Pharmaceutical metabolite profiling using quadrupole/ion mobility spectrometry/time‐of‐flight mass spectrometry

The use of hybrid quadrupole ion mobility spectrometry time‐of‐flight mass spectrometry (Q/IMS/TOFMS) in the metabolite profiling of leflunomide (LEF) and acetaminophen (APAP) is presented. The IMS drift times (T_d) of the drugs and their metabolites were determined in the IMS/TOFMS experiments and correlated with their exact monoisotopic masses and other in silico generated structural properties, such as connolly molecular area (CMA), connolly solvent‐excluded volume (CSEV), principal moments of inertia along the X, Y and Z Cartesian coordinates (MI‐X, MI‐Y and MI‐Z), inverse mobility and collision cross‐section (CCS). The correlation of T_d with these parameters is presented and discussed. IMS/TOF tandem mass spectrometry experiments (MS² and MS³) were successfully performed on the N‐acetyl‐p‐benzoquinoneimine glutathione (NAPQI‐GSH) adduct derived from the in vitro microsomal metabolism of APAP. As comparison, similar experiments were also performed using hybrid triple quadrupole linear ion trap mass spectrometry (QTRAPMS) and quadrupole time‐of‐flight mass spectrometry (QTOFMS). The abilities to resolve the product ions of the metabolite within the drift tube and fragment the ion mobility resolved product ions in the transfer travelling wave‐enabled stacked ring ion guide (TWIG) demonstrated the potential applicability of the Q/IMS/TOFMS technique in pharmaceutical metabolite profiling. Copyright © 2009 John Wiley & Sons, Ltd.     

Synthesis,Anticancer Evaluation,and Molecular Docking Studies of Novel (4‐Hydroxy‐2‐Thioxo‐3,4‐Dihydro‐2H‐[1,3]Thiazin‐6‐Yl)‐Chromen‐2‐Ones via a Multicomponent Approach

A series of coumarin‐substituted 1,3‐thiazine‐2‐thione derivatives ( 4a–m ) were synthesized via the multicomponent reaction of 3‐chloro‐3‐(2‐oxo‐2H‐chromen‐3‐yl)acrylaldehyde ( 1 ) carbon disulfide ( 2 ), and various primary amines ( 3 ), in presence of triethylamine and acetonitrile under stirring with good yields. The structures of all the synthesized compounds were characterized by analytical and spectral studies. Further, the synthesized compounds were screened for their in vitro antiproliferative activities against different cancer cell lines (A549, MDA‐MB‐231, MCF7, HeLa, and B16F10). Studies on the molecular interactions to recognize the hypothetical binding motif of the title compounds with the target Hsp 100 were carried out employing the Schrodinger software. Compounds 4a , 4c and 4m showed activity against all the five cell lines compared with the reference drug, and 4a exhibited the least IC₅₀ concentration of 7.56 ± 1.07 μg/mL against MCF7. This in vitro anticancer result was supported by in silico docking and in silico ADME (absorption, distribution, metabolism, and excretion) studies as well.     

Design,Synthesis, and Biological Evaluation of 3,5‐Disubstituted 2‐Pyrazineamide Derivatives as Antitubercular Agents

A novel series of 3,5‐disubstituted‐2‐pyrazineamide derivatives ( 5a–5o ) were synthesized and studied for their potential as antitubercular agents. Among them, the compounds 5a , 5g , and 5m showed the good minimal inhibitory concentration of 20, 25, and 25 μg/mL, respectively. The compound 5a displayed excellent minimum inhibitory concentration of 10 μg/mL and is four times more potent compared with the standard drug, rifampicin concentration. In silico docking studies revealed that the compounds 5a and 5c can bind strongly in the active site of 2FUM enzyme and prevent enzyme–substrate interactions. In addition, in silico docking studies were calculated, and based on the data obtained, compound 5a displayed excellent drug‐like properties.     

Synthesis,Docking, and Bioavailability of 2′‐Oxo‐3‐phenylspiro[cyclopropane‐1,3′‐indoline]‐2,2‐dicarbonitriles as Antibacterial Agents In Silico

An efficient method has been developed for the synthesis of N‐alkylated 2′‐oxo‐3‐phenylspiro[cyclopropane‐1,3′‐indoline]‐2,2‐dicarbonitrile from 3‐chloroindolin‐2‐one and 2‐benzylidenemalononitrile by using triethylamine as a base at room temperature and obtained the products in moderate to good yields. In extension, the scope of the reaction has been investigated by stepwise and one‐pot methods. Furthermore, in silico antibacterial activity was carried out in order to understand possible binding modes of novel derivatives with the active site of DNA gyrase A enzyme, and the results were well complemented. Additionally, absorption, distribution, metabolism, and excretion properties of compounds have shown drug likeness with good oral absorption and moderate blood–brain barrier permeability.     

3,5‐Dihydro‐2H‐thieno[2,3‐c]pyrrole 1,1‐Dioxide – A New Simple Pyrrole Unit. Preliminary Communication

2,3‐Dihydrothiophene 1,1‐dioxide (‘2‐sulfolene’) reacted with tosylmethyl isocyanide (TsMIC) in the presence of a base to give the hitherto unknown 3,5‐dihydro‐2H‐thieno[2,3‐c]pyrrole 1,1‐dioxide (‘β′‐sulfolenopyrrole’) from the expected cyclocondensation. A serendipitous formation of this β′‐sulfolenopyrrole was found earlier, when we investigated synthetic routes to a 3,5‐dihydro‐1H‐thieno[3,4‐c]pyrrole 2,2‐dioxide (a ‘β″‐sulfolenopyrrole’) from TsMIC and 2,5‐dihydrothiophene 1,1‐dioxide (‘3‐sulfolene’). Here, we present the synthesis and characterization of β′‐sulfolenopyrrole. The X‐ray crystal‐structure analyses of β′‐sulfolenopyrrole and the isomeric β″‐sulfolenopyrrole are also reported here. This β′‐sulfolenopyrrole is a new type of a functionalized pyrrole, which is likely to be of interest for pharmaceutical purposes.     

A pH‐dependent computational approach to the effect of mutations on protein stability

This article describes a novel software implementation for high‐throughput scanning mutagenesis with a focus on protein stability. The approach combines molecular mechanics calculations with calculations of protein ionization and a Gaussian‐chain model of electrostatic interactions in unfolded state. Comprehensive testing demonstrates a state‐of‐the‐art accuracy for predicted free energy differences on single, double, and triple mutations with a correlation coefficient R above 0.7, which takes about 1.5 min per mutation on a single CPU. Unlike most of existing in silico methods for fast mutagenesis, the stability changes are reported as a continuous function of solution pH for wide pH intervals. We also propose a novel in silico strategy for searching stabilized protein variants that is based on combinatorial scanning mutagenesis using representative amino acid types. Our in silico predictions are in excellent agreement with the hyper‐stabilized variants of mesophilic cold shock protein found using the Proside method of direct evolution. © 2016 Wiley Periodicals, Inc.     

A Novel d‐Peptide Identified by Mirror‐Image Phage Display Blocks TIGIT/PVR for Cancer Immunotherapy

The low response rate and adaptive resistance of PD‐1/PD‐L1 blockade demands the studies on novel therapeutic targets for cancer immunotherapy. We discovered that a novel immune checkpoint TIGIT expressed higher than PD‐1 in many tumors especially anti‐PD‐1 resistant tumors. Here, mirror‐image phage display bio‐panning was performed using the d ‐enantiomer of TIGIT synthesized by hydrazide‐based native chemical ligation. d ‐peptide ^DTBP‐3 was identified, which could occupy the binding interface and effectively block the interaction of TIGIT with its ligand PVR. ^DTBP‐3 showed proteolytic resistance, tumor tissue penetrating ability, and significant tumor suppressing effects in a CD8⁺ T cell dependent manner. More importantly, ^DTBP‐3 could inhibit tumor growth and metastasis in anti‐PD‐1 resistant tumor model. This is the first d ‐peptide targeting TIGIT, which could serve as a potential candidate for cancer immunotherapy.     

The application of gas chromatography/atmospheric pressure chemical ionisation time‐of‐flight mass spectrometry to impurity identification in Pharmaceutical Development

Accurate mass measurement (used to determine elemental formulae) is an essential tool for impurity identification in pharmaceutical development for process understanding. Accurate mass liquid chromatography/mass spectrometry (LC/MS) is used widely for these types of analyses; however, there are still many occasions when gas chromatography (GC)/MS is the appropriate technique. Therefore, the provision of robust technology to provide accurate mass GC/MS (and GC/MS/MS) for this type of activity is essential. In this report we describe the optimisation and application of a newly available atmospheric pressure chemical ionisation (APCI) interface to couple GC to time‐of‐flight (TOF) MS. To fully test the potential of the new interface the APCI source conditions were optimised, using a number of standard compounds, with a variety of structures, as used in synthesis at AstraZeneca. These compounds were subsequently analysed by GC/APCI‐TOF MS. This study was carried out to evaluate the range of compounds that are amenable to analysis using this technique. The range of compounds that can be detected and characterised using the technique was found to be extremely broad and include apolar hydrocarbons such as toluene. Both protonated molecules ([M + H]⁺) and radical cations (M^+.) were observed in the mass spectra produced by APCI, along with additional ion signals such as [M + H + O]⁺. The technique has been successfully applied to the identification of impurities in reaction mixtures from organic synthesis in process development. A typical mass accuracy of 1–2 mm/zunits (m/z 80–500) was achieved allowing the reaction impurities to be identified based on their elemental formulae. These results clearly demonstrate the potential of the technique as a tool for problem solving and process understanding in pharmaceutical development. The reaction mixtures were also analysed by GC/electron ionisation (EI)‐MS and GC/chemical ionisation (CI)‐MS to understand the capability of GC/APCI‐MS relative to these two firmly established techniques. Copyright © 2010 John Wiley & Sons, Ltd.     

Simple in‐house flow‐injection capillary electrophoresis with capacitively coupled contactless conductivity method for the determination of colistin

An in‐house flow‐injection capillary electrophoresis with capacitively coupled contactless conductivity detection method was developed for the direct measurement of colistin in pharmaceutical samples. The flow injection and capillary electrophoresis systems are connected by an acrylic interface. Capillary electrophoresis separation is achieved within 2 min using a background electrolyte solution of 5 mM 2‐morpholinoethanesulfonic acid and 5 mM histidine (pH 6). The flow‐injection section allows for convenient filling of the capillary and sample introduction without the use of a pressure/vacuum manifold. Capacitively coupled contactless conductivity detection is employed since colistin has no chromophore but is cationic at pH 6. Calibration curve is linear from 20 to 150 mg/L, with a correlation coefficient (r²) of 0.997. The limit of quantitation is 20 mg/L. The developed method provides precision, simplicity, and short analysis time.     

Microwave Induced Synthesis of 3‐Aryl‐6‐(6‐/8‐substituted 4‐chloroquinoline‐3‐yl) ‐ s ‐triazolo [3,4‐b] −1,3,4‐thiadiazoles

The condensation of 4‐amino‐3‐aryl‐5‐mercapto‐1, 2, 4‐triazoles (1a‐f) with 6‐/8‐substituted 1,4‐dihydro‐4‐oxo‐quinoline‐3‐carboxylic adds (2a‐d) in the presence of phosphorus oxychloride on refluxng or under microwave irradiation gave twenty four novel 3‐aryl‐6‐ (6‐/8‐substituted 4‐chloroquinoline‐3‐yl)‐s‐triazolo[3,4‐b]‐1, 3,4‐thiadiazoles (4a‐x), Considerable increase in the reaction rate has been observed with improved yields under microwave irradiation. The structures of the compounds synthesized were determined by elemental analyses, IR, ¹H NMR and MS spectra. Their spectral properties and the reaction mechanism were also discussed. The preliminary biological test showed that some of compounds bad moderate antibacterial activities.     

A mixed DFT‐MD methodology for the in silico development of drug releasing macrocycles. Calix and thia‐calix[N]arenes as carriers for Bosutinib and Sorafenib

Interaction energies between a family of 36 calix[n]arenes, their corresponding thia‐ analogues, and two commercially available second generation tyrosine kinase III inhibitors—Bosutinib and Sorafenib—were calculated through DFT methods at the B97D/6‐31G(d,p) level of theory, based on Natural Population Analysis, for the in silico development of suitable drug carriers based on the aforementioned macrocycles which can increase their bioavailability and in turn their pharmaceutical efficiency. Molecular Dynamics simulations (production runs: +500 ns) using the General Amber Force Field were also carried out in order to assess the releasing process of these drugs in an explicit aqueous environment. In total, 144 host–guest complexes are examined. According to our results, five‐membered ? SO₃H and i–Pr functionalized‐calixarenes are the best candidates for Sorafenib‐carriers while six‐membered ones ? SO₃H and C₂H₄NH₂ functionalized– are the lead candidates for Bosutinib‐carriers. © 2015 Wiley Periodicals, Inc.     

Synthesis,experimental and in silico studies of N‐fluorenylmethoxycarbonyl‐O‐tert‐butyl‐N‐methyltyrosine,coupled with CSD data: a survey of interactions in the crystal structures of Fmoc–amino acids

Recently, fluorenylmethoxycarbonyl (Fmoc) amino acids (e.g. Fmoc–tyrosine or Fmoc–phenylalanine) have attracted growing interest in biomedical research and industry, with special emphasis directed towards the design and development of novel effective hydrogelators, biomaterials or therapeutics. With this in mind, a systematic knowledge of the structural and supramolecular features in recognition of those properties is essential. This work is the first comprehensive summary of noncovalent interactions combined with a library of supramolecular synthon patterns in all crystal structures of amino acids with the Fmoc moiety reported so far. Moreover, a new Fmoc‐protected amino acid, namely, 2‐{[(9H‐fluoren‐9‐ylmethoxy)carbonyl](methyl)amino}‐3‐{4‐[(2‐hydroxypropan‐2‐yl)oxy]phenyl}propanoic acid or N‐fluorenylmethoxycarbonyl‐O‐tert‐butyl‐N‐methyltyrosine, Fmoc‐N‐Me‐Tyr(t‐Bu)‐OH, C₂₉H₃₁NO₅, was successfully synthesized and the structure of its unsolvated form was determined by single‐crystal X‐ray diffraction. The structural, conformational and energy landscape was investigated in detail by combined experimental and in silico approaches, and further compared to N‐Fmoc‐phenylalanine [Draper et al. (2015). CrystEngComm, 42 , 8047–8057]. Geometries were optimized by the density functional theory (DFT) method either in vacuo or in solutio. The polarizable conductor calculation model was exploited for the evaluation of the hydration effect. Hirshfeld surface analysis revealed that H…H, C…H/H…C and O…H/H…O interactions constitute the major contributions to the total Hirshfeld surface area in all the investigated systems. The molecular electrostatic potentials mapped over the surfaces identified the electrostatic complementarities in the crystal packing. The prediction of weak hydrogen‐bonded patterns via Full Interaction Maps was computed. Supramolecular motifs formed via C—H…O, C—H…π, (fluorenyl)C—H…Cl(I), C—Br…π(fluorenyl) and C—I…π(fluorenyl) interactions are observed. Basic synthons, in combination with the Long‐Range Synthon Aufbau Modules, further supported by energy‐framework calculations, are discussed. Furthermore, the relevance of Fmoc‐based supramolecular hydrogen‐bonding patterns in biocomplexes are emphasized, for the first time.     

On‐Surface Self‐Assembly of a C3‐Symmetric π‐Conjugated Molecule Family Studied by STM: Two‐Dimensional Nanoporous Frameworks

The on‐surface self‐assembled behavior of four C ₃‐symmetric π‐conjugated planar molecules ( Tp , T12 , T18 , and Ex ) has been investigated. These molecules are excellent building blocks for the construction of noncovalent organic frameworks in the bulk phase. Their hydrogen‐bonded 2D on‐surface self‐assemblies are observed under STM at the solid/liquid interface; these structures are very different to those in the bulk crystal. Upon combining the results of STM measurements and DFT calculations, the formation mechanism of different assemblies is revealed; in particular, the critical role of hydrogen bonding in the assemblies. This research provides us with not only a deep insight into the self‐assembled behavior of these novel functional molecules, but also a convenient approach toward the construction of 2D multiporous networks.     

Towards Molecular Design Rationalization in Branched Multi‐Thiophene Semiconductors: The 2‐Thienyl‐Persubstituted α‐Oligothiophenes

The introduction of branching in multi‐thiophene semiconductors, although granting the required solubility for processing, results in an increased molecular fluxionality and a higher level of distortion, thus hampering π conjugation. Accordingly, branched oligothiophenes require rationalization of their structure–reactivity relationships for target‐oriented design and optimization of the synthetic effort. Our current research on spiderlike oligothiophenes affords deep insight into the subject, and introduces new, easily accessible molecules with attractive functional properties. In particular, a regular series, T′X _Y , of five new multi‐thiophene systems, T′5₃ , T′8₄ , T′11₅ , T′14₆ , and T′17₇ , constituted by five, eight, 11, 14, and 17 thiophene units, respectively, their longest α‐conjugated chain consisting of tri‐, tetra‐, penta‐, hexa‐, and heptathiophene moieties, respectively, has been synthesized and fully characterized from the structural, spectroscopic, and electrochemical point of view. The electronic properties of the monomers and their electropolymerization ability are discussed and rationalized as a function of their molecular structure, particularly in comparison with the series of 5‐(2,2′‐dithiophene)yl‐persubstituted α‐oligothiophenes ( TX _Y ) previously reported by us. These oligothiophenes are easily accessible materials, with promising properties for applications as active layers in multifunctional organic devices including solar cells.     

Physiological activities of chitosan and N‐trimethyl chitosan chloride in U937 and 3T3‐L1 cells

Chitosan (CH) is a biopolymer with biocompatible, biodegradable, and bioactive properties. N,N,N‐trimethyl chitosan chloride (TMC) is a quaternized form of CH that is highly cationic and more water soluble than unmodified CH. The physiological activities of CHs with different molecular weights (M_w) and degrees of TMCs quaternization were investigated in U937 and 3T3‐L1 cell lines. ¹H‐NMR spectrometry and size exclusion chromatography were used for characterization of the biopolymers. The half inhibition concentration (IC₅₀) of DPPH‐radical‐scavenging activity was below 0.9 mg/m with quaternized CHs. The IC₅₀ values of chitooligosaccharides, low‐ and medium‐molecular‐weight CHs were 8.4, 10.9, and 13.9 mg/ml, respectively. High‐molecular‐weight CHs and TMCs showed apoptotic activity on U937 cells. T41, a TMC of 549 kDa with a 41% degree of quaternization (DQ), yielded 30.7% apoptotic cell death in U937 at 20 µg/ml and effectively repressed cell differentiation and triglyceride accumulation in 3T3‐L1. Depolymerized CHs reduced triglyceride accumulation but also caused cell differentiation. TMCs showed repressor activity to both cell differentiation and triglyceride accumulation. Increasing the molecular weight of CHs and TMCs generally resulted in increased physiological activity. Copyright © 2010 John Wiley & Sons, Ltd.     

Determination of ligand efficiency indices in a group of 7H‐purine‐2,6‐dione derivatives with psychotropic activity using micellar electrokinetic chromatography

Discovering hit compounds and optimization processes in medicinal chemistry nowadays could be improved by predictive tools, based on the relationship between structure of molecules and lipophilic properties. Lipophilicity of drug candidate can affect both the pharmacokinetic and pharmacodynamics properties, in particular, the ability of a molecule to cross the cell membrane. Among the new methods for determination of the lipophilicity of compounds, micellar electrokinetic chromatography (MEKC) is considered to be an appropriate one for bioactive molecules, as it closely mimics the physiological conditions. In this paper MEKC was used for the estimation of the lipophilicity of 24 derivatives of 8‐alkoxy‐7H‐purine‐2,6‐dione, designed and synthesized as potential antidepressant/anxiolytic and antipsychotic agents. The results of experimental method were compared with calculated in silico parameters (AlogPs and milogP by Virtual Computational Laboratory website, log P_Pallas by Pallas 3.1, Mlog P by Marvin, log P_ChemS by ChemSketch, log P_ChemDraw by ChemBioUltra) using Principal Component Analysis (PCA) method. Finally, using estimated log P values for selected compounds ligand – lipophilicity efficiency (LLE), per cent efficiency index (PEI), and binding efficiency index (BEI) parameters were calculated. Applied MEKC procedure could be used for selection of potential lead structure in a group of 7H‐purine‐2,6‐dione derivatives.     

A model validation and consensus building environment

Over half of the failures in drug development are due to problems with the absorption, distribution, metabolism, excretion, and toxicity, or ADME/Tox properties of a candidate compound. The utilization of in silico tools to predict ADME/Tox and physicochemical properties holds great potential for reducing the attrition rate in drug research and development, as this technology can prioritize candidate compounds in the pharmaceutical R&D pipeline. However, a major concern surrounding the use of in silico ADME/Tox technology is the reliability of the property predictions. Bio-Rad Laboratories, Inc. has created a computational environment that addresses these concerns. This environment is referred to as KnowItAll®. Within this platform are encoded a number of ADME/Tox predictors, the ability to validate these predictors with/without in-house data and models, as well as build a ‘consensus’ model that may be a much better model than any of the individual predictive model. The KnowItAll® system can handle two types of predictions: real number and categorical classification.     

Characterization of green‐tissue protein extract from alfalfa (Medicago sativa) exploiting a 3‐D technique

There is a growing interest of pharmaceutical companies for plant‐based production systems. To facilitate the general acceptance of plants as bioreactors, the establishment of efficient downstream operations is critical. It has been proposed that a better understanding of the properties of the contaminant proteins can benefit downstream processing design and operation. The coupled application of 2‐DE with aqueous two‐phase partitioning has been suggested as a practical 3‐D method to characterize potential contaminant proteins from plant extracts. The application of this novel 3‐D approach to a complex protein extract from alfalfa (Medicago sativa) containing a model recombinant protein (human granulocyte colony stimulating factor (hG‐CSF)) resulted in the quantification of 55 protein spots. The 3‐D properties (M_r, pI, and K_p) obtained for 17 proteins comprising 69% of the alfalfa proteins, allowed the proposal of a prefractionation step as well as the identification of the target molecule (rG‐CSF) from bulk of alfalfa proteins. The information obtained from this experimental approach was useful for the identification of the potential contaminant proteins that will occur in alfalfa when this plant is used as a host for recombinant proteins. Additionally, this method will assist in the design of adequate purification strategies for recombinant proteins expressed in alfalfa green tissue.