Amino Keto Research Articles

General Designs Reveal Distinct Codes in Protein-Coding and Non-Coding Human DNA.

This study seeks to investigate distinct signatures and codes within different genomic sequence locations of the human genome. The promoter and other non-coding regions contain sites for the binding of biological particles, for processes such as transcription regulation. The specific rules and sequence codes that govern this remain poorly understood. To derive these (codes), the general designs of sequence are investigated. Genomic signatures are a powerful tool for assessing the general designs of sequence, and cross-comparing different genomic regions for their distinct sequence properties. Through these genomic signatures, the relative non-random properties of sequences are also assessed. Furthermore, a binary components analysis is carried out making use of information theory ideas, to study the RY (purine/pyrimidine), WS (weak/strong) and KM (keto/amino) signatures in the sequences. From this comparison, it is possible to identify the relative importance of these properties within the various protein-coding and non-coding genomic locations. The results show that coding DNA has a strongly non-random WS signature, which reflects the genetic code, and the hydrogen-bond base pairing of codon-anti-codon interactions. In contrast, non-coding locations, such as the promoter, contain a distinct genomic signature. A prominent feature throughout non-coding DNA is a highly non-random RY signature, which is very different in nature to coding DNA, and suggests a structural-based RY code. This marks progress towards deciphering the unknown code(s) in non-protein-coding DNA, and a further understanding of the coding DNA. Additionally, it unravels how DNA carries information. These findings have implications for the most fundamental principles of biology, including knowledge of gene regulation, development and disease.

Alteration of Inflammation Marker Levels with Alfa Keto Analogs in Diabetic Rats

Diabetes mellitus is the most well-known and common cause of end-stage renal disease. Excessive inflammatory processes were hypothesized to be one of the reasons for progression to end-stage disease. Even though progression to end stage disease tried to be prevented with some dietary measures such as lowering nitrogen in diet, none of the methods tried were successful enough. In our study, we aimed to determine the effects of alfa keto analog use in altering levels of inflammatory markers when added to dietary program in a diabetic rat model. The study was performed on 22 male Sprague Dawley rats with streptozocine induced diabetic nephropathy. Both groups were fed with low protein diet except for study group with added alfa keto analogs. Biochemical values and inflammatory markers were studied with ELISA assay. Significant difference in serum albumin was found between study group and control group following administration of alfa keto analogs (p <.001). Also mentioned dietary modification made a significant difference in suppression of inflammatory reactions for interleukin (IL)-1, IL-6, IL-10, IL-18 and tumor necrosis factor-α. Adding keto amino acids to diets that are already low on protein, can slow progression to end-stage renal disease by reducing inflammation and protein loss in an animal model.

General Designs Reveal a Purine-Pyrimidine Structural Code in Human DNA

The human genome carries a vast amount of information within its DNA sequences. The chemical bases A, T, C, and G are the basic units of information content, that are arranged into patterns and codes. Expansive areas of the genome contain codes that are not yet well understood. To decipher these, mathematical and computational tools are applied here to study genomic signatures or general designs of sequences. A novel binary components analysis is devised and utilized. This seeks to isolate the physical and chemical properties of DNA bases, which reveals sequence design and function. Here, information theory tools break down the information content within DNA bases, in order to study them in isolation for their genomic signatures and non-random properties. In this way, the RY (purine/pyrimidine), WS (weak/strong), and KM (keto/amino) general designs are observed in the sequences. The results show that RY, KM, and WS components have a similar and stable overall profile across all human chromosomes. It reveals that the RY property of a sequence is most distant from randomness in the human genome with respect to the genomic signatures. This is true across all human chromosomes. It is concluded that there exists a widespread potential RY code, and furthermore, that this is likely a structural code. Ascertaining this feature of general design, and potential RY structural code has far-reaching implications. This is because it aids in the understanding of cell biology, growth, and development, as well as downstream in the study of human disease and potential drug design.

Guanine Tautomerism in Ionic Complexes with Ag+ Investigated by IRMPD Spectroscopy and Mass Spectrometry.

In this paper, we present the IRMPD spectra of three ionic complexes between guanine (G) and silver (Ag+): [GAg-H2O]+, [GAgG]+ produced in the electrospray ionization source of the mass spectrometer, and [GAg]+ produced by collision induced dissociation of the [GAgG]+ complex. On the basis of the comparison of theoretically calculated IR spectra, we show that there are two isomers of each complex containing two different keto-amino (KA) tautomers of G (GKA(1,9) and GKA(1,7)). The observed isomers are the most stable structures in aqueous solution, and their experimentally estimated relative populations are in better agreement with the calculated relative populations in solution than in the gas phase, both at 298 K. We concluded that these observations suggest that GKA(1,9) and GKA(1,7) coexist in solution according to previous theoretical reports (Colominas, C.; et al. J. Am. Chem. Soc. 1996, 118, 6811). We were unable to find any evidence of the presence of the GEA(9), GKA(3,7), GKA(3,9), or GKA(7,9), whose relative stabilities in solution are strongly dependent on the theoretical method used to account for the solvent effect (Hanus, M.; et al. J. Am. Chem. Soc. 2003, 125, 7678).

Exploratory-Data and Statistical Analyses of AB070597, an Amino Acid/Peptide Complex, on Blood-Serum Creatinine Concentration and Estimated Glomerular Filtration Rate: A Non-Randomized Pilot Trial of Five Humans with Declining Renal Function

ABSTRACT&#x0D; Background:&#x0D; Chronic kidney disease (CKD) develops from persistent, irremediable loss of renal function (RF). Animal studies show that dietary supplement, AB070597, an amino acid/ peptide complex, can stabilize, and in some instances, reverse CKD. Previous human CKD studies demonstrate that dietary treatment with specific keto acids and amino acids can lower blood-serum creatinine concentration (SCr) and increase glomerular filtration rate (GFR). This pilot trial was performed to determine whether a future randomized controlled human clinical trial of AB070597’s effect on CKD was justified.&#x0D; Methods: &#x0D; The trial was structured as a consecutive case series to evaluate whether oral treatment with AB070597 could slow CKD progression, as gaged by SCr, and estimated glomerular filtration rate (eGFR). Eligibility requirements: Non-diabetic white males under current medical care in the United States, diagnosed with CKD, or with histories of increasing SCr and declining eGFR, resulting from CKD or natural consequence of aging. Exclusion criteria: Concurrent or suspected comorbidities unrelated to CKD. Participants ingested 6-g bi-daily doses of AB070597 for periods up to 24 months. SCr was measured and eGFR calculated at approximate tri-monthly intervals. &#x0D; Results:&#x0D; Results were presented as individual-participant and group SCr and eGFR vectors, and initial-data-analysis diagrams.&#x0D; Treatment reversed SCr slopes from positive to negative, and eGFR slopes from negative to positive. When individual participant’s median monthly eGFR rate-of-change (positive) was compared with the median monthly eGFR rate-of-change (negative) in a sample of 2870 humans with CKD, differences were significant in favor of the AB070597 treatment group in 4 of 5 participants: (P = 0.0625, 95% CI: 0.368-8.368), (P = 0.0313, 95% CI: 0.368-1.038), (P = 0.0039, 95% CI: 0.368-0.698), (P = 0.0010, 95% CI: 0.118-2.868),&#x0D; (P &lt;0.0001, 95% CI: 0.368-10.370).&#x0D; Conclusion:&#x0D; Oral AB070597 treatment produced an apparently favorable change in CKD trajectory in 4 humans and in 1 with naturally age-related declining RF. The magnitude and direction of change hint that treatment may have had a beneficial effect on CKD progression and age-related RF. In and of themselves, this pilot trial’s results seem to favor CKD treatment with AB070597, but because there was no randomization, no control group, and a small sample size , it is not possible to extend results beyond its bounds. They do, however, support the rationale for a future randomized controlled trial

Excited-State Dynamics of Thienoguanosine, an Isomorphic Highly Fluorescent Analogue of Guanosine.

Thienoguanosine (th G) is an isomorphic analogue of guanosine with promising potentialities as fluorescent DNA label. As a free probe in protic solvents, th G exists in two tautomeric forms, identified as the H1, being the only one observed in nonprotic solvents, and H3 keto-amino tautomers. We herein investigate the photophysics of th G in solvents of different polarity, from water to dioxane, by combining time-resolved fluorescence with PCM/TD-DFT and CASSCF calculations. Fluorescence lifetimes of 14.5-20.5 and 7-13 ns were observed for the H1 and H3 tautomers, respectively, in the tested solvents. In methanol and ethanol, an additional fluorescent decay lifetime (≈3 ns) at the blue emission side (λ≈430 nm) as well as a 0.5 ns component with negative amplitude at the red edge of the spectrum, typical of an excited-state reaction, were observed. Our computational analysis explains the solvent effects observed on the tautomeric equilibrium. The main radiative and nonradiative deactivation routes have been mapped by PCM/TD-DFT calculations in solution and CASSCF in the gas phase. The most easily accessible conical intersection, involving an out-of plane motion of the sulfur atom in the five-membered ring of th G, is separated by a sizeable energy barrier (≥0.4 eV) from the minimum of the spectroscopic state, which explains the large experimental fluorescence quantum yield.

On the thermodynamics of triazines. A DFT and topological study

Tautomerism is the relation between isomeric organic compounds, which readily interconvert, usually by relocation of a proton. It plays an important role in the biological activity of compounds. In the series of tautomeric triazines (monoxime and dioxime derivatives) energy computations have been performed. The results have shown that for the monoxime, the amino keto tautomer is favored by 10.9 kJ/mol vs. the enol form; for the dioxime tautomer, the imino keto form is 17.6 kJ/mol lower in energy in comparison with the most stable amino keto tautomer. Topological aspects have been considered. Computations have been done at DFT M06-2X/6-311G(d,p) level of theory.

Stable Europium(III) Complexes with Short Linkers for Site-Specific Labeling of Biomolecules.

In this study, two new terpyridine‐based EuIII complexes were synthesized, the structures of which were optimized for luminescence resonance energy‐transfer (LRET) experiments. The complexes showed high quantum yields (32 %); a single long lifetime (1.25 ms), which was not influenced by coupling to protein; very high stability in the presence of chelators such as ethylenediamine‐N,N,N′,N′‐tetraacetate and ethylene glycol‐bis(2‐aminoethylether)‐N,N,N′,N′‐tetraacetic acid; and no interaction with cofactors such as adenosine triphosphate and guanosine triphosphate. A special feature is the short length of the linker between the EuIII ion and the maleimide or hydrazide function, which allows for site‐specific coupling of cysteine mutants or unnatural keto amino acids. As a consequence, the new complexes appear particularly suited for accurate distance measurements in biomolecules by LRET.

Thermodynamic investigation of tautomerism in triazine oximes

The geometric and energetic preference of the possible isomers of four tautomeric triazine derivatives has been investigated by density functional theory and topological calculations and their thermodynamic stability was assessed. For the monoxime series the amino keto tautomer is favored by 2.6 kcal/mol (10.9 kJ/mol) as compared to the enol form, while the lowest energy imino isomer is 4.1 kcal/mol (17.1 kJ/mol) higher in energy. However, for the dioxime tautomer series the imino keto tautomer is 4.2 kcal/mol (17.6 kJ/mol) lower in energy as compared to the most stable amino keto tautomer. The computed excitation energies for the first electron transitions agree with the experimental observations.

Raman spectroscopy and quantum-mechanical analysis of tautomeric forms in cytosine and 5-methylcytosine on gold surfaces

Spectral differences between cytosine (Cyt) and 5-methylcytosine (5MC) were investigated by means of Raman spectroscopy with a combination of density functional theory (DFT) calculations. Surface-enhanced Raman scattering (SERS) revealed discriminating peaks of 5MC from those of Cyt upon adsorption on gold nanoparticles (AuNPs). Among the notable features, the multiple bands between 850 and 700cm−1 for the ring-breathing modes of 5MC and Cyt could be correlated well with the simulated spectra based on the DFT calculations of the adsorbates on the gold cluster atoms. The relative energetic stabilities of the enol/keto and the amino/imino tautomeric forms of Cyt and 5MC have been estimated using DFT calculations, before and after binding six atom gold clusters. Among the six tautomeric forms, the 7H keto amino and the 4H imino trans forms are expected to be predominant in binding gold atoms, whereas the enol trans/cis conformers would coexist in the free gas phase. Our approach may provide useful theoretical guidelines for identifying 5MC from Cyt by analyzing Raman spectra on gold surfaces on the basis of quantum-mechanical calculations.

Optimisation of a system for the co-translational incorporation of a keto amino acid and its application to a tumour-specific Anticalin

The bioorthogonal keto group has attracted interest for the site-specific chemical conjugation of recombinant proteins under mild conditions, e.g. with aminooxy-functionalised fluorescent probes, radiometal chelates, toxins or polymers. However, the cotranslational incorporation of the corresponding non-canonical amino acid p-acetyl-L-phenylalanine (Apa) into proteins expressed in Escherichia coli by means of amber suppression using a previously described system with a mutated tRNA and an engineered tyrosyl-tRNA synthetase from Methanococcus jannaschii shows limited efficiency and considerable promiscuity towards endogenous amino acids. Employing a one-plasmid system that encodes all three components required for selection, i.e. the modified aminoacyl-tRNA synthetase (aaRS), the cognate amber suppressor tRNA and the enhanced green fluorescent protein equipped with an amber stop codon and serving as reporter, we have generated an Apa-specific aaRS&tRNA pair with considerably improved efficiency (17-fold increased expression) and also fidelity (6-fold). To this end, both the aaRS and the tRNA were subjected to doped random mutagenesis and selection in altogether four evolutionary cycles using fluorescence-activated bacterial cell sorting as well as automated screening of microcultures. The resulting aaRS&tRNA pair was applied to the functionalisation of an Anticalin with specificity towards oncofetal fibronectin by introducing a keto group at a permissible site for subsequent conjugation with a fluorescent dye, thus allowing visualisation of this tumour target under the microscope.

Crystal structure of disodium 2-amino-6-oxo-6,7-di-hydro-1H-purine-1,7-diide hepta-hydrate.

In the title compound, disodium 2-amino-6-oxo-6,7-di-hydro-1H-purine-1,7-diide hepta-hydrate, 2Na(+)·C5H3N5O(2-)·7H2O, the structure is composed of alternating (100) layers of guanine mol-ecules and hydrated Na(+) ions. Within the guanine layer, the mol-ecules are arranged in centrosymmetric pairs, with a partial overlap between the guanine rings. In this compound, guanine exists as the amino-keto tautomer from which deprotonation from N1 and N7 has occurred (purine numbering). There are no direct inter-actions between the Na(+) cations and the guanine anions. Guanine mol-ecules are linked to neighboring water mol-ecules by O-H⋯N and O-H⋯O hydrogen bonds into a network structure.

On the Ag(+)-cytosine interaction: the effect of microhydration probed by IR optical spectroscopy and density functional theory.

The gas-phase structures of cytosine-Ag(+) [CAg](+) and cytosine-Ag(+)-H2O [CAg-H2O](+) complexes have been studied by mass-selected infrared multiphoton dissociation (IRMPD) spectroscopy in the 900-1800 cm(-1) spectral region using the Free Electron Laser facility in Orsay (CLIO). The IRMPD experimental spectra have been compared with the calculated IR absorption spectra of the different low-lying isomers (computed at the DFT level using the B3LYP functional and the 6-311G++(d,p) basis set for C, H, N and O atoms and the Stuttgart effective core potential for Ag). For the [CAg](+) complex, only one isomer with cytosine in the keto-amino (KA) tautomeric form and Ag(+) interacting simultaneously with the C(2)[double bond, length as m-dash]O(7) group and N(3) of cytosine was observed. However, the mono-hydration of the complex in the gas phase leads to the stabilization of a two quasi-isoenergetic structure of the [CAg-H2O](+) complex, in which Ag(+) interacts with the O atom of the water molecule and with the N(3) or C(2)[double bond, length as m-dash]O(7) group of cytosine. The relative populations of the two isomers determined from the IRMPD kinetics plot are in good agreement with the calculated values. Comparison of these results with those of protonated cytosine [CH](+) and its mono-hydrated complex [CH-H2O](+) shows some interesting differences between H(+) and Ag(+). In particular, while a single water molecule catalyzes the isomerization reaction in the case of [CH-H2O](+), it is found that in the case of [CAg-H2O](+) the addition of water leads to the stabilization of two isomers separated by small energy barrier (0.05 eV).

Excited-State Structure and Dynamics of Keto–Amino Cytosine: The 1ππ* State Is Nonplanar and Its Radiationless Decay Is Not Ultrafast

We have measured the mass- and tautomer-specific S0 → S1 vibronic spectra and S1 state lifetimes of the keto–amino tautomer of cytosine cooled in supersonic jets, using two-color resonant two-photon ionization (R2PI) spectroscopy at 0.05 cm(–1) resolution. The rotational contours of the 0(0)(0) band and nine vibronic bands up to +437 cm(–1) are polarized in the pyrimidinone plane, proving that the electronic excitation is to a 1ππ* state. All vibronic excitations up to +437 cm(–1) are overtone and combination bands of the low-frequency out-of-plane ν1′ (butterfly), ν2′ (boat), and ν3′ (H–N–C6–H twist) vibrations. UV vibronic spectrum simulations based on approximate second-order coupled-cluster (CC2) calculations of the ground and 1ππ* states are in good agreement with the experimental R2PI spectrum, but only if the calculated ν1′ and ν2′ frequencies are reduced by a factor of 4 and anharmonicity is included. Together with the high intensity of the ν1′ and ν2′ overtone vibronic excitations, this implies that the 1ππ* potential energy surface is much softer and much more anharmonic in the out-of-plane directions than predicted by the CC2 method. The 1ππ* state lifetime is determined from the Lorentzian line broadening necessary to reproduce the rotational band contours: at the 0(0)(0) band it is τ = 44 ps, remains at τ = 35–45 ps up to +205 cm(–1), and decreases to 25–30 ps up to +437 cm(–1). These lifetimes are 20–40 times longer than the 0.5–1.5 ps lifetimes previously measured with femtosecond pump–probe techniques at higher vibrational energies (1500–3800 cm(–1)). Thus, the nonradiative relaxation rate of keto–amino cytosine close to the 1ππ* state minimum is k(nr) 2.5 × 10(10) s(–1), much smaller than at higher energies. An additional nonradiative decay channel opens at +500 cm(–1) excess energy. Since high overtone bands of ν1′ and ν2′ are observed in the R2PI spectrum but only a single weak 2ν3′ band, we propose that ν3′ is a promoting mode for nonradiative decay, consistent with the observation that the ν3′ normal-mode eigenvector points toward the “C6-puckered” conical intersection geometry.

Effect of keto amino acids on asymmetric dimethyl arginine, muscle and fat tissue in chronic kidney disease

Levels of endogenous nitric oxide synthase inhibitor asymmetric dimethylarginine (ADMA) are elevated in chronic kidney disease (CKD) and may contribute to vascular complications. In this study we tested the hypothesis that elevated ADMA can be reduced in CKD patients by long-term administration of low-protein diet (LPD) supplemented with keto amino acids (KA). In a long-term prospective double blind placebo controlled randomized trial, we evaluated a total of 120 CKD patients (62/58F) aged 22-76 yrs with creatinine clearance 22-40mL/min/1.73m 2 for a period of 36 months. All patients were on low-protein diet containing 0.6 protein/kg/IBW/day and 120-125/kJ/kg/IBW/day. LPD was randomly supplemented with KA at dosage of 100 mg/kg/IBW/day (61 patients, Group I) while 59 patients (Group II) received placebo. During the study period, glomerular filtration rate (GFR) slightly decreased (C cr from 34.2±11.6 to 29.9±9.2 mL/min and 33.5±11.6 to 22.2±10.4 mL/min in Group I and II, respectively); this however was more marked in Group II (p<0.01). Fat in muscle measured by MR spectroscopy (MRS, m.tibialis anterior) significantly decreased in Group I and was linked to reduced volume of visceral fat measured by MRI (p<0.01). Reduction of fat in Group II was not significant. In Group I, there was a significant decrease in the plasma level of ADMA (from 2.4±0.4 to 1.2±0.3 μmol/L, p<0.01), but ADMA remained unchanged in Group II. A further remarkable finding was reduction in the plasma concentration of pentosidine (from 486±168 to 325±127 μg/L, p<0.01) and decrease of proteinuria (from 3.7±2.20 to 1.6±1.2 g/24hrs, p<0.01) in Group I. Plasma adiponectin (ADPN) in Group I rose (p<0.01). Analysis of lipid spectrum revealed a mild yet significant decrease in total cholesterol and LPD-cholesterol (p<0.01), more pronounced in Group I. In Group I, there was a decrease in plasma triglycerides (from 3.8±1.5 down to 2.3±0.5 mmol/L, p<0.01), whereas glycated hemoglobin (HbAc1) decreased from 7.0±1.3 to 4.1±0.9 %, (p<0.01) nIn conclusion,comparing to placebo group long term co-administration of LPD and KA in CKD patients led to decrease of ADMA,fat in muscle and visceral body fat, and proteinuria. Concomitant decreases of glycated haemoglobin, LDL-c and pentosidine may also contribute to the delay in progression of renal failure and decrease of cardiovascular risk factors..The study was supported by Research Project MZO 00023001 awarded by Ministry of Health of the Czech Republic

BENEFICIAL EFFECT OF KETO AMINO ACIDS FOR DIALYSIS PATIENTS

Nutritional status is an important predictor of clinical outcome in dialysed patients. Beside decreased serum protein/albumin,lower BMI with decreased muscle mass is the most significant predictor of morbidity and mortality. Keto amino acids (KA) represent an additional source for protein anabolism influencing indirectly also carbohydrate and lipid metabolism,Ca-P and acid base balance.Additionaly,by concominant metabolic and hemodynamic effect on residual nefrons, KA can help to slow progression of residual renal function (RRF) mainly in peritoneal dialysis patients. We conducted a long-term prospective randomized placebo controlled trial to test whether a modified low-protein diet (LPD) with or without keto acids (KA) would be safe ,well tolerated and associated with an increase of metabolic status and preservation of RRF in peritoneal dialysis (PD). We evaluated a total of 62 PD patients (32M/30F) aged 26-72 yrs with creatinine clearance (Ccr) 7.9-5.7 mL/min/1.73m2 for a period of 12 months. All patients were on modified LPD containing 0.8 protein/kg/IBW/day and 135/kJ/kg/IBW/day. LPD was randomly supplemented with KA at dosage of 100 mg/kg/IBW/day (30 patients, Group I) while 30 patients (Group II) received placebo. We analysed also muscle and fat metabolism by MR spectroscopy (MRS, m.tibialis anterior)) and imagining (MRI,visceral fat).Patients from Group I were before enrolment on conservative management using LPD + KA (0.6g P + 0.1g KA/kg/IBW/day) for longer time (18-48 months, median 28) with good compliance (SGA). Patients from group II were never treated with LPD and KA.All patients were monitored at the beginning of PD and at every 3 months for 12 months.;A neutral or positive long- term nitrogen balance (nPCR in g/kg IBW/day) was achieved in Group I (p

Tautomeric transitions of isocytosine isolated in argon and neon matrices induced by UV irradiation

The tautomeric equilibrium of the isocytosine molecules in the low temperature Ar and Ne matrices has been investigated by the FTIR matrix isolation spectroscopy and quantum-chemical calculations at the DFT, MP2, and CCSD(T) levels of theory. Broad-band UV irradiation of matrix isolated isocytosine results in an increase of the abundance of the minor isocytosine tautomer, KA1. After UV irradiation the intensity of the spectral bands assigned to this tautomer increases more than 1.5 times and the bands of other minor conformers are not observed. The values of ΔH (6.6kJ/mol) and ΔG (6.8kJ/mol) determined based on the experimental data are close to the ΔE value (8.3kJ/mol) calculated at the CCSD/aug-cc-pVDZ level of theory. Two Fermi resonances involving the νCO vibration of the minor tautomer KA1 (2-amino-4-oxo-pyrimidine or keto–amino) and four Fermi resonances involving the ring stretching vibrations of the most abundant tautomer EA1 (2-amino-4-hydroxy-pyrimidine or enol–amino) are found. The performance of the different computational methods in predicting the vibrational spectra of isocytosine is evaluated.

Click to Join Peptides/Proteins Together

Copper(I) is able to catalyze Huisgen 1,3-dipolar cycloaddition in a "click" fashion. This copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction presents excellent chemoselectivity and occurs over a wide-range of reaction conditions. It shows tolerance to variation in both pH and solvent polarity, thereby facilitating the ligation of peptides and proteins to produce peptidomimetics and synthetic proteins. In addition, the only product formed is a 1,4-disubstituted-1,2,3-triazole moiety, in many aspects resembling the natural peptide bond, including hydrogen-bonding capability, planarity, distance between the 1 and 4 substituents, and conformational restriction of the peptide backbone; thus the triazole-backbone-modified peptide, in which a triazole replaces the amide bond, may be anticipated to present a secondary structure similar to that of its natural counterpart. This Focus Review describes the scope and applications of copper(I)-catalyzed alkyne–azide cycloaddition in synthetic peptide/protein chemistry.

Evolution of cyclic peptide protease inhibitors

We report a bacterial system for the evolution of cyclic peptides that makes use of an expanded set of amino acid building blocks. Orthogonal aminoacyl-tRNA synthetase/tRNA(CUA) pairs, together with a split intein system were used to biosynthesize a library of ribosomal peptides containing amino acids with unique structures and reactivities. This peptide library was subsequently used to evolve an inhibitor of HIV protease using a selection based on cellular viability. Two of three cyclic peptides isolated after two rounds of selection contained the keto amino acid p-benzoylphenylalanine (pBzF). The most potent peptide (G12: GIXVSL; X=pBzF) inhibited HIV protease through the formation of a covalent Schiff base adduct of the pBzF residue with the ε-amino group of Lys 14 on the protease. This result suggests that an expanded genetic code can confer an evolutionary advantage in response to selective pressure. Moreover, the combination of natural evolutionary processes with chemically biased building blocks provides another strategy for the generation of biologically active peptides using microbial systems.

Keto–enol tautomerism in asymmetric Schiff bases derived from p-phenylenediamine

Reaction of dehydroacetic acid and p-phenylenediamine afforded a monosubstituted Schiff base, I, with the other amino group free. In further reactions with various salicylaldehyde derivatives, I served as a precursor for synthesis of asymmetric bis-Schiff bases. The synthesized compounds are thus comprised of two subunits, dehydroacetic ( dha) and salicylidene ( sal), which are bridged by the phenylene linker. All products were investigated by means of elemental analysis, FT-IR and NMR spectroscopy, thermal methods, powder X-ray diffraction and, when possible, by single crystal X-ray crystallography. Structural and spectroscopic studies revealed that in the bis-products, the dha subunit adopts the keto–amino tautomeric form, while the sal subunit adopts the enol–imino form. Tautomeric forms were not affected if a methoxo group was introduced on the salicylidene ring. Both tautomeric subunits are stabilized by strong resonance-assisted hydrogen bonds, RAHB. The two subunits of the prepared bis-Schiff bases predominantly retain in solution the same tautomeric forms as found in the solid state.