Live-cell biosensors based on the fluorescence lifetime of environment-sensing dyes.

In this work, we examine the use of environment-sensitive fluorescent dyes in fluorescence lifetime imaging microscopy (FLIM) biosensors. We screened merocyanine dyes to find an optimal combination of environment-induced lifetime changes, photostability, and brightness at wavelengths suitable for live-cell imaging. FLIM was used to monitor a biosensor reporting conformational changes of endogenous Cdc42 in living cells. The ability to quantify activity using phasor analysis of a single fluorophore (e.g., rather than ratio imaging) eliminated potential artifacts. We leveraged these properties to determine specific concentrations of activated Cdc42 across the cell.

Design, dynamic docking, synthesis, and in vitro validation of a novel DNA gyrase B inhibitor.

Methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-intermediate-resistant Staphylococcus aureus (VRSA) are among the WHO's high priority pathogens. Among these two, MRSA is the most globally documented pathogen that necessitates the pressing demand for new classes of anti-MRSA drugs. Bacterial gyrase targeted therapeutics are unique strategies to overcome cross-resistance as they are present only in bacteria and absent in higher eukaryotes. The GyrB subunit is essential for the catalytic functions of the bacterial enzyme DNA Gyrase, thereby constituting a promising druggable target. The current study performed a structure-based virtual screening to designing GyrB target-specific candidate molecules. The de novo ligand design of novel hit molecules was performed using a rhodanine scaffold. Through a systematic in silico screening process, the hit molecules were screened for their synthetic accessibility, drug-likeness and pharmacokinetics properties in addition to its target specific interactions. Of the 374 hit molecules obtained through de novo ligand design, qsl-304 emerged as the most promising ligand. The molecular dynamic simulation studies confirmed the stable interaction between the key residues and qsl-304. qsl-304 was synthesized through a one-step chemical synthesis procedure, and the in vitro activity was proven, with an IC50 of 31.23 µg/mL against the novobiocin resistant clinical isolate, Staphylococcus aureus sa-P2003. Further studies on time-kill kinetics showed the bacteriostatic nature with the diminished recurrence of resistance. The on-target gyrB inhibition further proved the efficacy of qsl-304.Communicated by Ramaswamy H. Sarma.

Why an integrated approach between search algorithms and chemical intuition is necessary?

Though search algorithms are appropriate tools for identifying low-energy isomers, fixing several constraints seems to be a fundamental prerequisite to successfully running any structural search program. This causes some potential setbacks as far as identifying all possible isomers, close to the lowest-energy isomer, for any elemental composition. The number of explored candidates, the choice of method, basis set, and availability of CPU time needed to analyze the various initial test structures become necessary restrictions in resolving the issues of structural isomerism reasonably. While one could arrive at new structures through chemical intuition, reproducing or achieving those exact same structures requires increasing the number of variables in any given program, which causes further constraints in exploring the potential energy surface in a reasonable amount of time. Thus, it is emphasized here that an integrated approach between search algorithms and chemical intuition is necessary by taking the C12O2Mg2 system as an example. Our initial search through the AUTOMATON program yielded 1450 different geometries. However, through chemical intuition, we found eighteen new geometries within 40.0 kcal mol-1 at the PBE0-D3/def2-TZVP level. These results indirectly emphasize that an integrated approach between search algorithms and chemical intuition is necessary to further our knowledge in chemical space for any given elemental composition.

Development of an Antibiotic Resistance Breaker to Resensitize Drug-Resistant Staphylococcus aureus: In Silico and In Vitro Approach.

Efflux pumps are one of the predominant microbial resistant mechanisms leading to the development of multidrug resistance. In Staphylococcus aureus, overexpression of NorA protein enables the efflux of antibiotics belonging to the class of fluoroquinolones and, thus, makes S. aureus resistant. Hence, NorA efflux pumps are being extensively exploited as the potential drug target to evade bacterial resistance and resensitize bacteria to the existing antibiotics. Although several molecules are reported to inhibit NorA efflux pump effectively, boronic acid derivatives were shown to have promising NorA efflux pump inhibition. In this regard, the current study exploits 6-(3-phenylpropoxy)pyridine-3-boronic acid to further improve the activity and reduce cytotoxicity using the bioisostere approach, a classical medicinal chemistry concept. Using the SWISS-Bioisostere online tool, from the parent compound, 42 compounds were obtained upon the replacement of the boronic acid. The 42 compounds were docked with modeled NorA protein, and key molecular interactions of the prominent compounds were assessed. The top hit compounds were further analyzed for their drug-like properties using ADMET studies. The identified potent lead, 5-nitro-2-(3-phenylpropoxy)pyridine (5-NPPP), was synthesized, and in vitro efficacy studies have been proven to show enhanced efflux inhibition, thus acting as a potent antibiotic breaker to resensitize S. aureus without elucidating any cytotoxic effect to the host Hep-G2 cell lines.

MgC6H2 Isomers: Potential Candidates for Laboratory and Radioastronomical Studies.

Eighty three stationary points of MgC6H2 isomers spanning from 0 to 215 kcal mol-1 have been theoretically identified using density functional theory at the B3LYP/6-311++G(2d,2p) level of theory. Among them, four low-lying isomers lying within 23.06 kcal mol-1 (1 eV) have been further characterized in detail using high-level coupled-cluster (CC) methods. The thermodynamically most stable isomer turns out to be 1-magnesacyclohepta-4-en-2,6-diyne (1). The other three isomers, 3-magnesahepta-1,4,6-triyne (2), 1-magnesacyclohepta-2,3,4-trien-6-yne (3), and 1-magnesahepta-2,4,6-triyne (4) lie 8.24, 19.76, and 21.36 kcal mol-1, respectively, above 1 at the ae-CCSD(T)/cc-pCVTZ level of theory. All the four isomers are polar with a permanent electric dipole moment (µ ≠ 0). Hence, they are potential candidates for rotational spectroscopic studies. Considering the recent identification of magnesium-bearing hydrocarbons such as, MgC2H and MgC4H in IRC+10216, it is believed that the current theoretical data may be of relevance to laboratory molecular spectroscopic and radioastronomical studies on MgC6H2 isomers. The energetic and spectroscopic information gathered in this study would aid the detection of low-lying MgC6H2 isomers in the laboratory, which are indispensable for radioastronomical studies. It is also noted here that neither the National Institute of Standards and Technology Chemistry WebBook nor the Kinetic Database for Astrochemistry lists any isomer of MgC6H2 at the moment. Therefore, these isomers are studied here theoretically for the very first time.

Amyloid-like Nanofibrillation of Metal-Organic Complex Arrays Ruled by Their Precisely Designed Metal Sequences.

Self-assembly of a series of dimetallic sequences constructed on a backbone with two successive tyrosine moieties (Fmoc-M1 -M2 -CO2 H) revealed that the resultant morphology is clearly dependent on the metal sequence, where Re-containing sequences such as homometallic Fmoc-Re-Re-CO2 H specifically afforded amyloid-like nanofibers. These findings further allowed to achieve the fibrillation of a longer metal sequence containing three different metals (Fmoc-Rh-Pt-Re-Re-CO2 H). Cyclic voltammetry of the fibrillated Fmoc-Re-Re-CO2 H demonstrated that the redox activity of the metal complexes in the sequence is preserved in the nanofibrous forms.

5-Hydroxymethylfurfural-Derived Boron-Dipyrromethene Immobilized on Resin Support as a Sustainable Catalyst for C-H Arylation of Heterocycles.

5-Hydroxymethylfurfural (HMF) was used as a sustainable raw material in the development of a resin-supported boron-dipyrromethene (BODIPY)-based photocatalyst. In the development of the catalyst, the brominated product (HMF-BODIPY-Br) and photocatalyst (HMF-BODIPY-Br-Suc) were isolated under a chromatography-free condition. The photocatalyst was loaded on polymeric resin by bridging alcohol functionality in HMF and amine functionality in polymeric resin using succinic anhydride. The resin-supported photocatalyst was used in light-mediated C-H arylation of various heterocycles using aryldiazonium salt. For representative examples, diazotization and photoarylation were carried out in one pot, and arylated furans were obtained in very good yields. C-H arylation was found to proceed via a photogenerated radical intermediate, and the radical intermediate was trapped by forming an adduct with TEMPO.

Simple admixture of 4-nitrobenzaldehyde and 2,4-dimethylpyrrole for efficient colorimetric sensing of copper(II) ions.

An easily accessible chemo-probe based on physical mixture of 2,4-dimethylpyrrole and 4-nitrobenzaldehyde has been developed. Based on NMR spectroscopic analysis, catalyst free formation of dipyrromethane was observed in the physical mixture of chemo-probe. The probe is utilized in effective colorimetric sensing of copper(II) ions present in environmental solutions by instantaneous appearance of red colour, even in the co-existence of various metal ions. The lowest detection limit of 2.51 µM for this chemo-probe towards copper(II) sensing is significantly lower than the WHO prescribed level (<30 µM of copper(II) ions) in potable water. The sensing mechanism is explained via rapid formation of bis(dipyrrinato)copper(II) complex, as confirmed by Jobs plot, UV-Vis spectroscopy and IR spectroscopy.

A Glutathione-Responsive Short Sequence of Metal-Organic Complex Array.

A short metal-organic complex array (MOCA) containing a sequence of RPtRRu (1Cl ) was found to exhibit unique responses to a major biothiol, glutathione (GSH). Upon binding of GSH to 1Cl , the resultant 1:1 complex (1GS ) formed nanofibrous assemblies that suggested supramolecular polymerization through the double-salt-bridge structure formation. The binding behavior of this MOCA sequence to calf thymus DNA was also dependent on GSH; a larger conformational change of DNA was observed upon binding with 1GS , relative to that with 1Cl .

TfOH mediated intermolecular electrocyclization for the synthesis of pyrazolines and its application in alkaloid synthesis.

TfOH mediated easy access to interesting pyrazolines starting from an aldehyde, phenylhydrazine and styrene has been developed. The scope of this synthetic methodology has been explored by synthesizing various 1,3,5-trisubstituted pyrazolines in very good yields with very high regioselectivity. The origin of regioselectivity has been explained by comparing the stability of possible intermediate carbocations. The synthetic utility of a green solvent has been explored by synthesizing some of pyrazolines in a DES medium. The synthetic application of the present methodology is employed in the synthesis of a pyrazoline alkaloid.

C-H oxidation and chelation of a dipyrromethane mediated rapid colorimetric naked-eye Cu(ii) chemosensor.

Copper(ii) ion mediated C-H oxidation of dipyrromethanes (DPMs) to the corresponding dipyrrins followed by complexation invoked the selective sensing of copper(ii) ions in aqueous solutions. On the addition of copper, the colour of the DPM solution instantaneously changes from yellow to pink with the detection limit of 0.104 µM measured by absorption spectroscopy, whereas visible colour changes could be observed by the naked eye for concentrations as low as 3 µM.

Copper-coordination polymer-controlled Cu@N-rGO and CuO@C nanoparticle formation: reusable green catalyst for A3-coupling and nitroarene-reduction reactions.

The intriguing structural properties of coordination polymers (COPs), together with the huge variety of metal ions and organic linkers to choose from, make COPs potential precursors for fabricating carbon-encapsulated metal and metal oxide nanoparticles (NPs). Herein, we have studied the role of the COP structural assembly, prepared through making subtle changes to the ligand structure, on the formation of NPs in a carbon matrix. Cu-COPs (Cu-COP-1-Cu-COP-7), generated using different amino acid-based reduced Schiff base phenolic chelating ligands, exhibited crystalline structures with differing structural organization in the solid state. Interestingly, the calcination of Cu-COP-1 and Cu-COP-5 at 330 °C produced pure CuNPs, whereas Cu-COP-2, Cu-COP-3, Cu-COP-4 and Cu-COP-7 gave CuONPs encapsulated by carbon matrix. The calcination of Cu-COP-6 produced both CuNPs and CuONPs together in the carbon matrix. The formation of CuNPs and CuONPs in the carbon matrices was unambiguously confirmed by PXRD and XPS studies. The sizes and morphologies of the Cu/CuONPs were analyzed using HR-TEM and FE-SEM. BET studies revealed higher surface areas with small pores for the CuNPs encapsulated by carbon and lower surface areas with higher porosity for the CuONP-carbon matrix. Raman spectra revealed the formation of a nitrogen-doped reduced graphene oxide (N-rGO) carbon matrix in CuNPs-1. The N-rGO coverage and high surface area with small pores provided CuNPs-1 with good stability in strong acid (10 M H2SO4). Importantly, the fabricated N-rGO-encapsulated CuNPs-1 and carbon-covered CuONPs-4 nanocomposites were used as green catalysts in solvent-free neat A3-coupling and nitroarene-reduction reactions, respectively. The products were confirmed using 1H-NMR spectra. The recovered CuNPs-1 and CuONPs-4 catalysts, after the completion of the reactions, also showed similar catalytic activity at up to five cycles, without significant loss of catalytic activity. Thus, the present studies demonstrate the influence of Cu-COP structural assembly on the formation of Cu/CuONPs as well as the carbon matrix, and open the possibility of fabricating functional nanomaterials from the vast number of available COPs with intriguing structural motifs.

Staphylococcus aureus Quorum Regulator SarA Targeted Compound, 2-[(Methylamino)methyl]phenol Inhibits Biofilm and Down-Regulates Virulence Genes.

Staphylococcus aureus is a widely acknowledged Gram-positive pathogen for forming biofilm and virulence gene expressions by quorum sensing (QS), a cell to cell communication process. The quorum regulator SarA of S. aureus up-regulates the expression of many virulence factors including biofilm formation to mediate pathogenesis and evasion of the host immune system in the late phases of growth. Thus, inhibiting the production or blocking SarA protein might influence the down-regulation of biofilm and virulence factors. In this context, here we have synthesized 2-[(Methylamino)methyl]phenol, which was specifically targeted toward the quorum regulator SarA through in silico approach in our previous study. The molecule has been evaluated in vitro to validate its antibiofilm activity against clinical S. aureus strains. In addition, antivirulence properties of the inhibitor were confirmed with the observation of a significant reduction in the expression of representative virulence genes like fnbA, hla and hld that are governed under S. aureus QS. Interestingly, the SarA targeted inhibitor showed negligible antimicrobial activity and markedly reduced the minimum inhibitory concentration of conventional antibiotics when used in combination making it a more attractive lead for further clinical tests.

Self-Assembled Light-Harvesting System from Chromophores in Lipid Vesicles.

Lipid vesicles are used as the organizational structure of self-assembled light-harvesting systems. Following analysis of 17 chromophores, six were selected for inclusion in vesicle-based antennas. The complementary absorption features of the chromophores span the near-ultraviolet, visible, and near-infrared region. Although the overall concentration of the pigments is low (~1 µM for quantitative spectroscopic studies) in a cuvette, the lipid-vesicle system affords high concentration (≥10 mM) in the bilayer for efficient energy flow from donor to acceptor. Energy transfer was characterized in 13 representative binary mixtures using static techniques (fluorescence-excitation versus absorptance spectra, quenching of donor fluorescence, modeling emission spectra of a mixture versus components) and time-resolved spectroscopy (fluorescence, ultrafast absorption). Binary donor-acceptor systems that employ a boron-dipyrrin donor (S0 ↔ S1 absorption/emission in the blue-green) and a chlorin or bacteriochlorin acceptor (S0 ↔ S1 absorption/emission in the red or near-infrared) have an average excitation-energy-transfer efficiency (ΦEET) of ~50%. Binary systems with a chlorin donor and a chlorin or bacteriochlorin acceptor have ΦEET ∼ 85%. The differences in ΦEET generally track the donor-fluorescence/acceptor-absorption spectral overlap within a dipole-dipole coupling (Förster) mechanism. Substantial deviation from single-exponential decay of the excited donor (due to the dispersion of donor-acceptor distances) is expected and observed. The time profiles and resulting ΦEET are modeled on the basis of (Förster) energy transfer between chromophores relatively densely packed in a two-dimensional compartment. Initial studies of two ternary and one quaternary combination of chromophores show the enhanced spectral coverage and energy-transfer efficacy expected on the basis of the binary systems. Collectively, this approach may provide one of the simplest designs for self-assembled light-harvesting systems that afford broad solar collection and efficient energy transfer.

Extending the short and long wavelength limits of bacteriochlorin near-infrared absorption via dioxo- and bisimide-functionalization.

Six new bacteriochlorins expanding the range of the strong near-infrared (NIR) absorption (Qy band) to both shorter and longer wavelengths (∼690 to ∼900 nm) have been synthesized and characterized. The architectures include bacteriochlorin-bisimides that have six-membered imide rings spanning the 3,5- and 13,15-macrocycle positions or five-membered imide rings spanning the ß-pyrrolic 2,3- and 12,13-positions. Both bisimide types absorb at significantly longer wavelength than the bacteriochlorin precursors (no fused rings), whereas oxo-groups at the 7- or 7,17-positions shift the Qy band to a new short wavelength limit. Surprisingly, bacteriochlorin-bisimides with five-membered ß-pyrrolic-centered imide rings have a Qy band closer to that of six-membered bacteriochlorin-monoimides. However, the five-membered bisimides (versus the six-membered bacteriochlorin-monoimides) have significantly enhanced absorption intensity that is paralleled by an ∼2-fold higher fluorescence yield (∼0.16 vs ∼0.07) and longer singlet excited-state lifetime (∼4 ns vs ∼2 ns). The photophysical enhancements derive in part from mixing of the lowest unoccupied frontier molecular orbitals of the five-membered imide ring with those of the bacteriochlorin framework. In general, all of the new bacteriochlorins have excited-state lifetimes (1-4 ns) that are sufficiently long for use in molecular-based systems for photochemical applications.

Diblock copolymer micelles and supported films with noncovalently incorporated chromophores: a modular platform for efficient energy transfer.

We report generation of modular, artificial light-harvesting assemblies where an amphiphilic diblock copolymer, poly(ethylene oxide)-block-poly(butadiene), serves as the framework for noncovalent organization of BODIPY-based energy donor and bacteriochlorin-based energy acceptor chromophores. The assemblies are adaptive and form well-defined micelles in aqueous solution and high-quality monolayer and bilayer films on solid supports, with the latter showing greater than 90% energy transfer efficiency. This study lays the groundwork for further development of modular, polymer-based materials for light harvesting and other photonic applications.

Enhanced light-harvesting capacity by micellar assembly of free accessory chromophores and LH1-like antennas.

Biohybrid light-harvesting antennas are an emerging platform technology with versatile tailorability for solar-energy conversion. These systems combine the proven peptide scaffold unit utilized for light harvesting by purple photosynthetic bacteria with attached synthetic chromophores to extend solar coverage beyond that of the natural systems. Herein, synthetic unattached chromophores are employed that partition into the organized milieu (e.g. detergent micelles) that house the LH1-like biohybrid architectures. The synthetic chromophores include a hydrophobic boron-dipyrrin dye (A1) and an amphiphilic bacteriochlorin (A2), which transfer energy with reasonable efficiency to the bacteriochlorophyll acceptor array (B875) of the LH1-like cyclic oligomers. The energy-transfer efficiencies are markedly increased upon covalent attachment of a bacteriochlorin (B1 or B2) to the peptide scaffold, where the latter likely acts as an energy-transfer relay site for the (potentially diffusing) free chromophores. The efficiencies are consistent with a Förster (through-space) mechanism for energy transfer. The overall energy-transfer efficiency from the free chromophores via the relay to the target site can approach those obtained previously by relay-assisted energy transfer from chromophores attached at distant sites on the peptides. Thus, the use of free accessory chromophores affords a simple design to enhance the overall light-harvesting capacity of biohybrid LH1-like architectures.

Hydrophilic tetracarboxy bacteriochlorins for photonics applications.

Bacteriochlorins absorb strongly in the near-infrared (NIR, 700-900 nm) region and hence are well suited for photophysical studies and photomedical applications, yet such endeavors heretofore have been largely limited by the intrinsic lipophilicity of the bacteriochlorin macrocycle. Here, a new molecular design is investigated wherein 3,5-dicarboxyphenyl units are appended to the ß-pyrrolic positions of the bacteriochlorin. Use of the 3,5-aryl substitution motif places the carboxylic acid groups, which are anionic at neutral pH, above and below the plane of the bacteriochlorin macrocycle. A de novo synthesis has been employed to create five such bacteriochlorins, which uses as intermediates two new 2,12-dibromobacteriochlorin building blocks and a known 3,13-dibromobacteriochlorin. The aryl groups with protected carboxylate moieties were introduced by Suzuki coupling; subsequent deprotection afforded the hydrophilic bacteriochlorins. The latter were characterized by absorption and fluorescence spectroscopy in DMF and in aqueous phosphate buffer (pH 7). In most cases, comparable sharp emission (FWHM of ∼25 nm) and modest fluorescence yields (0.060-0.11) were observed in aqueous phosphate buffer medium and in DMF. Aqueous solubility was examined by absorption spectral interrogation of samples over a 1000-fold concentration range with reciprocal change in pathlength (∼0.5, 5, 50, and 500 µM; 10, 1, 0.1, and 0.01 cm pathlength cuvettes). One hydrophilic bacteriochlorin was prepared that contains a single maleimido-terminated tether for bioconjugation; the tether was installed by the sequence of 15-bromination of the bacteriochlorin, Suzuki coupling, and DCC-mediated amide formation. The maleimido-bacteriochlorin was conjugated to a 48-residue cysteine-containing peptide analogue of a constituent from a bacterial photosynthetic light-harvesting complex. Taken together, the results show a new molecular design and facile de novo synthetic route for obtaining hydrophilic bacteriochlorins including a bioconjugatable group if desired.

Convenient methods for the synthesis of chiral amino alcohols and amines.

Simple, convenient methods have been developed using readily available, easy-to-handle reagents to access a variety of chiral amino alcohols and amines, which have considerable potential for applications in asymmetric organic transformations. Scholars from this laboratory in India have made significant contributions to this field, which is the subject of the current review.

Synthesis of metal−organic complex arrays.

The Merrifield solid-phase peptide synthesis technique has been adapted to the synthesis of homo- and heterometallic metal−organic complex arrays (MOCAs). A terpyridine-appended and Fmoc-protected L-tyrosine derivative was metalated with Pt(II), Rh(III), or Ru(II) ions in solution and sequentially coupled at the surface of functionalized polymeric resin to give a metal complex triad (Rh−Pt−Ru), tetrad (Ru−Rh−Pt−Pt), pentad (Rh−Pt−Ru−Pt−Rh), and hexad (Rh−Pt−Ru−Pt−Rh−Pt) with specific metal sequence arrangements. These were cleaved from the resin, and their character was confirmed by mass spectrometry.