scholarly journals Bifunctional intercalation and sequence specificity in the binding of quinomycin and triostin antibiotics to deoxyribonucleic acid

1978 ◽  
Vol 173 (1) ◽  
pp. 115-128 ◽  
Author(s):  
J S Lee ◽  
M J Waring
Keyword(s):  
Binding Constant ◽  
Binding Constants ◽  
Sequence Specificity ◽  
Peptide Antibiotics ◽  
Naturally Occurring ◽  
Binding Isotherms ◽  
Triostin A ◽  
Specificity Pattern ◽  
Intercalating Agents ◽  
Binding Curves

Quinomycin C, triostin A and triostin C are peptide antibiotics of the quinoxaline family, of which echinomycin (quinomycin A) is also a member. They all remove and reverse the supercoiling of closed circular duplex DNA from bacteriophage PM2 in the fashion characteristic of intercalating drugs, and the unwinding angle at I 0.01 is, in all cases, almost twice that of ethidium. Thus, as with echinomycin, they can be characterized as bifunctional intercalating agents. For the triostins this conclusion has been confirmed by measurements of changes in the viscosity of sonicated rod-like DNA fragments; the helix extension was found to be almost double that expected for a simple monofunctional intercalation process. For triostin A, further evidence for bifunctionality was derived from the cross-over point of binding isotherms to nicked circular and closed circular bacteriophage-PM2DNA. Binding curves for the interaction of quinomycin C and triostin A with a variety of synthetic and naturally occurring nucleic acids were determined by solvent-partition analysis, but triostin C was too insoluble in aqueous solution to make this method applicable. For quinomycin C the highest binding constant was found with Micrococcus lysodeikticus DNA, and its pattern of specificity among natural DNA species was broadly similar to that of echinomycin, although the binding constants were 2–6 times as large. For triostin A the highest binding constant was again found for M. lysodeikticus DNA, but the specificity pattern was quite different from that of the quinomycins. In particular, triostin A bound better to poly(dA-dT) than to the poly(dG-dC) whereas this order was reversed for quinomycin C. There was also evidence that the binding to poly(dA-dT) might be co-operative in nature. No significant interaction could be detected with poly(dA).poly(dT) or with RNA from Escherichia coli. Poly(dG).poly(dC) gave variable results, depending on the source of the polymer. The different patterns of specificity displayed by the quinomycins and triostins are tentatively ascribed to differences in their conformations in solution.

scholarly journals Interaction between synthetic analogues of quinoxaline antibiotics and nucleic acids. Changes in mechanism and specificity related to structural alterations

1978 ◽  
Vol 173 (1) ◽  
pp. 129-144 ◽  
Author(s):  
J S Lee ◽  
M J Waring
Keyword(s):  
Binding Constant ◽  
Dimethyl Ester ◽  
Sedimentation Coefficient ◽  
Binding Constants ◽  
The Other ◽  
Sequence Specificity ◽  
Synthetic Dna ◽  
Cross Bridge ◽  
Naturally Occurring ◽  
Triostin A

The interaction with DNA of six chemically synthesized derivatives of the quinoxaline antibiotics was investigated. Five of the compounds bound only weakly to DNA or not at all; for these substances spectrophotometric measurements, sedimentation studies with closed circular duplex bacteriophage-PM2 DNA and thermal-denaturation profiles were used to determine limits fot the binding constants. No interaction could be detected with two products of degradation of echinomycin (quinomycin A), one of which, echinomycinic acid dimethyl ester, had the lactone linkages opened, whereas the other retained an intact octapeptide ring but had a broken cross-bridge. The other compounds studied were des-N-tetramethyl-triostin A (‘TANDEM’) and its derivatives. A derivative of ‘TANDEM’ IN WHICH benzyloxycarbonyl moieties replace both quinoxaline chromophores had binding constants to nucelic acids in the range 10(2)–10(3)-1, whereas no interaction could be detected for a benzyloxycarbonyl derivative that, in addition, had the cross-bridge broken. The derivative of ‘TANDEM’ with L-serine in place of D-serine in both positions showed no detectable interaction with Clostridium perfringens DNA, whereas the binding constant to poly(dA-dT) was approx 2 × 10(3)M-1. ‘TANDEM’ itself bound strongly to DNA, and the bathochromic and hypochromic shifts in its u.v.-absorption spectrum in the presence of DNA were similar to those seen with echinomycin. From the effect on the sedimentation coefficient of closed circular duplex bacteriophage-PM2 DNA the mechanism of binding was shown to involve bifunctional intercalation, typical of the naturally occurring quinoxaline antibiotics. Solvent-partition analysis was used to determine binding constants for the interaction between ‘TANDEM’ and a variety of natural and synthetic DNA species. The pattern of specificity thus revealed differed markedly from that previously found with the naturally occurring quinoxaline antibiotics. Most striking was the evident large preference for (A + T)-rich DNA species, in complete contrast with echinomycin and triostin A. The highest binding constant was found for poly(dA-dT), the interaction with which appeared highly co-operative in character. The conformations adopted by those quinoxaline compounds that bind strongly to DNA were examined withe aid of molecular models on the basis of results derived from n.m.r. and computer studies. It appears that the observed patterns of base-sequence specificity are determined, at least in part, by the structure and conformation of the sulphur-containing cross-bridge.

scholarly journals The use of radiolabelled triostin antibiotics to measure low levels of binding to deoxyribonucleic acid

1983 ◽  
Vol 211 (3) ◽  
pp. 543-551 ◽  
Author(s):  
K R Fox ◽  
A Cornish ◽  
R C Williams ◽  
M J Waring
Keyword(s):  
Cyclic Peptide ◽  
Tight Binding ◽  
Binding Constants ◽  
Biologically Relevant ◽  
Low Concentrations ◽  
Binding Isotherms ◽  
Triostin A ◽  
Ranking Order ◽  
Partition Method ◽  
First Time

Triostin antibiotics, which contain a cyclic peptide with a disulphide bridge, have been prepared by growing Streptomyces triostinicus in the presence of inorganic [35S]-sulphate. The labelled triostin A has been shown to behave in all respects similarly to the authentic natural product and to enable a much more sensitive radiochemical adaptation of the solvent-partition method for determining antibiotic binding to DNA. By this means, binding isotherms at low, biologically relevant levels (down to one antibiotic molecule per gene) have been measured. The results indicate the existence of some tight binding sites in natural DNA species that are preferentially occupied at low concentrations. No evidence has been found for any allosteric transitions provoked by interaction between these antibiotics and natural DNA species, though there is evidence for co-operativity in the binding of triostin A to poly(dA-dT). For the first time accurate isotherms have been determined for the binding of triostin C to DNA; its binding constants for a variety of polydeoxynucleotides are uniformly tighter than those of triostin A but fall into the same ranking order when different species of natural DNA are compared.

Host-guest interactions of cyclodextrins and metalloporphyrins: supramolecular building blocks toward artificial heme proteins

2004 ◽  
Vol 08 (02) ◽  
pp. 125-140 ◽  
Author(s):  
Huchen Zhou ◽  
John T. Groves
Keyword(s):  
Binding Constant ◽  
Molecular Design ◽  
Covalent Binding ◽  
Binding Constants ◽  
Building Blocks ◽  
Binding Pocket ◽  
Axial Ligand ◽  
Pyridyl Nitrogen ◽  
H Nmr ◽  
Self Assembled

Cyclodextrins are versatile building blocks for a variety of macromolecules due to the inclusion complexes that are formed with hydrophobic organic molecules. Cyclodextrin-porphyrin interactions are of particular interest since cyclodextrins can serve as a non-covalent binding pocket while metalloporphyrins could serve as the heme analogs in the construction of heme protein model compounds. Various approaches to the design and assembly of biomimetic porphyrin constructs are compared and contrasted in this minireview with a particular emphasis on self-assembled and porphyrin-cyclodextrin systems. Several recent advances from our laboratories are described in this context. A sensitive fluorescent binding probe, 6A-N-dansyl-permethylated-β-cyclodextrin (Dan-NH-TMCD), was found to form 2:1 complexes with the meso-tetraphenylporphyrins Mn(III)TCPP , Mn(III)TPPS and Mn(III)TF 4 TMAP with high binding constants. A perPEGylated cyclodextrin, heptakis(2,3,6-tri-O-2-(2-(2-methoxyethoxy)ethoxy)ethyl)-β-cyclodextrin (TPCD), has been shown by 1 H NMR spectroscopy to form a 1:1 complex with H 2 TCPP with a binding constant above 108M-1. Such a strong binding constant is the largest found for a 1:1 complex between a monomeric cyclodextrin and a guest. TPCD was also found to bind Mn(III)TCPP with a binding constant of 1.2 × 106 M -1. A novel, self-assembled hemoprotein model, hemodextrin is also described. The molecular design is based on a PEGylated cyclodextrin scaffold that bears both a heme-binding pocket and an axial ligand that binds an iron porphyrin. The binding constant for Fe (III) TPPS (iron(III) meso-tetra(4-sulfonatophenyl)porphyrin) by py-PPCD was determined to be 2 × 106 M -1. The pyridyl nitrogen of py-PPCD was shown to ligate to the iron center by observing signal changes in the Fe(II) -porphyrin 1 H NMR spectrum. This hemodextrin ensemble, a minimalist myoglobin, was shown to bind dioxygen reversibly and to form a stable ferryl species.

scholarly journals Natural Cyclic Peptides as an Attractive Modality for Therapeutics: A Mini Review

Molecules ◽  
2018 ◽  
Vol 23 (8) ◽  
pp. 2080 ◽  
Author(s):  
Muna Abdalla ◽  
Lyndy McGaw
Keyword(s):  
Drug Discovery ◽  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
Pharmacological Properties ◽  
Biological Processes ◽  
Peptide Antibiotics ◽  
Natural Sources ◽  
Biological Targets ◽  
Naturally Occurring ◽  
Wide Range

Peptides are important biomolecules which facilitate the understanding of complex biological processes, which in turn could be serendipitous biological targets for future drugs. They are classified as a unique therapeutic niche and will play an important role as fascinating agents in the pharmaceutical landscape. Until now, more than 40 cyclic peptide drugs are currently in the market, and approximately one new cyclopeptide drug enters the market annually on average. Interestingly, the majority of clinically approved cyclic peptides are derived from natural sources, such as peptide antibiotics and human peptide hormones. In this report, the importance of cyclic peptides is discussed, and their role in drug discovery as interesting therapeutic biomolecules will be highlighted. Recently isolated naturally occurring cyclic peptides from microorganisms, sponges, and other sources with a wide range of pharmacological properties are reviewed herein.

Binding of calcium ions to bovine αsl-casein and precipitability of the protein–calcium ion complexes

1980 ◽  
Vol 47 (1) ◽  
pp. 113-122 ◽  
Author(s):  
Douglas G. Dalgleish ◽  
Thomas G. Parker
Keyword(s):  
Ionic Strength ◽  
Calcium Ions ◽  
Calcium Ion ◽  
Calcium Binding ◽  
Calcium Concentration ◽  
Binding Constants ◽  
Substitution Effects ◽  
Binding Isotherms ◽  
Decreasing Ph ◽  
Increasing Temperature

SummaryBinding isotherms for the calcium ion–αsl-casein system have been measured, as functions of ionic strength, temperature, and pH, and the isotherms have been analysed in terms of binding constants modified by substitution effects. The results demonstrate that the strength of binding is increased with increasing temperature and decreased by increasing ionic strength or decreasing pH, all of which may be explained semi-quantitatively. Parallel studies on the precipitability of the αsl-casein–Ca2+ complexes showed that there is considerable variation in the extent of calcium binding required to initiate precipitation of the protein, and in the calcium concentration necessary to achieve the required extent of ligand binding.

Binding constants for tetramethylammonium ion determined with irreversible inhibitors of acetylcholinesterase

1976 ◽  
Vol 54 (10) ◽  
pp. 918-920 ◽  
Author(s):  
F. Iverson
Keyword(s):  
Rate Constant ◽  
Binding Constant ◽  
Binding Constants ◽  
Single Site ◽  
Reversible Binding ◽  
Bimolecular Rate Constant ◽  
Irreversible Inhibitors ◽  
Carbamate Inhibitors

The reversible binding constant (Ki) for tetramethylammonium ion (TMA) was determined from the decrease in the bimolecular rate constant (ki) observed with each of 21 organophosphate or carbamate inhibitors of acetylcholinesterase (EC 3.1.1.7). The Ki values obtained were reasonably constant (5.8 × 10−4 ± 0.38 M), and this is consistent with reports indicating that TMA binds to a single site on the enzyme.

The use of β-cyclodextrins to enhance the aqueous solubility of trichloroethylene and perchloroethylene and their removal from soil organic matter: Effect of substituents

2003 ◽  
Vol 81 (1) ◽  
pp. 45-52 ◽  
Author(s):  
Salma Shirin ◽  
Erwin Buncel ◽  
Gary W vanLoon
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Binding Constant ◽  
Binding Constants ◽  
Aqueous Solubility ◽  
Solubility Enhancement ◽  
Degree Of Substitution ◽  
Water Remediation ◽  
Effective Removal ◽  
Matter Effect

This paper describes a systematic study for the evaluation of different substituted β-cyclodextrins (β-CDs), as agents for the enhancement of the aqueous solubility of two major organic pollutants, trichloroethylene (TCE) and perchloroethylene (PCE). The aqueous solubility enhancement occurs through the formation of host–guest inclusion complexes between the CD molecule (host) and the polychloroethylene (guest) and is driven primarily by hydrophobic forces. The CDs evaluated are: methyl-β-CD (Mβ-CD), hydroxypropyl-β-CD (HPβ-CD), carboxymethyl-β-CD (CMβ-CD1, CMβ-CD2), and sulfated-β-CD (Sβ-CD1, Sβ-CD2); the degree of substitution was also varied. Using a 5% (w/v) aqueous CD solution, solubility enhancement factors (St/So) up to 5.5 and 14 were determined for TCE and PCE, respectively. Binding constants (K11) for TCE with the substituted CDs were evaluated using an 1H NMR technique; these were found to range from 3 to 120 M–1. It was shown that solubility enhancement, as well as the binding constant, is dependent on the type and degree of substitution of the β-CD molecule; the determining factors are discussed. The CDs are also capable of effective removal of PCE and TCE retained by soil organic matter. Thus, a suitably substituted β-CD may be a valuable additive in pump-and-treat protocols for site remediation of polychlorinated organics. Key words: Cyclodextrin, trichloroethylene, perchloroethylene, solubility enhancement, binding constant, soil and water remediation.

scholarly journals The binding of cupric ions to 1-carboxymethylhistidine-119-ribonuclease

1968 ◽  
Vol 108 (4) ◽  
pp. 583-586 ◽  
Author(s):  
R. H. Saundry ◽  
W D Stein
Keyword(s):  
Binding Site ◽  
Binding Constant ◽  
Metal Ion ◽  
Binding Constants ◽  
Enzymic Activity

Binding of Cu2+ by 1-carboxymethylhistidine-119-ribonuclease was investigated by using diligand metal ion buffers. A single Cu2+-binding site was found over the Cu2+ concentration range studied. The binding constants for this site were 8·33×105 (±2%)m−1 and 1·57×104 (±6%)m−1 at pH7·0 and 6·1 respectively. An estimate of the pH-independent Cu2+-binding constant suggests that the most avid Cu2+-binding site has disappeared after carboxymethylation. This is consistent with an earlier report that binding of Cu2+ at the most avid site is associated with the loss of enzymic activity.

scholarly journals Kinetic and structural analysis of the increased affinity of enoyl-ACP (acyl-carrier protein) reductase for triclosan in the presence of NAD+

2004 ◽  
Vol 381 (3) ◽  
pp. 725-733 ◽  
Author(s):  
Mili KAPOOR ◽  
P. L. Swarna MUKHI ◽  
Namita SUROLIA ◽  
K. SUGUNA ◽  
Avadhesha SUROLIA
Keyword(s):  
Rate Constant ◽  
Binding Constant ◽  
Ternary Complex ◽  
Acyl Carrier Protein ◽  
Binding Constants ◽  
Fold Increase ◽  
Dissociation Rate ◽  
Carrier Protein ◽  
Binary And Ternary Complexes ◽  
Steady State Kinetic

The binding of enoyl-ACP (acyl-carrier protein) reductase from Plasmodium falciparum (PfENR) with its substrates and inhibitors has been analysed by SPR (surface plasmon resonance). The binding of the substrate analogue crotonoyl-CoA and coenzyme NADH to PfENR was monitored in real time by observing changes in response units. The binding constants determined for crotonoyl-CoA and NADH were 1.6×104 M−1 and 1.9×104 M−1 respectively. Triclosan, which has recently been demonstrated as a potent antimalarial agent, bound to the enzyme with a binding constant of 1.08×105 M−1. However, there was a 300-fold increase in the binding constant in the presence of NAD+. The increase in the binding constant was due to a 17 times increase in the association rate constant (k1) from 741 M−1·s−1 to 1.3×104 M−1 ·s−1 and a 16 times decrease in the dissociation rate constant (k−1) from 6.84×10−3 s−1 to 4.2×10−4 s−1. These values are in agreement with those determined by steady-state kinetic analysis of the inhibition reaction [Kapoor, Reddy, Krishnasastry, N. Surolia and A. Surolia (2004) Biochem. J. 381, 719–724]. In SPR experiments, the binding of NAD+ to PfENR was not detected. However, a binding constant of 6.5×104 M−1 was obtained in the presence of triclosan. Further support for these observations was provided by the crystal structures of the binary and ternary complexes of PfENR. Thus the dramatic enhancement in the binding affinity of both triclosan and NAD+ in the ternary complex can be explained by increased van der Waals contacts in the ternary complex, facilitated by the movement of residues 318–324 of the substrate-binding loop and the nicotinamide ring of NAD+. Interestingly, the results of the present study also provide a rationale for the increased affinity of NAD+ for the enzyme in the ternary complex.

The topological trapping of circular DNAs on agarose: Unexpected restrictions on DNA rotation

1978 ◽  
Vol 56 (6) ◽  
pp. 585-591 ◽  
Author(s):  
Jeremy S. Lee ◽  
A. Richard Morgan
Keyword(s):  
Secondary Structure ◽  
Binding Constant ◽  
Binding Assay ◽  
Sodium Perchlorate ◽  
Binding Constants ◽  
The Other ◽  
Calf Thymus ◽  
Potential Applications ◽  
Open Circular ◽  
Circular Dnas

DNA linked to an insoluble matrix has many potential applications. In some cases, it is highly desirable that the DNA be chemically unaltered, and for this reason, we have developed methods for topologically trapping circular DNAs on agarose. Open circular (oc) DNA containing at least one nick is readily trapped on agarose which has been heated or dissolved in sodium perchlorate to destroy secondary structure and then gelled by cooling or dialysis respectively. On the other hand, covalently closed circular (ccc) DNA of superhelix density −0.12 (PM2 DNA) is only poorly trapped unless first relaxed by topoisomerases or with the appropriate addition of an intercalating drug. When the oc DNA – agarose was used in a procedure for rapidly obtaining binding constants of drugs to DNA, the binding constant of ethidium was found to be considerably less than that expected. On addition of calf thymus topoisomerase to the binding-assay mixture, the ethidium-binding constant increased to the expected value. Thus, although free oc DNA is topologically unrestricted, oc DNA trapped in agarose must be rotationally constrained such that addition of ethidium introduced supercoils. The nature of these constraints is discussed with respect to the known structure of agarose bihelices.

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