The crystal structure of penicillopepsin at 6Åresolution

A 6Åresolution electron density map of crystals of penicillopepsin, an acid protease from Penicillium janthinellum, has been computed from multiple isomorphous replacement phases determined from two heavy metal derivatives, K₂PtCl₆ and UO₂Cl₂. The mean figure of merit of the map is 0.939. The boundaries of the molecules, of which there are four per unit cell, are readily discernible. The molecule is highly asymmetric with approximate dimensions 60Å× 40Å× 30Å. The molecule consists of two distinct lobes separated by a deep cleft, which is probably the extended substrate binding site.     

Platinum(II) complexes with 2,4-diaminobutyric acid,ornithine, lysine and 4,5-diaminovaleric acid

L-2,4-Diaminobutyric acid (Dab) reacts with K₂PtCl₄ yielding PtCl₂(N,O-Dab), which rearranges to PtCl₂(N,N-Dab). Reaction with L-ornithine and L-lysine yields the corresponding PtCl₂(N,O-Orn) and PtCl₂(N,O-Lys), respectively, whereas reaction with 4,5-diaminovaleric acid (Dav) yields PtCl₂(N,N- Dav).     

Platinum(II) complexes with diaminopropionic acid as oxygen-bound unidentate,nitrogen—oxygen and nitrogen—2nitrogen chelate complexes

Reaction of diaminopropionic acid (Dap) monohydrochloride with K₂PtCl₄ in water gives two isomeric PtCl₂(O-Dap·HCl)₂ complexes co-ordinated through oxygen only which can be isolated in solid form; both isomers are converted upon short heating to PtCl₂(N,O-Dap), whereas prolonged heating yields PtCl₂(N,N-Dap).     

Platinum(IV) isocyanide complexes

Neutral and cationic platinum(IV) isocyanide complexes of the type [PtCl₄(CNR)₂], [PtCl₄(CNR) (PMe₂Ph)], [PtCl₃(CNR)(PMe₂Ph)₂]⁺, [PtCl₂(CNR)₂ (PMe₂Ph)₂]²⁺, where R = methyl, t-butyl, cyclohexyl, p-tolyl, have been prepared by chlorine addition to the corresponding platinum(II) derivatives. The complexes [PtCl₂(CN)₂(CNR)₂] and [PtCl₂(CN)(CNR) (PMe₂Ph)₂]⁺ (R = t-butyl), are also reported. The cationic t-butylisocyanide derivatives are noteworthy in the way they readily lose the t-butyl cation at room temperature to give the corresponding cyano complexes. The compounds have been characterized by elemental analysis, molecular weights and conductivity measurements, and their i.r. and n.m.r. data are discussed in relation to structures and to the nature of the platinum-isocyanide bond.     

Platinum(II) complexes with aryl tellurols and diaryl ditellurides: Syntheses and spectral investigations

Arytellurol complexes [PtCl(TeAr)(PPh₃)₂] (I) and [Pt(TeAr)₂(PPh₃)₂] (II) are readily obtained from cis-[PtCl₂(PPh)₃)₂] and NaTeAr (Ar = C₆H₅, 4-CH₃OC₆H₄ and 4-CH₃CH₂OC₆H₄) in ethanolbenzene at room temperature. ³¹P NMR spectra of (I) and (II) indicate their trans configuration in solution. Metathetical reactions between I (Ar = 4-CH₃OC₆H₄) and NaX (X = I, Br, SCN) occur in methanol to give [Pt(X)(TeC₆H₄OCH₃-4)(PPh₃)₂]. ¹H NMR shows that equimolar proportions of NaTeC₆H₅, NaTeC₆H₄OCH₂CH₃-4 and cis-[PtCl₂(PPh₃)₂] give a mixture of three complexes: II, Ar = C₆H₅; II, Ar = 4-CH₃CH₂OC₆H₄; and [Pt(TeC₆H₅)(TeC₆H₄OCH₂CH₃-4)(PPh₃)₂]. Polymeric complexes [PtCl(TeAr)]_n (III) and [Pt(TeAr)₂]_n (IV) result from reaction between K₂[PtCl₄] and NaTeAr in aqueaous ethanol. They react with excess of PPh₃ in CDCl₃ to yield monomeric complexes I and II respectively which were characterized in situ by ¹H and ³¹P NMR of the reaction mixtures. IR spectra indicate the presence of bridging chloride ligands in III. An alternating chloride and tellurol bridged chain structure for III and a tellurol bridged for IV have been proposed. Reaction between equimolar amounts of III and PPh₃ in dichloromethane yielded a tellurol bridged dimeric complex [PtCl(μ-TeAr)(PPh₃)]₂ (V) with terminal chloride ligand as suggested by IR study. Ethanolic solutions of diarylditellurides also react readily with an aqueous solution of K₂[PtCl₄] at 10 °C to give complexes for which the structure trans-[PtCl₂(ArTeTeAr)₂] (VI) is suggested from their elemental analyses, IR, Raman (in one case only), ¹H, ¹²⁵Te (in one case only), and ¹⁹⁵Pt NMR spectra and reactions with triphenylphosphine which liberated free ditellurides. At 40 °C or above the same ditellurides form polymeric complexes III with K₂[PtCl₄] in aquaeous ethanol.     

Properties of the Mg2+-induced low-affinity nucleotide binding site of (Na++ K+)-activated ATPase

(1) The Mg²⁺-induced low-affinity nucleotide binding by (Na⁺ + K⁺)-ATPase has been further investigated. Both heat treatment (50–65°C) and treatment with N-ethylmaleimide reduce the binding capacity irreversibly without altering the K_d value. The rate constant of inactivation is about one-third of that for the high-affinity site and for the (Na⁺ + K⁺)-ATPase activity. (2) Thermodynamic parameters (ΔH° and ΔS°) for the apparent affinity in the ATPase reaction (K_m ATP) and for the true affinity in the binding of AdoPP[NH]P (K_d and K_i) differ greatly in sign and magnitude, indicating that one or more reaction steps following binding significantly contribute to the K_m value, which thus is smaller than the K_d value. (3) Ouabain does not affect the capacity of low-affinity nucleotide binding, but only increases the K_d value to an extent depending on the nucleotide used. GTP and CTP appear to be most sensitive, ATP and ADP intermediately sensitive and AdoPP[NH]P and least sensitive to ouabain. Ouabain reduces the high-affinity nucleotide binding capacity without affecting the K_d value. (4) The nucleotide specificity of low-affinity binding site is the same for binding (competition with AdoPP[NH]P) and for the ATPase activity (competition with ATP): AdoPP[NH]P > ATP > ADP > AMP. (5) The low-affinity nucleotide binding capacity is preserved in the ouabain-stabilized phosphorylated state, and the K_d value is not increased more than by ouabain alone. (6) It is inferred that the low-affinity site is Iocated on the enzyme, more specifically its α-subunit, and not on the surrounding phospholipids. It is situated outside the phosphorylation centre. The possible functional role of the low-affinity binding is discussed.     

Influence of cis-[PtCl<Subscript>2</Subscript>(Me<Subscript>2</Subscript>SO)<Subscript>2</Subscript>] on thermal denaturation of albumin

The interaction of cis-[PtCl₂(Me₂SO)₂] with human serum albumin (HSA) and the sensitivity of the complex to heat denaturation as dependent on the duration of incubation have been studied by UV absorption and fluorescence spectroscopy. Optimal conditions for cis-[PtCl₂(Me₂SO)₂] binding to HSA have been determined. The results are compared with the data for the HSA-cisplatin complex. It has been found that binding of HSA with cis-[PtCl₂(Me₂SO)₂] does not result in significant structural changes of the protein.     

Discovery and development of substituted tyrosine derivatives as Bcl-2/Mcl-1 inhibitors

Anti-apoptotic Bcl-2 family proteins are vital for cancer cells to escape apoptosis, which make them attractive targets for cancer therapy. Recently, a lead compound 1 was found to modestly inhibit the binding of BH3 peptide to Bcl-2 protein with a K_i value of 5.2?µM. Based on this, a series of substituted tyrosine derivatives were developed and tested for their binding affinities to Bcl-2 protein. Results indicated that these compounds exhibited potent binding affinities to Bcl-2 and Mcl-1 protein but not to Bcl-X_L protein. Promisingly, compound 6i inhibited the binding of BH3 peptide to Bcl-2 and Mcl-1 protein with a K_i value of 450 and 190?nM respectively, and showed obvious anti-proliferative activities against tested cancer cells.     

The first pincer-aryl [M-(NCN)] complexes {M = Pd(II); Pt(II)} with chiral pyridine donors: Synthesis and catalytic activity in C-C bond formation

The first chiral bis(pyridine) N-C(H)-N pincer ligand, (5S,7S)-1,3-bis(6,6-dimethyl-5,6,7,8-tetrahydro-5,7-methanquinolin-2-yl)benzene (HL) has been synthesized and characterized by a thorough ¹H NMR analysis. Reaction of HL with K₂[PtCl₄] in acetic acid gives [Pt(L)Cl] (1), where L acts as a tridentate N-C-N pincer ligand. The analogous palladium(II) derivatives [Pd(L)Cl] (2), and [Pd(L)(OAc)] (3), were first prepared through a transmetalation reaction between Pd(OAc)₂ and the organomercury compound [Hg(L)Cl] (4). The structures of compounds 1 (Pt) and 2 (Pd), as determined by X-ray diffraction, are reported and compared. Compound 2 can also be obtained from Na₂[PdCl₄] and HL in refluxing acetic acid, i.e., under the same conditions used for compound 1. Apparently, this is the first palladium pincer derivative of a 1,3-bis(pyridyl)benzene ligand synthesized by direct C-H activation.The neutral complexes 1-3 are catalysts of modest activity, but devoid of enantioselectivity in the Heck reaction between iodobenzene and methyl acrylate and in the aldol condensation of benzaldehyde with methyl isocyanoacetate.     

Novel trans-platinum complexes of the histone deacetylase inhibitor valproic acid; synthesis, in vitro cytotoxicity and mutagenicity

The first examples of Pt complexes of the well known anti-epilepsy drug and histone deacetylase inhibitor, valproic acid (VPA), are reported. Reaction of the Pt(II) am(m)ine precursors trans-[PtCl₂(NH₃)(py)] and trans-[PtCl₂(py)₂] with silver nitrate and subsequently sodium valproate gave trans-[Pt(VPA_−1H)₂(NH₃)(py)] and trans-[Pt(VPA_−1H)₂(py)₂], respectively. The valproato ligands in both complexes are bound to the Pt(II) centres via the carboxylato functionality and in a monodentate manner. The X-ray crystal structure of trans-[Pt(VPA_−1H)₂(NH₃)(py)] is described. Replacement of the dichlorido ligands in trans-[PtCl₂(py)₂] and trans-[PtCl₂(NH₃)(py)] by valproato ligands (VPA_−1H) to yield trans-[Pt(VPA_−1H)₂(py)₂] and trans-[Pt(VPA_−1H)₂(NH₃)(py)] respectively, significantly enhanced cytotoxicity against A2780 (parental) and A2780 cisR (cisplatin resistant) ovarian cancer cells. The mutagenicity of trans-[Pt(VPA_−1H)₂(NH₃)(py)] and trans-[Pt(VPA_−1H)₂(py)₂] was determined using the Ames test and is also reported.     

The interaction of methylcobalamin with tetracyanoplatinate(II), tetrathiocyanoplatinate(II) and tetrachloroplatinate(II)

The interactions of methylcobalamin (CH₃-B₁₂) with Pt(CN)₄^2?, PtCl₄^2?, and Pt(SCN)₄^2? in aqueous solution were studied by UV-visible and ¹H NMR spectroscopy. Together with earlier results on the mechanism of the Pt(IV)-dependent methyl-transfer reaction from CH₃-B₁₂ to Pt(II), these studies suggest at least three Pt binding sites on CH₃-B₁₂. One site, which is occupied by all three complexes (K₁ = 4 X 10³ M^?1 for Pt(CN)₄^2? and 3 X 10³ M^?1 for PtCl₄^2?), is located on the CoCH₃ side of the corrin macrocycle, and is involved in the methyl-transfer process in the presence of a Pt(IV) complex. An additional site for Pt(SCN)₄^2? is the N-3 of the benzimidazole group, resulting in dissociation of this group from the cobalt. An additional site for Pt(CN)₄^2? has a binding constant of 16 M^1? and ¹H NMR changes indicate perturbation but not dissociation of the benzimidazole group. Only the first interaction is discerned for PtCl₄^2?.     

X-ray crystal structure and properties of tris(tetrathiafulvalenium) hexachloroplatinate

The title salt has been prepared by the diffusion of tetrathiafulvalene (TTF) and [NBuⁿ₄]₂[PtCl₆] in acetonitrile. Crystals (black plates) are tetragonal, space group P4/mbm, with a=11.757(2), c=11.707(2) Å, and Z=2. The block-diagonal least-squares refinement, based on 804 independent reflections with ∣F_o∣> 3σ(F), yields an R factor of 0.11. The structure is comprised of TTF-trimer units which are arranged perpendicularly to each other, forming a two-dimensional layer with somewhat close sulfur- sulfur contact among the trimers. The salt exhibits the electrical resistivity of 87 Ω cm as a compacted pellet at 25 °C. Binding energies of platinum 4f electrons of the [PtCl₆]²⁻ anion suggest an extreme reduction from the platinum(IV) state.     

The interaction of proteins with hydroxyapatite: II. Role of acidic and basic groups

The elution behavior from hydroxyapatite columns of the modification products of seven basic and three acidic proteins has been investigated. Three classes of NH₂ derivatives were prepared. These consisted of (1) replacement by a guanidyl group with no change in charge; (2) blocking with loss of charge; and (3) replacement of positive charges by negative ones. Two types of COOH derivatives were prepared: (1) blocking with loss of charge; and (2) replacement of COOH by SO₃H with no change in charge. The elution behavior of the derivatives in PO₄, F^?, Cl^?, ClO₄^?, and Ca²⁺ ion eluants showed that (1) the elution patterns are determined by the isoelectric points of the proteins, there being no symmetry between the binding or elution behavior of acidic and basic proteins; (2) the binding of basic proteins requires the presence of a high density of positively charged groups; (3) the binding of all proteins to hydroxyapatite equilibrated with phosphate buffer is enhanced by a decrease in the number of their negative charges; and (4) calcium ions affect the binding of proteins to hydroxyapatite at the level of carboxyls, since clusters of carboxyls strengthen both the interaction with Ca²⁺ and the binding to hydroxyapatite.     

Chemical evolution of iron containing enzymes: Mixed ligand complexes of iron as intermediary steps

Activities of the iron complexes of evolutionary importance like K₄[Fe(CN)₆], K₄[Fe(CN)₅(gly)], and K₄[Fe(CN)₅(trigly)] have been tested towards some redox reactions of biological significance, namely, decomposition of hydrogen peroxide, dehydrogenation of NADH and ascorbic acid both coupled with reduction of methylene blue. It has been observed that the catalytic activities of iron (II) complexes towards the redox reactions studied at pH 9.18 followed the order, K₄[Fe(CN)₆]4[Fe(CN)₅(gly)]4[Fe(CN)₅(trigly)]. Decomposition of H₂O₂ catalysed by cyanocomplexes of iron (II) has been discussed through the formation of an innersphere complex in which loosly bound ligands like, glycine and triglycine are replaced by hydroperoxide ion. A tentative mechanism for the catalysed decomposition of H₂O₂ has been discussed.Based upon the experimental observations a hypothesis on the evolution of iron containing enzymes has been envisaged as: iron(II) ion iron(II) cyanide complexes mixed ligand iron(II) cyanide and amino acid complexes iron(II) complexes of macromolecules proenzyme or early enzyme containing iron(II).     

Pt(II) and Ag(I) complexes with acesulfame: Crystal structure and a study of their antitumoral, antimicrobial and antiviral activities

Two new complexes of platinum(II) and silver(I) with acesulfame were synthesized. Acesulfame is in the anionic form acesulfamate (ace). The structures of both complexes were determined by X-ray crystallography. For K₂[PtCl₂(ace)₂] the platinum atom is coordinated to two Cl⁻ and two N-acesulfamate atoms forming a trans-square planar geometry. Each K⁺ ion interacts with two oxygen atoms of the S(O)₂ group of each acesulfamate. For the polymeric complex [Ag(ace)]_n the water molecule bridges between two crystallographic equivalent Ag1 atoms which are related each other by a twofold symmetry axis. Two Ag1 atoms, related to each other by a symmetry centre, make bond contact with two equivalent oxygen atoms. These bonds give rise to infinite chains along the unit cell diagonal in the ac plane. The in vitro cytotoxic analyses for the platinum complex using HeLa (human cervix cancer) cells show its low activity when compared to the vehicle-treated cells. The Ag(I) complex submitted to in vitro antimycobacterial tests, using the Microplate Alamar Blue (MABA) method, showed a good activity against Mycobacterium tuberculosis, responsible for tuberculosis, with a minimal inhibitory concentration (MIC) value of 11.6 μM. The Ag(I) complex also presented a promising activity against Gram negative (Escherichia coli and Pseudomonas aeruginosa) and Gram positive (Enterococcus faecalis) microorganisms. The complex K₂[PtCl₂(ace)₂] was also evaluated for antiviral properties against dengue virus type 2 (New Guinea C strain) in Vero cells and showed a good inhibition of dengue virus type 2 (New Guinea C strain) replication at 200 μM, when compared to vehicle-treated cells.     

Structural characterization and DNA interactions of new cytotoxic transplatin analogues containing one planar and one nonplanar heterocyclic amine ligand

trans-Diaminedicholoroplatinum(II) complexes with one planar and one non-planar heterocyclic amine ligand were designed as new potential antitumor drugs. The X-ray crystallographic structures of trans-[PtCl₂(4-picoline)(piperidine)] and trans-[PtCl₂(4-picoline)(piperazine)]·HCl revealed that the piperidine and piperazine ligands bind to the platinum through the equatorial position and that the ligands adopt the chair conformation. The nonplatinated amine of the piperazine can form hydrogen bonds with atoms that are approximately 7.5 Å away from the Pt binding site. DNA is considered a major pharmacological target of platinum compounds. Hence, to expand the database correlating structural features of platinum compounds and DNA distortions induced by these compounds, which may facilitate identification of more effective anticancer platinum drugs, we describe the DNA binding mode in a cell-free medium of trans-[PtCl₂(4-picoline)(piperidine)] and trans-[PtCl₂(4-picoline)(piperazine)]·HCl. Interestingly, the overall impact of the replacement of the second ammine group in transplatin by the heterocyclic ligands appears to change the character of the global conformational changes induced in DNA towards that induced by cisplatin. The clinical ineffectiveness of the parent transplatin has been proposed to be also associated with its reduced capability to form bifunctional adducts in double-helical DNA. The results of the present work support the view that replacement of both ammine groups of transplatin by heterocyclic ligands enhances cytotoxicity probably due to the marked enhancement of the stability of intrastrand cross-links in double-helical DNA.     

Directed evolution reveals the binding motif preference of the LC8/DYNLL hub protein and predicts large numbers of novel binders in the human proteome

LC8 dynein light chain (DYNLL) is a eukaryotic hub protein that is thought to function as a dimerization engine. Its interacting partners are involved in a wide range of cellular functions. In its dozens of hitherto identified binding partners DYNLL binds to a linear peptide segment. The known segments define a loosely characterized binding motif: [D/S]_-4K_-3X_-2[T/V/I]_-1Q₀[T/V]₁[D/E]₂. The motifs are localized in disordered segments of the DYNLL-binding proteins and are often flanked by coiled coil or other potential dimerization domains. Based on a directed evolution approach, here we provide the first quantitative characterization of the binding preference of the DYNLL binding site. We displayed on M13 phage a naïve peptide library with seven fully randomized positions around a fixed, naturally conserved glutamine. The peptides were presented in a bivalent manner fused to a leucine zipper mimicking the natural dimer to dimer binding stoichiometry of DYNLL-partner complexes. The phage-selected consensus sequence V_-5S_-4R_-3G_-2T_-1Q₀T₁E₂ resembles the natural one, but is extended by an additional N-terminal valine, which increases the affinity of the monomeric peptide twentyfold. Leu-zipper dimerization increases the affinity into the subnanomolar range. By comparing crystal structures of an SRGTQTE-DYNLL and a dimeric VSRGTQTE-DYNLL complex we find that the affinity enhancing valine is accommodated in a binding pocket on DYNLL. Based on the in vitro evolved sequence pattern we predict a large number of novel DYNLL binding partners in the human proteome. Among these EML3, a microtubule-binding protein involved in mitosis contains an exact match of the phage-evolved consensus and binds to DYNLL with nanomolar affinity. These results significantly widen the scope of the human interactome around DYNLL and will certainly shed more light on the biological functions and organizing role of DYNLL in the human and other eukaryotic interactomes.     

Complex of cis-(NH3)2PtCl2 with guanylyl(3′-5′)-cytidine

The predominant complex formed by the reaction of cis-(NH₃)₂PtCl₂ and guanylyl(3′-5′)cytidine has been isolated. The molar ratio of the binding of cis-(NH₃)₂PtCl₂ to guanylyl(3′-5′)-cytidine is 1:2. The values of proton dissociation constant due to guanine and cytosine bases provide useful information for determining the binding site of the isolated complex. In addition, nmr and ir spectral data were used to determine the binding site. cis-(NH₃)₂PtCl₂ coordinates to guanylyl(3′-5′)cytidine through N(7) position of the guanine base, but cytosine base does not participate in the binding to cis-(NH₃)₂Pt²⁺. Interbase crosslink has not been detected. The binding specificity of cis-(NH₃)₂PtCl₂ to guanine base is discussed.     

Cis-diamminedichloroplatinum(II) modified DNA stimulates far greater levels of S1 nuclease sensitive regions than does the modification produced by the trans- isomer

S1 endonuclease recognizes distortions in DNA structure produced by both cis- and trans-diamminedichloroplatinum(II) binding. However, cis-(NH₃)₂PtCl₂ binding stimulates far greater levels of S1 digestion than does the trans-isomer. This supports the view that the modes of binding for the two isomers differ and shows that cis-(NH₃)₂PtCl₂ causes a greater disruption of the secondary structure. The S1 digestion products include acid soluble DNA fragments with bound platinum, with the latter providing evidence that (NH₃)₂PtCl₂ is directly responsible for the structural alteration. These findings also reveal that at low levels of binding, the average number of nucleotides excised for each platinum excised in cis-(NH₃)₂PtCl₂ modified DNA is twice as large as for the trans-isomer.     

Unraveling the stability of plasma proteins upon interaction of synthesized uridine products: biophysical and molecular dynamics approach

Abstract

Most of the drugs binding to human serum albumin (HSA) are transported to various parts of the body. Here, we have studied the molecular interaction between HSA and synthesized uridine derivatives, 1-[(3R, 4S, 5?R)-2-methyl-3, 4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dion.)(C-MU); [(2R,3R,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxy-4-methyl-tetrahydrofuran-2-yl] methyl methyl phosphochloridate (CM-MU) and [(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-2-methyl-3,4-dihydroxyoxolan-2-yl] methyl dihydrogen phosphate (P-MU). Cytotoxic studies of these synthesized compounds with mouse macrophages (RAW 246.7) and HeLa cells (human cervical cancer cells) and binding mechanism of these uridine derivatives with HSA were performed. Subsequently, fluorescence quenching was observed upon titration of uridine derivatives with HSA via static mode of quenching, and the binding constants (K_2-C-MU = 4?±?0.03?×?10⁴M^?1, K_5-CM-MU = 1.95?±?0.03?×?10⁴ M^?1 and K_5-P-MU =1.56?±?0.03?×?10⁴ M^?1) were found to be in sync with the computational results. Further, molecular displacement and molecular docking data revealed that all the derivatives are binding in the subdomain IIA and IIB regions of HSA. The protein secondary structure of complexes was determined by circular dichroism, indicating partial unfolding of the protein upon addition of the uridine derivatives. Furthermore, atomic force microscopy data reveal the change in topology upon binding of 2-C-MU, 5-CM-MU and 5-P-MU with HSA, indicating change in the microenvironment around tryptophan region. Additionally, cytotoxicity studies on HeLa and Raw Cell lines suggested that these molecules have significant anti-proliferative and anti-inflammatory properties. Hence, the study may be of help for development of new drugs based on uridine derivatives which may be helpful for combating various potential diseases.

Communicated by Ramaswamy H. Sarma