Essential Functional Groups Research Articles

PHYTOCHEMICAL SCREENING, ELEMENTAL AND FUNCTIONAL GROUP ANALYSIS OF VITEX NEGUNDO L. LEAVES

Objective: To analyse elemental profile, evaluate functional groups and find out phytochemical constituents of Vitex negundo L. leaves.Methods: Determination of primary and secondary metabolites for various extracts by qualitative methods. Elemental analysis was carried out by using inductively coupled plasma mass spectrometry (ICP-MS) technique and the functional groups have been determined by using Fourier Transform Infrared Spectroscopy (FTIR) technique.Results: Soluble extractive percentage of material has been found the maximum in the aqueous extract (6.75%) followed by methanolic extract (4.35%) and acetone extract (1.8%). Phytochemical screening of material revealed the presence of carbohydrates, proteins, amino acids, steroids, cardiac and anthraquinone glycosides, saponins, flavonoids, tannins and phenolic compounds. The elemental analysis revealed Na, Mg, K, Ca, Cr, Mn, Fe, Co, Cu, Zn, Se, Mo, Li, B, Al, P, Cd, As, Ba, and Hg. FTIR technique was used to identify various functional groups present in three different extracts of the material.Conclusion: The phytochemical screening of three different extracts of the material showed the presence of most of the primary and secondary metabolites in aqueous and methanolic extract than acetone extract. The soluble extractive value was found the maximum in aqueous extract hence aqueous extract is most effective for studying the pharmacological activity of this plant. Elemental analysis showed the presence of trace elements in sufficient concentrations and traces of heavy and toxic metals. The FTIR study revealed the presence of essential functional groups in three different extracts of the material. The present investigation is most essential to discover innovative, dynamic and novel drugs for curing various newly emerged dangerous health problems.

Synthesis and evaluation of phenylisoserine derivatives for the SARS-CoV 3CL protease inhibitor

Synthesis and evaluation of new scaffold phenylisoserine derivatives connected with the essential functional groups against SARS CoV 3CL protease are described. The phenylisoserine backbone was found by simulation on GOLD software and the structure activity relationship study of phenylisoserine derivatives gave SK80 with an IC50 value of 43μM against SARS CoV 3CL R188I mutant protease.

Novel 4-thiazolidinone derivatives as agonists of benzodiazepine receptors: Design, synthesis and pharmacological evaluation.

A new series of 4-chloro-N-(2-(substitutedphenyl)-4-oxothiazolidin-3-yl)-2-phenoxybenzamide derivatives were designed, synthesized and biologically evaluated as anticonvulsant agents. The designed compounds have the main essential functional groups for binding to the benzodiazepine receptors and 4-thiazolidinone ring as an anticonvulsant pharmacophore. Some of the new synthesized compounds showed considerable anticonvulsant activity in electroshock and pentylenetetrazole-induced lethal convulsion tests. Compound 5i, 4-chloro-N-(2-(4-methoxyphenyl)-4-oxothiazolidin-3-yl)-2-phenoxybenzamide, with the best activity was selected for evaluation of other benzodiazepine pharmacological effects. This compound induced significant sedative-hypnotic activity. However, it does not impair the learning and memory in the experimental condition. Flumazenil was able to antagonize the sedative-hypnotic and anticonvulsant effects of compound 5i indicating that benzodiazepine receptors are highly involved in the pharmacological properties of the novel compounds.

Investigation on the optical, mechanical and magnetic properties of organic NLO single crystal: Pyridine 3-carboxylic acid

An organic nonlinear optical (NLO) single crystal of Pyridine 3-carboxylic acid, which has potential application in a variety of fields was grown by solution growth technique. The single crystal X-ray diffraction analysis confirms that the grown crystals possess lattice parameters of monoclinic system of space group (P21/c). The Fourier transform infrared (FTIR) study provides the evidence for the presence of essential functional groups in Pyridine 3-carboxylic acid single crystal. The optical parameters such as transmittance, absorption coefficient, refractive index and optical band gap of the grown crystals were obtained using ultraviolet visible (UV-Vis-NIR) spectroscopy. The red luminescence behavior and Second Harmonic generation (SHG) efficiency were measured. The soft ferromagnetic nature of the grown sample was ascertained from vibrational sample magnetometer analyses. In addition, the mechanical property was also examined.

Intercalated network of graphene oxide (GO)–CuO–polythiophene (PTh) hybrid nanocomposite for photocatalytic applications

This work aims in designing intercalated structure based carbon (Graphene oxide) photocatalytic nanocomposite integrating polythiophene (PTh) and cupric oxide, Graphene oxide serving the purpose of conducting electrons, PTh performing the dual role of donor and hole conducting layer. This nanocomposite was synthesized by aqueous chemical method. Structural properties of the nanocomposite were studied by XRD which shows good crystallinity. FTIR and RAMAN shifts confirm the presence of essential functional groups of each element in the nanocomposite. The optical study assures good absorbance in the UV–VIS region notably in the UV-C region. Morphological characterizations were studied by SEM and TEM analysis which shows a well ordered interconnecting network for the movement of excitons. The nanocomposite has a hydrogen production rate of 205.16 μmol h−1 showing quantum efficiency of 12.96 %, degradation efficiency of MB by 83.15 % and shows better UV-shielding property.

Selective membrane disruption by the cyclotide kalata B7: complex ions and essential functional groups in the phosphatidylethanolamine binding pocket

The cyclic cystine knot plant peptides called cyclotides are active against a wide variety of organisms. This is primarily achieved through membrane binding and disruption, in part deriving from a high affinity for phosphatidylethanolamine (PE) lipids. Some cyclotides, such as kalata B7 (kB7), form complexes with divalent cations in a pocket associated with the tyrosine residue at position 15 (Tyr15). In the current work we explore the effect of cations on membrane leakage caused by cyclotides kB1, kB2 and kB7, and we identify a functional group that is essential for PE selectivity. The presence of PE-lipids in liposomes increased the membrane permeabilizing potency of the cyclotides, with the potency of kB7 increasing by as much as 740-fold. The divalent cations Mn2+, Mg2+ and Ca2+ had no apparent effect on PE selectivity. However, amino acid substitutions in kB7 proved that Tyr15 is crucial for PE-selective membrane permeabilization on various liposome systems. Although the tertiary structure of kB7 was maintained, as reflected by the NMR solution structure, mutating Tyr into Ser at position 15 resulted in substantially reduced PE selectivity. Ala substitution at the same position produced a similar reduction in PE selectivity, while substitution with Phe maintained high selectivity. We conclude that the phenyl ring in Tyr15 is critical for the high PE selectivity of kB7. Our results suggest that PE-binding and divalent cation coordination occur in the same pocket without adverse effects of competitive binding for the phospholipid.

Design and synthesis of a series of serine derivatives as small molecule inhibitors of the SARS coronavirus 3CL protease

Synthesis of serine derivatives having the essential functional groups for the inhibitor of SARS 3CL protease and evaluation of their inhibitory activities using SARS 3CL R188I mutant protease are described. The lead compounds, functionalized serine derivatives, were designed based on the tetrapeptide aldehyde and Bai’s cinnamoly inhibitor, and additionally performed with simulation on GOLD softwear. Structure activity relationship studies of the candidate compounds were given reasonable inhibitors ent-3 and ent-7k against SARS 3CL R188I mutant protease. These inhibitors showed protease selectivity and no cytotoxicity.

Evaluation as antioxidant agents of 1,2,4-triazole derivatives: effects of essential functional groups

Swine Flu: An OverviewPriyanka Lokwani, Pramod Kumar, Yozana Upadhyay, Stuti Gupta, Renu Solanki, Nisha Singh

Tailoring Peptidomimetics for Targeting Protein–Protein Interactions

Protein-protein interactions (PPI) are a hallmark of cellular signaling. Such interactions occur abundantly within the cellular milieu and encompass interactions involved in vital cellular processes. Understanding the various types, mechanisms, and consequences of PPIs with respect to cellular signaling and function is vital for targeted drug therapy. Various types of small-molecule drugs and targeted approaches to drug design have been developed to modulate PPIs. Peptidomimetics offer an exciting class of therapeutics as they can be designed to target specific PPIs by mimicking key recognition motifs found at critical points in the interface of PPIs (e.g., hotspots). In contrast to peptides, peptidomimetics do not possess a natural peptide backbone structure but present essential functional groups in a required three-dimensional pattern complimentary to the protein-binding pocket. This design feature overcomes many limitations of peptide therapeutics including limited stability toward peptidases, poor transport across biologic membranes, and poor target specificity. Equally important is deciphering the structural requirements and amino acid residues critical to PPIs. This review provides an up-to-date perspective of the complexity of cellular signaling and strategies for targeting PPIs in disease states, particularly in cancer, using peptidomimetics, and highlights that the rational design of agents that target PPIs is not only feasible but is of the utmost clinical importance.

Effect of Various Pretreatment for Extracting Intracellular Lipid fromNannochloropsis oculataunder Nitrogen Replete and Depleted Conditions

Microalga is one of the most compelling microbial biomasses for biodiesel production. Various pretreatment processes, namely, enzyme treatment, lysis by acid, ultrasonicator, microwaves, autoclave, and 40% NaCl, for nitrogen replete and depleted algal cultures ofNannochloropsis oculatahad been carried out to check the most feasible and effective technique to disrupt cells for procuring lipids, for which concentrations were determined. Fatty acid composition, essential functional groups, and cell disruption were analyzed by GC-MS, FT-IR Spectroscopy, and Nile Red fluorescent microscopy, respectively. The present investigation showed that lipid yield was higher in nitrogen depleted cells than that in normally nourished cells. GC-MS revealed the presence of major fatty acids—palmitic, oleic, stearic, arachidic, lauric, and linoleic acids. Highest efficiency was found when cells were pretreated using acid for 3 h. The lipid content was calculated as 33.18% and 54.26% for nitrogen rich cells and nitrogen starved cells, respectively. This work thus aided in identifying the most eligible pretreatment process to avail lipids from cells, to convert them to eco-friendly and nonpolluting biodiesel.

Investigation of chemical modifications of micro- and macromolecules in bio-oil during hydrodeoxygenation with Pd/C catalyst in supercritical ethanol

Miscanthus bio-oil was subjected to hydrodeoxygenation (HDO) with Pd/C at different temperatures (250, 300 and 350°C) and times (30, 45 and 60min) to investigate the chemical modification of micro- and macromolecules in bio-oil. Four main products – char, gas and two immiscible oils (light and heavy oil) – were obtained from the HDO reaction. Yields of heavy oil as a targeting product of HDO varied from 60% to 13%, whereas those of gas and char were ranged from 7% to 36% and 6% to 17%, respectively. Water content was estimated to<1% and heating value was 26–31MJkg−1.Reduction of unstable oxygen-containing compounds such as acids (2-hydroxy-butanoic acid), aldehydes (furfural), alcohols (butanedial) and sugars (levoglucosan) were characteristic in heavey oil. Apart from hydrogenation and deoxygenation, micromolecules in bio-oil were plausibly modified to stable ketones, esters and saturated components via demethoxylation, dealkylation, decarbonylation, dehydroxylation and ring opening.Macromolecular lignin fragments (referred to as pyrolytic lignins in bio-oil and phenol polymers in heavy oil) were extracted and subjected to several analyses. Approximately 60% of the pyrolytic lignins were decomposed into low molecular weight compounds during HDO reaction. Moreover, essential functional groups, OCH3 and phen-OH groups attached to pyrolytic lignin, were severely modified during HDO reaction.

Fluorogenic small molecules requiring reaction with a specific protein to create a fluorescent conjugate for biological imaging–what we know and what we need to learn

We seek fluorogenic small molecules that generate a fluorescent conjugate signal if and only if they react with a given protein-of-interest (i.e., small molecules for which noncovalent binding to the protein-of-interest is insufficient to generate fluorescence). Consequently, it is the new chemical entity afforded by the generally irreversible reaction between the small molecule and the protein-of-interest that enables the energy of an electron occupying the lowest unoccupied molecular orbital (LUMO) of the chromophore to be given off as a photon instead of being dissipated by nonradiative mechanisms in complex biological environments. This category of fluorogenic small molecules is created by starting with environmentally sensitive fluorophores that are modified by an essential functional group that efficiently quenches the fluorescence until a chemoselective reaction between that functional group and the protein-of-interest occurs, yielding the fluorescent conjugate. Fluorogenic small molecules are envisioned to be useful for a wide variety of applications, including live cell imaging without the requirement for washing steps and pulse-chase kinetic analyses of protein synthesis, trafficking, degradation, etc.

Ab initio and metadynamics studies on the role of essential functional groups in biomineralization of calcium carbonate and environmental situations.

The interactions of proteins, polysaccharides and other biomolecules with Ca(2+), CO3(2-), and water are central to the understanding of biomineralization and crystallization of calcium carbonate (CaCO3), and their association with the natural organic matter (NOM) in the environment. A molecular-level investigation of how such interactions and thermodynamic forces drive the nucleation and growth of crystalline CaCO3 in living organisms remains elusive. This paper presents ab initio and metadynamics studies of the interactions of Ca(2+), CO3(2-), and water with the essential amino acids/functional groups, e.g. arginine/NH2(+), aspartate or glutamate/COO(-), aspartic or glutamic acid/COOH, and serine/OH, of protein/organic molecules that are likely to be critical to the biomineralization of CaCO3. These functional groups were modeled as guanidinium (Gdm(+)), acetate (AcO(-)), acetic acid (AcOH), and ethanol (EtOH) molecules, respectively. The Gdm(+)-Ca(2+)-CO3(2-) and AcO(-)-Ca(2+)-CO3(2-) systems were found to form stable ion-complexes irrespective of the presence of near neighbor water molecules. The strong electrostatic interactions of these functional groups with their counter-ions significantly affect the fundamental vibrational frequencies of the functional groups, mainly the NH2 stretching (str.) and degenerate (deg.) scissors modes of Gdm(+) and -C=OO, CC, and CO str. modes of AcO(-). The free-energy calculations reveal that EtOH forms weakly bound molecular complexes with the Ca(2+)-CO3(2-) ion pairs in water. However, the interaction strength of EtOH with crystalline CaCO3 can increase significantly due to combined effect of H-bond and electron donor acceptor (EDA) type of interactions. These results indicate that -NH2(+) and -COO(-) bearing molecules serve as potential nucleation sites promoting crystallization of CaCO3 phases while -OH bearing molecules are likely to control the morphology of the crystalline phases by attaching to the growing crystal surfaces.

Biogenic gold nanoparticles as fotillas to fire berberine hydrochloride using folic acid as molecular road map

Use of biologically modified gold nanoparticles (GNPs) as molecular vehicle to ferry potential anti-cancer drug berberine hydrochloride (BHC) using folic acid (FA) as targeting molecule is reported in this work. A tropical fruit peel, Trapa bispinosa is used to fabricate highly monodispersed GNPs, passivated with essential functional groups which were used as linkers to attach FA and BHC via amide linkage. Flocculation Parameter (FP) of biologically synthesized GNPs was calculated under different salt concentrations which were found to be very ideal under a physiological condition. Various statistical models were used to find drug release profile out of which Higuchi was found to be the most ideal. GNP–FA–BHC complexes were found to be active against folic acid expressing HeLa cells.

Synthesis and biological evaluation of substituted imidazoquinoline derivatives as mPGES-1 inhibitors

We have previously reported 7-bromo-2-(2-chrolophenyl)-imidazoquinolin-4(5H)-one (1) as a novel potent mPGES-1 inhibitor. To clarify the essential functional groups of 1 for inhibition of mPGES-1, we investigated this compound structure–activity relationship following substitution at the C(4)-position and N-alkylation at the N(1)-, the N(3)-, and the N(5)-positions of 1. To prepare the target compounds, we established a good methodology for selective N-alkylation of the imidazoquinolin-4-one, that is, selective alkylation of 1 at the N(3)- and N(5)-positions was achieved by use of an appropriate base and introduction of a protecting group at the nitrogen atom in the imidazole part, respectively. Replacement of the C(4)-oxo group with nitrogen- or sulfur- linked substituents gave decreased inhibitory activity for mPGES-1, and introduction of alkyl groups on the nitrogen atom at the N(1)-, the N(3)-, and the N(5)-positions resulted in even larger loss of inhibitory activity. These results revealed that the C(4)-oxo group, and the hydrogen atoms at the N(5)-position and the imidazole part were the best substituents.

Orthosteric versus allosteric GPCR activation: The great challenge of group-III mGluRs

Group-III metabotropic glutamate receptors (mGluRs) comprise four structurally related brain and retinal G protein-coupled receptors (GPCRs), mGluR4, mGluR6, mGluR7 and mGluR8, which receive much attention as promising targets for nervous system drugs. In particular, activation of mGluR4 is a major focus for the development of new therapeutics in Parkinson's disease, while mGluR7 activation is considered a potential approach for future treatments of specific psychiatric conditions. The first generation group-III mGluR agonists, e.g.l-AP4 and l-SOP, are characterized by an essential phosphonate functional group, which became a major limitation for the development of systemically active, potent and receptor subtype-selective drugs. Recently however, two approaches emerged in parallel providing resolution to this constraint: in silico high-throughput screening of chemical libraries against a 3D-model of the mGluR4 extracellular domain identified a hit that was optimized into a series of potent and subtype-selective orthosteric agonists with drug-like properties and novel chemotype structures; secondly, high-throughput random screening of chemical libraries against recombinantly expressed group-III receptors identified diverse chemical sets of allosteric agonists and positive modulators, which are drug-like, display selectivity for mGluR4, mGluR7, or mGluR8 and act via novel pharmacological sites.Here, we illustrate new scientific insights obtained via the use of those strategies. Also, we compare advantages and disadvantages of both approaches to identify the desired group-III mGluR activators and we conclude with suggestions how to employ those discovery strategies with success for the identification, optimization, and development of clinical drug candidates; this may have important implications for the entire field of GPCR research.

Probing Essential Nucleobase Functional Groups in Aptamers and Deoxyribozymes by Nucleotide Analogue Interference Mapping of DNA

Nucleotide analogue interference mapping of DNA (dNAIM) is here introduced as a new nonenzymatic interference-based approach that enables high-throughput identification of essential nucleobase functional groups in DNA aptamers and in the catalytic core of deoxyribozymes. Nucleobase-modified ribonucleotides are statistically incorporated into DNA by solid-phase synthesis, employing the 2'-OH group as a chemical tag for analysis of interference effects. This method is exemplified on an AMP-binding DNA aptamer and was further used to identify indispensable nucleobase functional groups for DNA-catalyzed RNA-ligation by the Mg(2+)-dependent deoxyribozymes 7S11 and 9DB1. dNAIM should prove broadly useful for facile structural probing of functional DNA for which active and inactive variants can be separated based on catalytic or ligand-binding activities.

Exploring aigialomycin d and its analogues as protein kinase inhibitors for cancer targets.

The natural product aigialomycin D (1) is a member of the resorcylic acid lactone (RAL) family possessing protein kinase inhibitory activities. This paper describes the synthesis of aigialomycin D and a series of its analogues and their activity for the inhibition of protein kinases related to cancer pathways. A preliminary study of these compounds in the inhibition of CDK2/cyclin A kinase has found that aigialomycin D and analogues 11 and 23 are moderate CDK2/cyclin A inhibitors with IC50 values of ca. 20 μM. Kinase profiling of aigialomycin D against a panel of kinases has led to the identification of MNK2 as a promising target (IC50 = 0.45 μM), and preliminary structure-activity relationship studies have been carried out to identify the essential functional groups for activity.

Conformational change in the Bacillus subtilis RNase P holoenzyme–pre-tRNA complex enhances substrate affinity and limits cleavage rate

Ribonuclease P (RNase P) is a ribonucleoprotein complex that catalyzes the 5' maturation of precursor tRNAs. To investigate the mechanism of substrate recognition in this enzyme, we characterize the thermodynamics and kinetics of Bacillus subtilis pre-tRNA(Asp) binding to B. subtilis RNase P holoenzyme using fluorescence techniques. Time courses for fluorescein-labeled pre-tRNA binding to RNase P are biphasic in the presence of both Ca(II) and Mg(II), requiring a minimal two-step association mechanism. In the first step, the apparent bimolecular rate constant for pre-tRNA associating with RNase P has a value that is near the diffusion limit and is independent of the length of the pre-tRNA leader. Following formation of the initial enzyme-substrate complex, a unimolecular step enhances the overall affinity of pre-tRNA by eight- to 300-fold as the length of the leader sequence increases from 2 to 5 nucleotides. This increase in affinity is due to a decrease in the reverse rate constant for the conformational change that correlates with the formation of an optimal leader-protein interaction in the RNase P holoenzyme-pre-tRNA complex. Furthermore, the forward rate constant for the conformational change becomes rate limiting for cleavage under single-turnover conditions at high pH, explaining the origin of the observed apparent pK(a) in the RNase P-catalyzed cleavage reaction. These data suggest that a conformational change in the RNase P*pre-tRNA complex is coupled to the interactions between the 5' leader and P protein and aligns essential functional groups at the cleavage active site to enhance efficient cleavage of pre-tRNA.

Structure-guided Mutational Analysis of the Nucleotidyltransferase Domain of Escherichia coli DNA Ligase (LigA)

NAD(+)-dependent DNA ligases (LigA) are ubiquitous in bacteria, where they are essential for growth and present attractive targets for antimicrobial drug discovery. LigA has a distinctive modular structure in which a nucleotidyltransferase catalytic domain is flanked by an upstream NMN-binding module and by downstream OB-fold, zinc finger, helix-hairpin-helix, and BRCT domains. Here we conducted a structure-function analysis of the nucleotidyltransferase domain of Escherichia coli LigA, guided by the crystal structure of the LigA-DNA-adenylate intermediate. We tested the effects of 29 alanine and conservative mutations at 15 amino acids on ligase activity in vitro and in vivo. We thereby identified essential functional groups that coordinate the reactive phosphates (Arg(136)), contact the AMP adenine (Lys(290)), engage the phosphodiester backbone flanking the nick (Arg(218), Arg(308), Arg(97) plus Arg(101)), or stabilize the active domain fold (Arg(171)). Finer analysis of the mutational effects revealed step-specific functions for Arg(136), which is essential for the reaction of LigA with NAD(+) to form the covalent ligase-AMP intermediate (step 1) and for the transfer of AMP to the nick 5'-PO(4) to form the DNA-adenylate intermediate (step 2) but is dispensable for phosphodiester formation at a preadenylylated nick (step 3).