Discovery of a Novel Mycobacterial F-ATP Synthase Inhibitor and its Potency in Combination with Diarylquinolines

The F₁F_O-ATP synthase is required for growth and viability of Mycobacterium tuberculosis and is a validated clinical target. A mycobacterium-specific loop of the enzyme's rotary γ subunit plays a role in the coupling of ATP synthesis within the enzyme complex. We report the discovery of a novel antimycobacterial, termed GaMF1, that targets this γ subunit loop. Biochemical and NMR studies show that GaMF1 inhibits ATP synthase activity by binding to the loop. GaMF1 is bactericidal and is active against multidrug- as well as bedaquiline-resistant strains. Chemistry efforts on the scaffold revealed a dynamic structure activity relationship and delivered analogues with nanomolar potencies. Combining GaMF1 with bedaquiline or novel diarylquinoline analogues showed potentiation without inducing genotoxicity or phenotypic changes in a human embryonic stem cell reporter assay. These results suggest that GaMF1 presents an attractive lead for the discovery of a novel class of anti-tuberculosis F-ATP synthase inhibitors.     

Structural fluctuation and concerted motions in F1‐ATPase: A molecular dynamics study

F₁‐ATPase is an adenosine tri‐phosphate (ATP)‐driven rotary motor enzyme. We investigated the structural fluctuations and concerted motions of subunits in F₁‐ATPase using molecular dynamics (MD) simulations. An MD simulation for the α₃β₃γ complex was carried out for 30 ns. Although large fluctuations of the N‐terminal domain observed in simulations of the isolated β_E subunit were suppressed in the complex simulation, the magnitude of fluctuations in the C‐terminal domain was clearly different among the three β subunits (β_E, β_TP, and β_DP). Despite fairly similar conformations of the β_TP and β_DP subunits, the β_DP subunit exhibits smaller fluctuations in the C‐terminal domain than the β_TP subunit due to their dissimilar interface configurations. Compared with the β_TP subunit, the β_DP subunit stably interacts with both the adjacent α_DP and α_E subunits. This sandwiched configuration in the β_DP subunit leads to strongly correlated motions between the β_DP and adjacent α subunits. The β_DP subunit exhibits an extensive network of highly correlated motions with bound ATP and the γ subunit, as well as with the adjacent α subunits, suggesting that the structural changes occurring in the catalytically active β_DP subunit can effectively induce movements of the γ subunit. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010     

Subcomplexes of mitochondrial complex V reveal mutations in mitochondrial DNA

Complex V, site of the final step in oxidative phosphorylation, uses the proton gradient across the inner mitochondrial membrane for the production of ATP. It is a multi‐subunit complex composed of a catalytic domain (F₁) and a membrane domain (F₀) linked by two stalks. Subcomplexes of complex V containing the F₁ domain have previously been reported in small series of patients. We report the results in tissue samples and/or cultured skin fibroblasts studied by blue native PAGE followed by activity staining in the gel. Catalytically active subcomplexes of complex V were detected in 66 tissues originating from 53 patients. In 29 of the latter (55%), a mitochondrial DNA (mtDNA) defect was identified. Twelve patients had a pathogenic point mutation in a mitochondrial tRNA, one a large mtDNA deletion, 12 showed mtDNA depletion and four had a mutation in the MT‐ATP6 gene. We conclude that the presence of subcomplexes of complex V is a valuable indicator in the detection of mtDNA defects.     

H2‐Fueled ATP Synthesis on an Electrode: Mimicking Cellular Respiration

ATP, the molecule used by living organisms to supply energy to many different metabolic processes, is synthesized mostly by the ATPase synthase using a proton or sodium gradient generated across a lipid membrane. We present evidence that a modified electrode surface integrating a NiFeSe hydrogenase and a F₁F₀‐ATPase in a lipid membrane can couple the electrochemical oxidation of H₂ to the synthesis of ATP. This electrode‐assisted conversion of H₂ gas into ATP could serve to generate this biochemical fuel locally when required in biomedical devices or enzymatic synthesis of valuable products.     

Dibutyltin-3-hydroxyflavone titrates a dissociable component (cofactor) of mitochondrial ATP synthase: An energy-transfer component linked to the ubiquinone pool

Dibutyltin-3-hydroxyflavone, Bu₂Sn(of), is a new fluorescence probe inhibitor of F₁F₀-ATPase and oxidative phosphorylation which inhibits by titration of an unidentified component of F₀. Its site of action is closely related to that of the trialkyltins and of venturicidin. This F₀ component is part of a pool of this component which is present in the heart mitochondrial inner membrane at levels of 5–7 nmol (mg protein)^?1 [18 ± 3 Bu₂Sn(of) sites per mol F₁F₀-ATPase]. However, ATPase activity in submitochondrial particles is near maximally inhibited by titration of approx. three Bu₂Sn(of) sites per mol F₁F₀-ATPase. Over 60% (60–80%) of the Bu₂Sn(of) interaction sites can be lost during the purification of F₁F₀-ATPase from submitochondrial particles. The number of Bu₂Sn(of) interaction sites in various F₁F₀-ATPase preparations is variable. The high numbers of Bu₂Sn(of) sites per mol F₁F₀-ATPase for heart mitochondria (18–21) and submitochondrial particles (15–19.5) decline in ATP synthase (11–15) to the low values obtained in Complex V (7–10.5) and the minimal values observed in highly purified F₁F₀?ATPase (3.5–5.6), thus indicating a variable dissociable component or cofactor of ATP synthase. The Bu₂Sn(of) interaction site, a component of ATP synthase, is responsive to the redox status of the respiratory chain and the interaction with Bu₂Sn(of) is with the reduced form of this component. Fluorescence titration studies show that this component is in redox equilibrium with the ubiquinone pool of the respiratory chain. It is proposed that this redox component serves as an inhibitor titratable cofactor pool which cycles through an F₀ interaction site (or sites) via a system which serves as an energy-transfer link between the respiratory chain and ATP synthase.     

Azidoperfluoroalkanes: Synthesis and Application in Copper(I)‐Catalyzed Azide–Alkyne Cycloaddition

We report an efficient and scalable synthesis of azidotrifluoromethane (CF₃N₃) and longer perfluorocarbon‐chain analogues (R_FN₃; R_F=C₂F₅, ⁿ C₃F₇, ⁿ C₈F₁₇), which enables the direct insertion of CF₃ and perfluoroalkyl groups into triazole ring systems. The azidoperfluoroalkanes show good reactivity with terminal alkynes in copper(I)‐catalyzed azide–alkyne cycloaddition (CuAAC), giving access to rare and stable N ‐perfluoroalkyl triazoles. Azidoperfluoroalkanes are thermally stable and the efficiency of their preparation should be attractive for discovery programs.     

ATP Synthesis by Rotary Catalysis (Nobel lecture)

The cyclic modulation of nucleotide-binding properties of the three catalytic β subunits by a series of conformational changes was an attractive explanation for the postulated binding change mechanism of ATP synthase. In the crystal structure of the catalytic F₁ domain of this enzyme there is indeed a complex made up of three α subunits and three β subunits arranged in alternation around a central α-helical segment of the γ subunit. This complex is asymmetric owing to the different conformations of the β subunits. The change in conformation is brought about by rotation of the rigid yet curved segment, which has meanwhile been proven experimentally.     

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.     

Proton gradient energy in the catalytic ATP synthesis

ATP synthesis assisted by the F₁F₀-ATP synthase enzyme is considered in the context of chemical thermodynamics. It is shown that the proton gradient itself has no energy. For this reason, ATP synthesis with the participation of protons’ gradient has no privileges in comparison with direct ATP synthesis.     

Design,synthesis of (Z)‐3‐benzyl‐5‐((1‐phenyl‐3‐(3‐((1‐ substituted phenyl‐1H‐1,2,3‐triazol‐4‐yl)methoxy)phenyl)‐1H‐pyrazol‐4‐yl)methylene)thiazolidine‐2,4‐dione analogues as potential cytotoxic agents

In an attempt to achieve promising cytotoxic agents, a series of new (Z)‐3‐benzyl‐5‐((1‐phenyl‐3‐(3‐((1‐substituted phenyl‐1H‐1,2,3‐triazol‐4‐yl)methoxy)phenyl)‐1H‐pyrazol‐4‐yl)methylene)thiazolidine‐2,4‐diones 10 a‐n were designed, synthesized, and characterized by ¹H NMR, ¹³C NMR, IR, and ESI‐MS techniques. These compounds synthesized from appropriate reaction procedures with better yields. All the novel synthesized compounds 10a‐n were evaluated for their cytotoxic activity against the MCF‐7 cell line (Human breast cancer cell line) at different concentrations of 0.625, 1.25, 2.5, 5, and 10 μM, respectively. The cytotoxic evaluation assay is presented in terms of IC₅₀ values and percentage cell viability reduction compared against standard drug cisplatin. Among all novel synthesized compounds 10a‐n , some of the representative analogues particularly 10g and 10e exhibit remarkable cytotoxic activity with IC₅₀ values 0.454 and 0.586 μM, comparable to that of the standard drug cisplatin, and some analogues 10d , 10f , 10k, and 10m also have shown significant activity.     

Divergent Solid-Phase Synthesis and Biological Evaluation of Yaku'amide B and Its Seven E/Z Isomers

Yaku′amide B ( 1 ) inhibits cancer cell growth through a unique mechanism of action. Compound 1 binds to mitochondrial F_oF₁-ATP synthase, inhibits ATP production, and enhances ATP hydrolysis. The presence of one (E)- and two (Z)-α,β-dehydroisoleucines (ΔIle) in the linear 13-mer sequence is the most unusual structural feature of 1 . To uncover the biological importance of these residues, we synthesized 1 and its seven E/Z isomers 2 – 8 by devising a new divergent solid-phase strategy. Both the (E)- and (Z)-ΔIle residues were stereoselectively constructed by traceless Staudinger ligation on resin to ultimately deliver 1 – 8 . All isomers 2 – 8 displayed effects on the inhibition of cell growth and ATP production, and enhanced ATP hydrolysis, thus indicating that 2 – 8 share the same mode of action as 1 . The least potent isomer, 8 , was isomeric at three ΔIle residues of the most potent 1 . These findings together indicate that the E/Z stereochemistry of the three ΔIle residues controls the magnitude of the biological functions of 1 .     

Synthesis and conformational analysis of efrapeptins

The efrapeptin family of peptide antibiotics produced by the fungus Tolypocladium niveum, and the neo‐efrapeptins from the fungus Geotrichum candidumare inhibitors of F₁‐ATPase with promising antitumor, antimalaria, and insecticidal activity. They are rich in C^α‐dialkyl amino acids (Aib, Iva, Acc) and contain one β‐alanine and several pipecolic acid residues. The C‐terminus bears an unusual heterocyclic cationic cap. The efrapeptins C–G and three analogues of efrapeptin C were synthesized using α‐azido carboxylic acids as masked amino acid derivatives. All compounds display inhibitory activity toward F₁‐ATPase. The conformation in solution of the peptides was investigated with electronic CD spectroscopy, FT‐IR spectroscopy, and VCD spectroscopy. All efrapeptins and most efrapeptin analogues were shown to adopt helical conformations in solution. In the case of efrapeptin C, VCD spectra proved that a 3₁₀‐helix prevails. In addition, efrapeptin C was conformationally studied in detail with NMR and molecular modeling. Besides NOE distance restraints, residual dipolar couplings (RDC) observed upon partial alignment with stretched PDMS gels were used for the conformational analysis and confirmed the 3₁₀‐helical conformation.     

Photophysical Analysis of 1,10‐Phenanthroline‐Embedded Porphyrin Analogues and Their Magnesium(II) Complexes

The synthesis, characterization, photophysical properties, and theoretical analysis of a series of tetraaza porphyrin analogues ( H? Pn : n=1–4) containing a dipyrrin subunit and an embedded 1,10‐phenanthroline subunit are described. The meso‐phenyl‐substituted derivative ( H? P1 ) interacts with a Mg²⁺ salt (e.g., MgCl₂, MgBr₂, MgI₂, Mg(ClO₄)₂, and Mg(OAc)₂) in MeCN solution, thereby giving rise to a cation‐dependent red‐shift in both the absorbance‐ and emission maxima. In this system, as well as in the other H? Pn porphyrin analogues used in this study, the four nitrogen atoms of the ligand interact with the bound magnesium cation to form Mg²⁺–dipyrrin–phenanthroline complexes of the general structure MgX? Pn (X=counteranion). Both single‐crystal X‐ray diffraction analysis of the corresponding zinc‐chloride derivative ( ZnCl? P1 ) and fluorescence spectroscopy of the Mg‐adducts that are formed from various metal salts provide support for the conclusion that, in complexes such as MgCl? P1 , a distorted square‐pyramidal geometry persists about the metal cation wherein a chloride anion acts as an axial counteranion. Several analogues ( H? Pn ) that contain electron‐donating and/or electron‐withdrawing dipyrrin moieties were prepared in an effort to understand the structure–property relationships and the photophysical attributes of these Mg–dipyrrin complexes. Analysis of various MgX? Pn (X=anion) systems revealed significant substitution effects on their chemical, electrochemical, and photophysical properties, as well as on the Mg²⁺‐cation affinities. The fluorescence properties of MgCl? Pn reflected the effect of donor‐excited photoinduced electron transfer (d‐PET) processes from the dipyrrin subunit (as a donor site) to the 1,10‐phenanthroline acceptor subunit. The proposed d‐PET process was analyzed by electron paramagnetic resonance (EPR) spectroscopy and by femtosecond transient absorption (TA) spectroscopy, as well as by theoretical DFT calculations. Taken together, these studies provide support for the suggestion that a radical species is produced as the result of an intramolecular charge‐transfer process, following photoexcitation. These photophysical effects, combined with a mixed dipyrrin–phenanthroline structure that is capable of effective Mg²⁺‐cation complexation, lead us to suggest that porphyrin‐inspired systems, such as H? Pn , have a role to play as magnesium‐cation sensors.     

High Fluorine Content Bis(fluoro‐Ponytailed) Bipyridine Palladium Complexes as Catalyst for Mizoroki‐Heck Reactions under Fluorous Biphasic Catalysis Conditions

Two highly fluorinated bipyridine derivatives, (4,4′‐bis(R_fCH₂OCH₂)‐2,2′‐bpy) {R_f = n‐C₁₀F₂₁ ( 1a ), n‐C₁₀F₂₃ ( 1b )}, have been synthesized starting from 4,4′‐bis(BrCH₂)‐2,2′‐bpy and the corresponding fluorinated alkoxides. The fluorine contents of ligands 1a‐b are 62.3% and 63.3%, respectively, both being white solids, virtually insoluble in CH₂Cl₂ or DMF and highly fluorophilic with a partition ratio between DMF and n‐C₈F₁₈ less than 1:1000. The reaction of ligands 1a‐b with [Pd(CH₃CN)₂Cl₂] results in novel Pd complexes [PdCl₂(4,4′‐bis‐(R_fCH₂OCH₂)‐2,2′‐bpy)] where R_f = n‐C₁₀F₂₁ ( 2a ), n‐C₁₀F₂₃ ( 2b ), respectively. The Pd complexes 2a‐b are pale yellow solids, soluble only in fluorinated solvents. The Pd complexes 2a‐b have been satisfactorily tested for Mizoroki‐Heck arylation under fluorous biphasic catalysis conditions in that the Pd complexes 2a‐b are easily recovered and maintain good catalytic activity after 8 consecutive cycles (> 90% yield). The TGA studies indicate that the Pd complexes 2a‐b are thermally stable up to 300 °C.     

Functional Genome Mining Reveals a Class V Lanthipeptide Containing a d‐Amino Acid Introduced by an F420H2‐Dependent Reductase

Lantibiotics are a type of ribosomally synthesized and post‐translationally modified peptides (termed lanthipeptides) with often potent antimicrobial activity. Herein, we report the discovery of a new lantibiotic, lexapeptide, using the library expression analysis system (LEXAS) approach. Lexapeptide has rare structural modifications, including N‐terminal (N,N)‐dimethyl phenylalanine, C‐terminal (2‐aminovinyl)‐3‐methyl‐cysteine, and d ‐Ala. The characteristic lanthionine moiety in lexapeptide is formed by three proteins (LxmK, LxmX, and LxmY), which are distinct from enzymes known to be involved in lanthipeptide biosynthesis. Furthermore, a novel F₄₂₀H₂‐dependent reductase (LxmJ) from the lexapeptide biosynthetic gene cluster (BGC) is identified to catalyze the reduction of dehydroalanine to install d ‐Ala. Our findings suggest that lexapeptide is the founding member of a new class of lanthipeptides that we designate as class V. We also identified further class V lanthipeptide BGCs in actinomycetes and cyanobacteria genomes, implying that other class V lantibiotics await discovery.     

Reversible Shape‐Morphing and Fluorescence‐Switching in Supramolecular Nanomaterials Consisting of Amphiphilic Cyanostilbene and Cucurbit[7]uril

We demonstrate a reversible shape‐morphing with concurrent fluorescence switching in the nanomaterials which are complexed with cucurbit[7]uril (CB[7]) in water. The cyanostilbene derivative alone forms ribbon‐like two‐dimensional (2D) nanocrystals with bright yellow excimeric emission in water (λ_em=540 nm, Φ_F=42 %). Upon CB[7] addition, however, the ribbon‐like 2D nanocrystals immediately transform to spherical nanoparticles with significant fluorescence quenching and blue‐shifting (λ_em=490 nm, Φ_F=1 %) through the supramolecular complexation of the cyanostilbene and CB[7]. Based on this reversible fluorescence switching and shape morphing, we could demonstrate a novel strategy of turn‐on fluorescence sensing of spermine and also monitoring of lysine decarboxylase activity.     

Planarity of heteroaryldithiocarbazic acid derivatives showing tuberculostatic activity. III. Mono‐ and diesters of 3‐(pyrazin‐2‐ylcarbonyl)dithiocarbazic acid

Methyl 2‐(pyrazin‐2‐ylcarbonyl)hydrazinecarbodithioate, C₇H₈N₄OS₂, (E1), N′‐[bis(methylsulfanyl)methylidene]pyrazine‐2‐carbohydrazide, C₈H₁₀N₄OS₂, (F1), N′‐[bis(methylsulfanyl)methylidene]‐6‐methoxypyrazine‐2‐carbohydrazide, C₉H₁₂N₄O₂S₂, (F2), and methyl 1‐methyl‐2‐(pyrazin‐2‐ylcarbonyl)hydrazinecarbodithioate, C₈H₁₀N₄OS₂, (G1), can be considered as derivatives of classical (thio)amide‐type tuberculostatics, and all are moderately active against Mycobacterium tuberculosis. This study was undertaken in a search for relationships between activity and specific intramolecular interactions, especially conjugations and hydrogen‐bond contacts, and the molecular structures were compared with respective amine analogues, also active against the pathogen. Despite the differences between the amine and carbonyl groups with opposite functions in the hydrogen bond, the two types of structure show a surprisingly similar planar geometry, mostly due to the conjugations aided by the bifurcated intramolecular hydrogen‐bond contact between the N—H group of the central hydrazide group as donor and a pyrazine N atom and an S atom of the dithio function as acceptors. Planarity was suggested to be crucial for the tuberculostatic activity of these compounds. The N‐methylated derivative (G1) showed a significant twist at the N—N bond [torsion angle = −121.9 (3)°] due to the methyl substitution, which precludes an intramolecular N—H...S contact and the planarity of the whole molecule. Nonetheless, the compound shows moderate tuberculostatic activity.     

Polymorphic phase transformations of 3‐chloro‐trans‐cinnamic acid and its solid solution with 3‐bromo‐trans‐cinnamic acid

We have investigated the polymorphic phase transformations above ambient temperature for 3‐chloro‐trans‐cinnamic acid (3‐ClCA, C₉H₇ClO₂) and a solid solution of 3‐ClCA and 3‐bromo‐trans‐cinnamic acid (3‐BrCA, C₉H₇BrO₂). At 413 K, the γ polymorph of 3‐ClCA transforms to the β polymorph. Interestingly, the structure of the β polymorph of 3‐ClCA obtained in this transformation is different from the structure of the β polymorph of 3‐BrCA obtained in the corresponding polymorphic transformation from the γ polymorph of 3‐BrCA, even though the γ polymorphs of 3‐ClCA and 3‐BrCA are isostructural. We also report a high‐temperature phase transformation from a γ‐type structure to a β‐type structure for a solid solution of 3‐ClCA and 3‐BrCA (with a molar ratio close to 1:1). The γ polymorph of the solid solution is isostructural with the γ polymorphs of pure 3‐ClCA and pure 3‐BrCA, while the β‐type structure produced in the phase transformation is structurally similar to the β polymorph of pure 3‐BrCA.     

A Chromium(III)‐Superoxo Complex as a Three‐Electron Oxidant with a Large Tunneling Effect in Multi‐Electron Oxidation of NADH Analogues

Metal‐superoxo species are involved in a variety of enzymatic oxidation reactions, and multi‐electron oxidation of substrates is frequently observed in those enzymatic reactions. A Cr^III‐superoxo complex, [Cr^III(O₂)(TMC)(Cl)]⁺ ( 1 ; TMC=1,4,8,11‐tetramethyl‐1,4,8,11‐tetraazacyclotetradecane), is described that acts as a novel three‐electron oxidant in the oxidation of dihydronicotinamide adenine dinucleotide (NADH) analogues. In the reactions of 1 with NADH analogues, a Cr^IV‐oxo complex, [Cr^IV(O)(TMC)(Cl)]⁺ ( 2 ), is formed by a heterolytic O−O bond cleavage of a putative Cr^II‐hydroperoxo complex, [Cr^II(OOH)(TMC)(Cl)], which is generated by hydride transfer from NADH analogues to 1 . The comparison of the reactivity of NADH analogues with 1 and p ‐chloranil (Cl₄Q) indicates that oxidation of NADH analogues by 1 proceeds by proton‐coupled electron transfer with a very large tunneling effect (for example, with a kinetic isotope effect of 470 at 233 K), followed by rapid electron transfer.     

Novel Symmetrical trans‐Bis‐Schiff Bases of N‐Substituted‐4‐ piperidones: Synthesis,Characterization, and Preliminary Antileukemia Activity Mensurations

A series of novel symmetrical trans‐bis‐Schiff bases ( 11a , 11b , 11c , 11d , 11e , 11f , 11g , 11h , 11i , 11j , 11k , 11l , 11m ) were designed and prepared as novel anticancer analogues, with the trans‐configuration confirmed by X‐ray diffraction. Preliminary inhibitory effects of these compounds on CML K562 cell growth were investigated, and the potential analogue 11e showed an excellent anti‐leukemia activity (IC₅₀=6.35 μg/mL), which is higher than that of the clinical drug 5‐fluorouracil (IC₅₀=8.48 μg/mL). Complete assignments had been achieved for the title compounds by spectroscopic techniques, and their structure–activity relationships have been studied.