Interaction Modes and Absolute Affinities of α‐Amino Acids for Mn2+: A Comprehensive Picture

Manganese is involved as a cofactor in the activation of numerous enzymes as well as the oxygen‐evolving complex of photosystem II. Full understanding of the role played by the Mn²⁺ ion requires detailed knowledge of the interaction modes and energies of manganese with its various environments, a knowledge that is far from complete. To bring detailed insight into the local interactions of Mn in metallopeptides and proteins, theoretical studies employing first‐principles quantum mechanical calculations are carried out on [Mn‐amino acid]²⁺ complexes involving all 20 natural α‐amino acids (AAs). Detailed investigation of [Mn‐serine]²⁺_, [Mn‐cysteine]²⁺, [Mn‐phenylalanine]²⁺, [Mn‐tyrosine]²⁺, and [Mn‐tryptophan]²⁺ indicates that with an electron‐rich side chain, the most stable species involves interaction of Mn²⁺ with carbonyl oxygen, amino nitrogen, and an electron‐rich section of the side chain of the AA in its canonical form. This is in sharp contrast with aliphatic side chains for which a salt bridge is formed. For aromatic AAs, complexation to manganese leads to partial oxidation as well as aromaticity reduction. Despite multisite binding, AAs do not generate strong enough ligand fields to switch the metal to a low‐ or even intermediate‐spin ground state. The affinities of Mn²⁺ for all AAs are reported at the B3LYP and CCSD(T) levels of theory, thereby providing the first complete series of affinities for a divalent metal ion. The trends are compared with those of other cations for which affinities of all AAs have been previously obtained.     

Controllable fabrication of a supramolecular polymer incorporating twisted cucurbit[14]uril and cucurbit[8]uril via self-sorting

A linear supramolecular polymer with controllable features based on twisted cucurbit[14]uril (tQ[14]) and cucurbit[8]uril (Q[8]) was firstly fabricated via an effective self-sorting strategy. Herein we designed a monomer, 1?butyl?1′-(naphthalen- 2-ylmethyl)-4,4′-bipyridinium bromide (BNB), that contains bipyridyl, aliphatic butyl and aromatic naphthyl groups, simultaneously. Two host molecules, tQ[14] and Q[8] were employed to develop an effective strategy for constructing a linear supramolecular polymer with controllable features. The alkyl groups on both sides of BNB could insert into the two cavities of tQ[14], the naphthyl part of BNB via π-π stacking in Q[8] cavity, serving as the driving force for supramolecular polymerization. Through self-sorting of the monomer, tQ[14] and Q[8], led to the formation of the linear supramolecular polymer. Depolymerization could be achieved by addition of adamantane hydrochloride (AH) which driven two BNB guest molecules out of the Q[8] cavity. This self-sorting strategy has great potential, not only for designing supramolecular polymer materials with different controllable structures through introduction of multiple functional groups, but also for broadening the application of twisted cucurbit[14]uril in supramolecular chemistry.     

Quadruplex–Duplex Junction: A High-Affinity Binding Site for Indoloquinoline Ligands

A parallel quadruplex derived from the Myc promoter sequence was extended by a stem-loop duplex at either its 5′- or 3′-terminus to mimic a quadruplex–duplex (Q–D) junction as a potential genomic target. High-resolution structures of the hybrids demonstrate continuous stacking of the duplex on the quadruplex core without significant perturbations. An indoloquinoline ligand carrying an aminoalkyl side chain was shown to bind the Q–D hybrids with a very high affinity in the order K_a≈10⁷ m ⁻¹ irrespective of the duplex location at the quadruplex 3′- or 5′-end. NMR chemical shift perturbations identified the tetrad face of the Q–D junction as specific binding site for the ligand. However, calorimetric analyses revealed significant differences in the thermodynamic profiles upon binding to hybrids with either a duplex extension at the quadruplex 3′- or 5′-terminus. A large enthalpic gain and considerable hydrophobic effects are accompanied by the binding of one ligand to the 3′-Q–D junction, whereas non-hydrophobic entropic contributions favor binding with formation of a 2:1 ligand-quadruplex complex in case of the 5′-Q–D hybrid.     

GC-MS of amino acids as their trimethylsilyl/t-butyldimethylsilyl Derivatives: In model solutions III

Summary Fragmentation patterns of the essential amino acids (AAs) as their silyl derivatives have been obtained with the aid of ion trap detection (ITD). Three derivatizing reagents, hexamethyldisilazane+trifluoroacetic acid (HMDS+TFAA),bis-(trimethylsilyl)trifluoroacetamide (BSTFA) andN-methyl-N-(t-butyldimethylsilyl)trifluoroacetamide (MTBSTFA) were used. Simple and multiple derivatives obtained with each reagent have been investigated, with regard to their sensitivity and selectivity. Our study performed in the concentration range of 5-2000 ng amino acids has shown that, contrary to literature data, thirteen of the twenty-two AAs investigated including the TBDMS derivatives give rise to more than one peak when eluted. As a result of ion/molecule interaction the very informative ions of high masses, ([M]⁺, [M+TMS/(TBDMS)]⁺, [M+1]⁺) are formed with considerable intensities. The fragments [M-CH₃]⁺, [M-C₄H₉]⁺, [M-(CH₃)₂Si]⁺, [M-TMS/(TBDMS)COO]⁺, [M-TBDMSOH]⁺, [M-TBDMSO]⁺, [M-TBDMSNH]⁺ and numerous others could be utilized for identification purposes. Presented at Balaton Symposium on High Performance Separation Methods, Siófok, Hungary, September 1–3, 1999     

Binding behaviors of para-dicyclohexanocucurbit[6]uril and meta-tricyclohexanocucurbit[6]uril with dialkyl viologens

The binding behaviours of para-dicyclohexanocucurbit[6]uril (Cy₂Q[6]) and meta-tricyclohexanocucurbit[6]uril (Cy₃Q[6]) with a series of dialkyl viologens (MV²⁺, EV²⁺, PV²⁺, BV²⁺, FV²⁺ and HV²⁺) have been investigated by various methods. In the aqueous solution, ¹H NMR spectra suggest that the alkyl chains are more favourably encapsulated into the hydrophobic cavities of both hosts than the aromatic rings. Cyclic voltammograms (CV) curves show that the Cy₂Q[6] or Cy₃Q[6] bind the charged viologens more strongly than the reduced viologens. Isothermal titration calorimetry (ITC) data reveal that the binding processes of both hosts with viologens are enthalpic driven. In the solid state, the PV²⁺, BV²⁺ guests and two Cy₃Q[6] hosts generated dumbbell-shaped structures, with two Cy₃Q[6] hosts residing over two terminal alkyl chains of the guests.     

Computational insights into the selectivity mechanism of APP-IP over matrix metalloproteinases

In this work, selectivity mechanism of APP-IP inhibitor (β-amyloid precursor protein-derived inhibitory peptide) over matrix metalloproteinases (MMPs including MMP-2, MMP-7, MMP-9 and MMP-14) was investigated by molecular modeling methods. Among MMPs, MMP-2 is the most favorable one for APP-IP interacting based on our calculations. The predicted binding affinities can give a good explanation of the activity difference of inhibitor APP-IP. In Comparison with MMP-2/APP-IP complex, the side chain of Tyr214^MMP-7 makes the binding pocket so shallow that the whole side chain of Tyr3^APP-IP can not be fully embraced, thus unfavorable for the N-terminal of APP-IP binding to MMP-7. The poor selectivity of APP-IP toward MMP-9 is mainly related with the decrease of interaction between the APP-IP C-terminal and MMP-9 due to the bulky side chains of Pro193 and Gln199, which is in agreement with experiment. The mutations at residues P193A and Q199G of MMP-9 alternate the binding pattern of the C-terminal of APP-IP by forming two new hydrogen bonds and hydrophobic interactions with MMP-9. The mutants favor the binding affinity of MMP-9 largely. For MMP-14/APP-IP, the large steric effect of Phe204^MMP-14 and the weak contributions of the polar residues Asn231^MMP-14 and Thr190^MMP-14 could explain why MMP-14 is non-selective for APP-IP interacting. Here, the molecular modeling methods were successfully employed to explore the selective inhibitor of MMPs, and our work gives valuable information for future rational design of selective peptide inhibitors toward individual MMP.     

Recognition of glycine by cucurbit[5]uril and cucurbit[6]uril: A comparative study of exo- and endo-binding

Recognition features of glycine (Gly) with cucurbit[5]uril (Q[5]) and cucurbit[6]uril (Q[6]) both in aqueous solution and solid state were investigated by ¹H NMR spectroscopy and X-ray crystallography. ¹H NMR data indicate that the Gly is located outside of the portals of the Q[5], exhibiting exo binding with the Q[5]. In the case of the Q[6], the Gly shows endo binding or a dual binding mode (endo and exo binding) with the host, which depends on the amount of the host in the aqueous solution. X-ray crystallography clearly display that the Gly forms 2:1 exclusion complex with the Q[5], and 2:1 inclusion complex with the Q[6]. Interestingly, hydrogen bondings between the encapsulated Gly molecules in the Q[6] were observed.     

Beiträge zur Chemie des Phosphors. 142. P6(t-Bu)5H – das erste Cyclotetraphosphan mit P2-Seitenkette

Contributions to the Chemistry of Phosphorus. 142. P₆(t-Bu)₅H – the First Cyclotetraphosphane with a P₂ Side Chain The thermolysis of 1, 2-di-tert-butyldiphosphane, H(t-Bu)P? P(t-Bu)H, leads to formation of the hitherto unknown hexaphosphane P₆(t-Bu)₅H ( 1 ). In the first instance the iso-P₅H₅ derivative P₅(t-Bu)₄H [3] is formed, which reacts further with H₂(t-BuP)₂ or H₂(t-BuP)₃ yielding 1 . Compound 1 has been isolated in the pure state and structurally characterized as 1-(1,2-di-tert-butyldiphosphino)-2, 3, 4-tri-tert-butyl-cyclotetraphosphane, i. e. as a four-membered ring compound with a P₂ side chain. Due to the chirality of the P atoms in the side chain, 1 exists as a mixture of two configurational isomers, the threo-and the erythro-form.     

Iron-mediated and -catalyzed metalative cyclization of electron-withdrawing-group-substituted alkynes and alkenes with Grignard reagents

Treatment of ethyl (E)‐5,5‐bis[(benzyloxy)methyl]‐8‐(N,N‐diethylcarbamoyl)‐2‐octen‐7‐ynoate with an iron reagent generated from FeCl₂ and tBuMgCl in a ratio of 1:4 (abbreviated as FeCl₂/4 tBuMgCl) afforded ethyl [4,4‐bis[(benzyloxy)methyl]‐2‐[(E)‐(N,N‐diethylcarbamoyl)methylene]cyclopent‐1‐yl]acetate in good yield. Deuteriolysis of an identical reaction mixture afforded the bis‐deuterated product ethyl [4,4‐bis[(benzyloxy)methyl]‐2‐[(E)‐(N,N‐diethylcarbamoyl)deuteriomethylene]cyclopent‐1‐yl]deuterioacetate, thus confirming the existence of the corresponding dimetalated intermediate. The latter intermediate can react with halogens or aldehydes to facilitate further synthetic transformations. The amount of FeCl₂ was reduced to catalytic levels (10 mol % relative to enyne), and catalytic cyclizations of this sort proceeded with yields comparable to those of the aforementioned stoichiometric reactions. The cyclization of diethyl (E,E)‐2,7‐nonadienedioate with a stoichiometric amount of FeCl₂/4 tBuMgCl, followed by the addition of sBuOH as a proton source, afforded a mixture of 2‐(ethoxycarbonyl)‐3‐bicyclo[3.3.0]octanone and its enol form in good yield. The use of aldehyde or ketone in place of sBuOH afforded 2‐(ethoxycarbonyl)‐3‐bicyclo[3.3.0]octanone, which has an additional hydroxyalkyl side chain. Additionally, the metalation of a carbon–carbon unsaturated bond in N,N‐diethyl‐5,5‐bis[(benzyloxy)methyl]‐7,8‐epoxy‐2‐octynamide or (E)‐3,3‐dimethyl‐6‐(N,N‐diethylcarbamoyl)‐5‐hexenyl p‐toluenesulfonate with FeCl₂/4 tBuMgCl or FeCl₂/4 PhMgBr was followed by an intramolecular alkylation with an epoxide or alkyl p‐toluenesulfonate to afford 5,5‐bis[(benzyloxy)methyl]‐3‐[(E)‐(N,N‐diethylcarbamoyl)methylene]‐1‐cyclohexanol or N,N‐diethyl(3,3‐dimethylcyclopentyl)acetamide after hydrolysis. In both cases, the remaining metalated portion α to the amide group was confirmed by deuteriolysis and could be utilized for an alkylation with methyl iodide.     

Interaction of Cucurbit[n = 6∼8]urils and Benzimidazole Derivatives

The structures and optical properties of host–guest complexes produced from cucurbit[n = 6–8]urils and some benzimidazole derivatives have been investigated by ¹H NMR spectroscopy, electronic absorption spectroscopy and fluorescence spectroscopy. The experimental results reveal that calculations of A∼N_Q[n]/N_guest and I_f∼N_Q[n]/N_guest for the same association complex both support a good fit to an identical binding model. In particular, the A∼N_Q[n]/N_guest, I_f∼N_Q[n]/N_guest calculations and the ¹H NMR determinations for three Q[6]–ge(1∼3) complexes and three Q[8]–ge(1∼3) complexes all support a binding model of 1:1 and 1:2 respectively.     

Voltammetric studies of the interaction of 6-mercaptopurine with cucurbit[7]uril and DNA

The interaction of 6-mercaptopurine (6-MP), an antitumor drug, with cucurbit[7]uril (Q[7]) and DNA in an acetate buffer solution was studied by differential pulse voltammetry (DPV) and cyclic voltammetry(CV). The electrochemical data indicated a 1:1 complex formation of 6-MP with Q[7] and DNA. The formation constants of these complexes were determined based on the variations in the current. Moreover, the interactions of the 6-MP-Q[7] inclusion complex with DNA have been investigated by means of voltammetry. The results suggested that 6-MP displayed a high affinity for Q[7] and that the inclusion complex did not decompose when it bound to DNA. It can be inferred from the experimental data that the binding model of 6-MP to DNA may be ??electrostatic binding??. In addition, the formation of inclusion complexes between Q[7] and 6-MP was confirmed by UV-Vis spectroscopy and the ¹H NMR technique.     

Modular Medical Imaging Agents Based on Azide–Alkyne Huisgen Cycloadditions: Synthesis and Pre-Clinical Evaluation of 18F-Labeled PSMA-Tracers for Prostate Cancer Imaging

Since the seminal contribution of Rolf Huisgen to develop the [3+2] cycloaddition of 1,3-dipolar compounds, its azide–alkyne variant has established itself as the key step in numerous organic syntheses and bioorthogonal processes in materials science and chemical biology. In the present study, the copper(I)-catalyzed azide–alkyne cycloaddition was applied for the development of a modular molecular platform for medical imaging of the prostate-specific membrane antigen (PSMA), using positron emission tomography. This process is shown from molecular design, through synthesis automation and in vitro studies, all the way to pre-clinical in vivo evaluation of fluorine-18- labeled PSMA-targeting ‘F-PSMA-MIC’ radiotracers (t_1/2=109.7 min). Pre-clinical data indicate that the modular PSMA-scaffold has similar binding affinity and imaging properties to the clinically used [⁶⁸Ga]PSMA-11. Furthermore, we demonstrated that targeting the arene-binding in PSMA, facilitated through the [3+2]cycloaddition, can improve binding affinity, which was rationalized by molecular modeling. The here presented PSMA-binding scaffold potentially facilitates easy coupling to other medical imaging moieties, enabling future developments of new modular imaging agents.     

Proxiphomine and protophomine, two new cytochalasans

Two new cytochalasans, proxiphomin and protophomin have been isolated from cultures of a Phoma species (strain S 298). They are shown to possess the same skeleton as deoxaphomin ( 4 ), which has been isolated recently. Thus they represent lower states of oxidation of 4 . On the basis of the spectral data, the structures 16-methyl-10-phenyl-[13]cytochalasa-6 (7), 13^t,21^t-triene-1,23-dione ( 1 ) and 16-methyl-10-phenyl-[13]cytochalasa-5 (6)13^t,21^t-triene-1,7,23-trione ( 2 ) are proposed for proxiphomin and protophomin respectively. On treatment with perchloric acid, substance 1 is isomerized to give 16-methyl-10-phenyl-10-pheny-10-phenyl-[13]cytochalasa-5(6)13^t,21^t-triene-1,23-dione ( 3 ). The assumption that the [13]cytochalasans are potential biogenetic precursors of the 24-oxa-[14]catochalasans is discussed.     

A hemicyanine and cucurbit[n]uril inclusion complex: competitive guest binding of cucurbit[7]uril and cucurbit[8]uril

The interaction between the hemicyanine indole derivative H and the cucubit[n]urils Q[7] and Q[8] has been studied using ¹H NMR and UV spectroscopy as well as by fluorescence experiments. Competitive studies on the inclusion of H by Q[7] and Q[8] have also been conducted, and reveal that on changing the size of the Q[n] cavity, the binding behaviour can be very different.     

Tricks of Light on Helices: Transformation of Helical Polymers by Photoirradiation

The following polymer structural transitions were achieved using light: preferred‐handed helix formation for poly(9,9‐di‐n‐octylfluoren‐2,7‐diyl), helix racemization (helix–helix transition) for poly(2,7‐bis(4‐t‐butylphenyl)fluoren‐9‐yl acrylate) and poly(2,5‐bis[4‐((S)‐2‐methylbutyloxy)phenyl]styrene), and helix decomposition for poly(2,7‐bis(4‐t‐butylphenyl)‐9‐methylfluoren‐9‐yl acrylate) and poly(2,7‐bis(4‐t‐butylphenyl)fluoren‐9‐ylmethyl methacrylate). Although these types of transitions and chemical transformations have been studied mainly using heat or chemicals as stimuli, light can also cause these structural alterations. In the helix construction and the helix–helix transition, a key transition is a twist‐coplanar conformational change of a biphenyl or an aryl–aryl unit in the side chain or the main chain of the polymer. Furthermore, the helix–helix transition was caused only by light and not by heat. The examples discussed in this review are expected to trigger off a new direction in synthesis and reaction of chiral polymers.     

Synthesis of 2‐amino‐4‐oxo‐5‐substitutedbenzylthiopyrrolo[2,3‐d]‐pyrimidines as potential inhibitors of thymidylate synthase

A series of ten novel 2‐amino‐4‐oxo‐5‐[(substitutedbenzyl)thio]pyrrolo[2,3‐d]pyrimidines 2‐11 were synthesized as potential inhibitors of thymidylate synthase and as antitumor agents. The analogues contain various electron withdrawing and electron donating substituents on the benzylsulfanyl ring of the side chains and were synthesized from the key intermediate 2‐amino‐4‐oxo‐6‐methylpyrrolo[2,3‐d]pyrimidine, 14 . Appropriately substituted benzyl mercaptans were appended to the 5‐position of 14 via an oxidative addition reaction using iodine, ethanol and water. The compounds were evaluated against human, Escherichia coli and Toxoplasma gondii thymidylate synthase and against human, Escherichia coli and Toxoplasma gondii dihydrofolate reductase. The most potent inhibitor, ( 6 ) which has a 4′‐methoxy substituent on the side chain, has an IC₅₀=25 μM against human thymidylate synthase. Contrary to analogues of general structure 1 , electron donating or electron withdrawing substituents on the side chain of 2‐11 had little or no influence on the human thymidylate synthase inhibitory activity.     

Synthesis of 3β-Hydroxy[21-14C]-5β-pregn-8(14)-en-20-one from Chenodeoxycholic Acid

3β-Hydroxy[21-¹⁴C]5β-pregn-8(14)-en-20-one ( 17 ) was prepared from chenodeoxycholic acid ( 1a ). The synthetic sequence involved: (i) degradation of the bile-acid side chain to an etianic acid; (ii) formation of the 8(14)-double bond; (iii) inversion of the configuration at C(3); (iv) construction of the acetyl side chain at C(17) with the required isotopic label at C(21). Structures of all described products were confirmed by chemical and spectroscopic (IR, ¹H-NMR, ¹³C-NMR, MS) methods.     

The Binding of Flavins by Apoflavodoxins from Peptostreptococcus elsdenii and Azotobacter vinelandii as Studied by Temperature-Jump Technique

The binding of various flavins by apoflavodoxins from P. elsdenii and A. vinelandii has been studied by the temperature-jump technique using fluorescence detection. P. elsdenii apoflavodoxin interacts only with flavins possessing 5 carbon atoms in the N(10) side chain and a terminal phosphate group. Employing a wide range of concentrations of deoxy-FMN

1 Flavin = 3,4-dimethyl-lO-substituted isoalloxazine = 3,4-dimethyl- lO-substituted-2,3,4,10-tetrahydro-benzo[g]-pteridine-2,4-dione; FMN = riboflavin-5′-monophosphate.

and apoflavodoxin only one relaxation process was observed, indicating a one-step binding mechanism. With native flavodoxin no relaxation could be observed. The kinetic parameters of the interaction of A. vinelandii apoflavodoxin with various flavin analogs (Structure I ) have also been investigated. The interaction between apoflavodoxin and flavin derivatives carrying an ionizable, terminal functional group on the side chain becomes very weak when the number of the side chain carbon atoms is decreased below 4. This observation is interpreted in terms of repulsive forces due to negatively charged amino acid residues located in the flavin side chain binding region of the apoflavodoxin. All complexes studied revealed only one relaxation process. This observation is in contradiction with published results [10]. The published traces are instrumental artifacts.     

Desoxaphomin,das erste [13]Cytochalasan,ein möglicher biogenetischer Vorläufer der 24-Oxa-[14]cytochalasane

From cultures of a Phoma species (strain S 298) the hitherto unknown metabolite deoxaphomine has been isolated. On the basis of the spectral data, structure 1 of the (7S, 16R, 20R)-7,20-dihydroxy-16-methyl-10-phenyl-[13]cytochalasa-6(12),13^t,21^t-triene-1,23-dione is assigned to deoxaphomine. This structure is confirmed by the chemical degradation of 1 , yielding the products 4 and 6 which are identical with derivatives of phomine ( 2 )((7S,16R,20R)-7,20-dihydroxy-16-methyl-10-phenyl-24-oxa-[14]cytochalasa-6(12), 13^t,21^t-triene-1,23-dione) and cytohalasin D ( 8 ) ((7S,16S,18R,21R)-21-acetoxy-7,18-dihydroxy-16,18-dimethyl-10-phenyl-[11]sytochalasa-6(12),13^t,19^t-triene-1,17-dione). Deoxaphomine ( 1 ) is a potential biogenetic precursor of the 24-oxa-[14]cytochalasans. Preliminary results of the biological activity of deoxaphomine are reported.     

Design,synthesis and biological evaluation of 2,4‐diamino‐6‐methyl‐5‐substitutedpyrrolo[2,3‐d]pyrimidines as dihydrofolate reductase inhibitors

Nine novel nonclassical 2,4‐diamino‐6‐methyl‐5‐mioarylsubstituted‐ 7H ‐pyrrolo[2,3‐d]pyrimidines 2‐10 were synthesized as potential inhibitors of dihydrofolate reductase and as antitumor agents. The analogues contain various electron donating and electron withdrawing substituents on the phenylsulfanyl ring of the side chains and were synthesized from the key intermediate 2,6‐diamino‐6‐methyl‐7H‐pyrrolo[2,3‐d]‐pyrimidine, 14 . Compound 14 , was in turn obtained by chlorination of 4‐position of 2‐amino‐6‐methylpyrrolo[2,3‐d]pyrimidin‐4(3H)‐one, 16 followed by displacement with ammonia. Appropriately substituted phenyl thiols were appended to the 5‐position of 14 via an oxidative addition reaction using iodine, ethanol and water. The compounds were evaluated against rat liver, rat‐derived Pneumocystis, Mycobacterium avium and Toxoplasma gondii dihydrofolate reductase. The most potent and selective inhibitor, (2) has a 1‐naphthyl side chain. In this series of compounds electron‐withdrawing and bulky substituents in the side chain afford marginally active dihydrofolate reductase inhibitors. The single atom sulfur bridge in the side chain of these compounds is not conducive to potent dihydrofolate reductase inhibition.