthesis of organic nanostructures. Tetrarosette assemblies 2(3).(BuCYA)(12) form quantitatively in CHCl(3) at room temperature upon mixing tetramelamine 2 with N-butylcyanurate (BuCYA) in the presence of 5,5-diethylbarbituric acid (DEB). Without the DEB units present, only oligomeric assemblies are formed that cannot rearrange to the tetrarosettes by themselves. The DEB units act as molecular "chaperones" by preorganizing the tetramelamine units for the spontaneous assembly of the tetrarosette structure.
Barbiturates↗
Guest encapsulation and self-assembly of molecular capsules in polar solvents via multiple ionic interactions.
Herein we report the formation and characterization of a novel type of capsules resulting from the self-association between oppositely charged complementary building blocks in MeOH/H2O. The assembly is based on the interaction between tetraamidinium calix[4]arenes 1a-d and tetrasulfonato calix[4]arene 2. Evidence for the formation of the expected 1:1 assemblies is provided by proton NMR, ESI-MS, and ITC. The association process is fast on the NMR time scale and strongly entropy driven, with association constants in the range of 10(6) M-1. The system 1a.2 shows binding affinity toward acetylcholine, tetramethylammonium, and N-methylquinuclidinium cations.
Journal Article↗
Diastereoselective noncovalent synthesis of hydrogen-bonded double-rosette assemblies.
Chiral centers present either in the dimelamine components of calix[4]arene 1 or in the cyanurate components CA quantitatively induce one handedness (P or M) in the corresponding hydrogen-bonded assemblies 1(3).(CA)(6) (de>98 %). The high degree of chiral induction results from the presence of six chiral centers in close proximity (C(alpha)) to the core of the assembly. A much lower level of chiral induction is observed for assemblies with chiral centers that are more remote (C(beta)). All diastereomerically pure assemblies 1(3).(CA)(6) exhibit very high CD activities (deltavarepsilon(max) approximately 100 L mol(-1) cm(-1)), in sharp contrast to the low CD activities (deltavarepsilon(max)<or=8 L mol(-1) cm(-1)) shown by the free components. The assemblies display spontaneous resolution under thermodynamically controlled conditions (i.e., heteromeric assemblies containing both peripheral R and S centers are not observed. Remarkable assembly behavior is observed if both components 1 and CA are chiral. In general, formation of well-defined assemblies is only observed when both components contain unidirectional information for the induction of either M or P chirality.
Journal Article↗
Enantioselective noncovalent synthesis of hydrogen-bonded double-rosette assemblies.
The noncovalent synthesis of enantiomerically pure hydrogen-bonded assemblies (M)- and (P)-1(3).(CA)(6) is described. These dynamic assemblies are of one single handedness (M or P), but do not contain any chiral components. They are prepared by using the "chiral memory" concept: the induction of supramolecular chirality is achieved through initial assembly with chiral barbiturates, which are subsequently replaced by achiral cyanurates. This exchange process occurs quantitatively and without loss of the M or P handedness of the assemblies. Racemization studies have been used to determine an activation energy for racemization of 105.9+/-6.4 kJ mol(-1) and a half-life time to racemization of 4.5 days in benzene at 18 degrees C. Kinetic studies have provided strong evidence that the rate-determining step in the racemization process is the dissociation of the first dimelamine component 1 from the assembly 1(3).(CA)(6). In addition to this, it was found that the expelled chiral barbiturate (RBAR or SBAR) acts as a catalyst in the racemization process. Blocking the dissociation process of dimelamines 1 from assembly 1(3).(CA)(6) by covalent capture through a ring-closing metathesis (RCM) reaction produces an increase of more than two orders of magnitude in the half-life time to racemization.
Journal Article↗
Unraveling the nanostructure of supramolecular assemblies of hydrogen-bonded rosettes on graphite: an atomic force microscopy study.
The self-organization of multicomponent tetrarosette assemblies into ordered nanostructures on graphite surfaces has been studied by atomic force microscopy (AFM). Real-space information on the level of individual molecules allowed us to analyze the underlying structure in unprecedented detail. In highly ordered nanorod domains, tetrarosettes 1(3) x (DEB)(12) arrange in the form of parallel rows with a spacing of 4.6 +/- 0.1 nm. High resolution AFM revealed the internal packing of the tetrarosette assemblies in these rows, which can be described by an oblique lattice with a = 2.5 +/- 0.3 nm, b = 5.0 +/- 0.1 nm, and gamma = 122 +/- 3 degrees. The results, together with recent improvements in synthetic approaches, contribute to the development of a general strategy to develop H-bonding-based nanostructures with molecular precision.
Graphite↗
Noncovalent Synthesis Using Hydrogen Bonding.
Hydrogen bonds are like human beings in the sense that they exhibit typical grouplike behavior. As an individual they are feeble, easy to break, and sometimes hard to detect. However, when acting together they become much stronger and lean on each other. This phenomenon, which in scientific terms is called cooperativity, is based on the fact that "1+1 is more than 2". By using this principle, chemists have developed a wide variety of chemically stable structures that are based on the reversible formation of multiple hydrogen bonds. More than 20 years of fundamental studies on these phenomena have gradually developed into a new discipline within the field of organic synthesis, and is nowadays called "noncovalent synthesis". This review describes noncovalent synthesis based on the reversible formation of multiple hydrogen bonds. Starting with a thorough description of what the "hydrogen bond" really is, it guides the reader through a variety of bimolecular and higher order assemblies and exemplifies the general principles that determine their stability. Special focus is given to reversible capsules based on hydrogen-bonding interactions that exhibit interesting encapsulation phenomena. Furthermore, the role of hydrogen-bond formation in self-replicating processes is actively discussed, and finally the review briefly summarizes the development of novel materials (nanotubes, liquid crystals, polymers, etc.) and principles (dynamic libraries) that recently have emanated from this intriguing field of research.
Journal Article↗