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Synthesis, Structure-Activity Relationship Studies Using Density Functional Theory and in silico Molecular Docking on Substituted Benzohydrazide Derivatives
Abstract
The present study demonstrates the utility of benzohydrazide derivatives based on an approach to identify potential targets for a series of synthesized compounds that show potent anticancer activities against four cancer cell lines compared to other structurally related molecules. Benzohydrazide compounds have been synthesized effectively by the condensation of aldehyde and hydrazide at a 1:1 molar ratio. The complete series of compounds 1a-j were characterized by FT-IR, NMR, and one of them by single-crystal X-ray diffraction. The crystal structure of compound 1a shows a trans configuration around the Cdouble bondN bond and crystallized in a monoclinic system with C 2/c space group. All compounds exhibited good anticancer activity against four cancer cell lines such as A375 (human malignant melanoma), A549 (human lung adenocarcinoma), HT-29 (human epithelial intestinal) and MDA-MB-232(human metastatic breast). Among them, compound 1e shows the highest cytotoxic effect against the HT29 (IC50 = 0.47 µM) and A375 (IC50 = 0.80 µM) cell lines. Other compounds also exhibited promising anticancer activity. In addition, the nontoxic action was verified using the cytocompatibility assay on the L929 normal cell line and the hemolysis assay on human red blood cells. Parameters such as HOMO-LUMO energies, Hirshfeld surface analysis, and Molecular Electrostatic Potential (MEP) surface have been calculated using DFT and compared to experimental values of compounds 1a-c. In silico molecular docking studies revealed that the compound 1 h interacted very strongly with the 1T46 protein, with a docking score of −9.7 kcal/mol and very good binding via π–π, π-alkyl and π–σ interactions as compared to the standard drug. As a result of their potent cytotoxicity activities and computational analysis, these can be considered promising anticancer agents.
... This rule considers factors such as molecular weight (MW), lipophilicity (logP), the number of hydrogen bond acceptors and donors (N and O atoms), and the number of rotatable bonds. Violations of these criteria may indicate challenges in terms of oral bioavailability [39]. Table 4 in the study reveals that the Schiff base derivative analyzed exhibited zero violations of Lipinski's rule of five. ...
The research described involves the synthesis and characterization of a new benzohydrazide based Schiff base compound namely 4-methyl-N'-(2,4,5-trimethoxybenzylidene) benzohydrazide (HL). The compound was synthesized by condensing a primary amine and an aldehyde functional group. The characterization of the compound was carried out using various spectroscopic techniques, including elemental analysis, Ultraviolet spectroscopy, nuclear magnetic resonance spectroscopy, and infrared spectroscopy. These techniques helped confirm the excellent quality of the synthesized molecules. In addition to the characterization, the Schiff base compound was subjected to docking studies and biological studies. The antibacterial activity of the compound was tested against three strains of bacteria, namely E. faecalis, B. subtills, and E.coli. The results of these tests provided information on the compound effectiveness against these bacterial strains. Furthermore, docking studies was performed to assess the interaction between the synthesized compound and three target enzymes like GlcN-6-p synthase, DNA polymerase, and EGFR tyrosine kinase. Docking studies are computational simulations that provide insights into the binding interactions between Schiff base ligand and target proteins. In this case, the docking studies helped understand the potential mechanisms of action of the synthesized compound by calculating binding constants and the number of binding modes. The biological activity studies revealed interesting fragmentation patterns, which could be further investigated to understand the compound modes of action. Moreover, the docking studies evaluated the compound's potential as a drug candidate by assessing its binding interactions with the target enzymes. The present study suggests that the synthesized benzohydrazide based Schiff base compound exhibits potential antibacterial activity and shows promising binding interactions with the target protein/enzymes. This information is valuable for designing and developing more potent compounds in the future.
A series of novel hydrazone compounds have been synthesized by the condensation of hydrazines and different substituted salicylaldehydes at a molar ratio of 1:1 in one step reaction and characterized by FT-IR, ESI-MS, ¹H NMR, and single crystal x-ray diffraction. The crystal structure of the compound shows a trans configuration around the C = N bond and triclinic system with P −1/-p 1. Synthesized compounds were screened for cytotoxicity activities against A375 (melanoma), HT-29 (Colon), and A549 (lung) cancer cell lines. Among them, compound 2 exhibited the highest cytotoxic effect against the A375 cell line (IC50 = 0.30 µM) and HT-29 cell line (1.68 µM), compared to those of apatinib as a reference standard drug (0.28, 1.49 µM, respectively). The cytocompatibility assay on the L929 normal cell line and the hemolysis assay on human RBC were used to validate the non-toxic action. From DFT calculation, the various parameters such as HOMO-LUMO energies, Hirshfeld, and MEP have been studied. Furthermore, in silico molecular docking with three receptors was studied. Among four compounds, compound 2 has the lowest binding energy against cyclin dependent kinase (ΔGb = −9.3 kcal/mol). In addition to this, molecular dynamics (MD) simulation was also performed. Based on this study, these novel hydrazones can be considered a promising anticancer agent due to their potent cytotoxicity activities and computational analysis.
Communicated by Ramaswamy H. Sarma
A new series of 1H-pyrrole (6a–c, 8a–c), pyrrolo[3,2-d]pyrimidines (9a–c) and pyrrolo[3,2-e][1, 4]diazepines (11a–c) were designed and synthesised. These compounds were designed to have the essential pharmacophoric features of EGFR Inhibitors, they have shown anticancer activities against HCT116, MCF-7 and Hep3B cancer cells with IC50 values ranging from 0.009 to 2.195 µM. IC50 value of doxorubicin is 0.008 µM, compounds 9a and 9c showed IC50 values of 0.011 and 0.009 µM respectively against HCT-116 cells. Compound 8b exerted broad-spectrum activity against all tested cell lines with an IC50 value less than 0.05 µM. Compound 8b was evaluated against a panel of kinases. This compound potently inhibited CDK2/Cyclin A1, DYRK3 and GSK3 alpha kinases with 10–23% compared to imatinib (1–10%). It has also arrested the cell cycle of MCF-7 cells at the S phase. Its antiproliferative activity was further augmented by molecular docking into the active sites of EGFR and CDK2 cyclin A1.
In continuation of our antecedent work against COVID-19, three natural compounds, namely, Luteoside C (130), Kahalalide E (184), and Streptovaricin B (278) were determined as the most promising SARS-CoV-2 main protease (Mpro) inhibitors among 310 naturally originated antiviral compounds. This was performed via a multi-step in silico method. At first, a molecular structure similarity study was done with PRD_002214, the co-crystallized ligand of Mpro (PDB ID: 6LU7), and favored thirty compounds. Subsequently, the fingerprint study performed with respect to PRD_002214 resulted in the election of sixteen compounds (7, 128, 130, 156, 157, 158, 180, 184, 203, 204, 210, 237, 264, 276, 277, and 278). Then, results of molecular docking versus Mpro PDB ID: 6LU7 favored eight compounds (128, 130, 156, 180, 184, 203, 204, and 278) based on their binding affinities. Then, in silico toxicity studies were performed for the promising compounds and revealed that all of them have good toxicity profiles. Finally, molecular dynamic (MD) simulation experiments were carried out for compounds 130, 184, and 278, which exhibited the best binding modes against Mpro. MD tests revealed that luteoside C (130) has the greatest potential to inhibit SARS-CoV-2 main protease.
Keratoconus (KC) is a serious disease that can affect people of any race or nationality, although the exact etiology and pathogenic mechanism are still unknown. In this study, thirty-two FDA-approved ophthalmic drugs were exposed to virtual screening using docking studies against both the MMP-2 and MMP-9 proteins to find the most promising inhibitors as a proposed computational mechanism to treat keratoconus. Matrix metalloproteinases (MMPs) are zinc-dependent proteases, and MMP inhibitors (MMPIs) are usually designed to interact with zinc ion in the catalytic (CAT) domain, thus interfering with enzymatic activity. In our research work, the FDA-approved ophthalmic medications will be investigated as MMPIs, to explore if they can be repurposed for KC treatment. The obtained findings of the docking study suggest that atenolol and ampicillin are able to accommodate into the active sites of MMP-2 and MMP-9. Additionally, both exhibited binding modes similar to inhibitors used as references, with an ability to bind to the zinc of the CAT. Molecular dynamic simulations and the MM-GBSA binding free-energy calculations revealed their stable binding over the course of 50 ns. An additional pharmacophoric study was carried out on MMP-9 (PDB ID: 1GKC) using the co-crystallized ligand as a reference for the future design and screening of the MMP-9 inhibitors. These promising results open the door to further biological research to confirm such theoretical results.
AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock Vina and AutoDock4, including the option of using the Autodock4Zn force field for metalloproteins. AMDock integrates several external programs (Open Babel, PDB2PQR, AutoLigand, ADT scripts) to accurately prepare the input structure files and to optimally define the search space, offering several alternatives and different degrees of user supervision. For visualization of molecular structures, AMDock uses PyMOL, starting it automatically with several predefined visualization schemes to aid in setting up the box defining the search space and to visualize and analyze the docking results. One particularly useful feature implemented in AMDock is the off-target docking procedure that allows to conduct ligand selectivity studies easily. In summary, AMDock’s functional versatility makes it a very useful tool to conduct different docking studies, especially for beginners. The program is available, either for Windows or Linux, at https://github.com/Valdes-Tresanco-MS .
Reviewers
This article was reviewed by Alexander Krah and Thomas Gaillard.
An unusual quinazoline alkaloid (1) was obtained when 2-aminobenzaldehyde was refluxed with pyrrolidine in ethanol for 12 h. The synthesized compound was characterized using spectral data analysis augmented with X-ray and literature precedent. Single crystal analysis depicted four conformations differing slightly in bond angles and bond lengths. Compound 1 crystallizes in a triclinic crystal system with a P space group having two molecules within the unit cell. The experimentally obtained parameters were compared to those obtained theoretically, which depicted a good agreement. Using the DFT/B3LYP/6-31G (d,p) level of theory, HOMO–LUMO energy gap, molecular electrostatic potential (MEP), vibrational (IR) and NMR analyses were carried out. The HOMO–LUMO energy gap allowed the calculation of chemical hardness, chemical inertness, electronegativity and the electrophilicity index of the molecule, which depicted its potential kinetic stability and reactivity. Prediction of activity spectra of the target compound revealed that compound 1 possesses notable antineoplastic activity with Pa = 0.884. The molecule was therefore evaluated against various cancerous cell lines in an in vitro SRB assay which depicted that compound 1 possesses the highest growth inhibition activity against THP-1 cell lines with an IC50 of 7 μM.
The effect of steric hindrance on reactivity towards biomolecules while designing Ru(II)-η(6)-p-cymene based anticancer agents seems to be an important parameter in improving the activity and inducing resistance against glutathione (GSH) deactivation. Herein we present the structure, hydrolysis, anticancer activity and the effect of steric hindrance on deactivation by glutathione for three complexes, [Ru(II)(η(6)-p-cym)()(Cl)](PF6) (), [Ru(II)(η(6)-p-cym)()(Cl)](PF6) () and [Ru(II)(η(6)-p-cym)()(Cl)](PF6) (). The ligands are Schiff bases which show increasing substitution in a benzene ring, such that two ortho hydrogens are replaced by -methyl in and by -isopropyl in . The cytotoxicity results strongly suggest that controlling the rate of hydrolysis through tuning of steric hindrance may be a feasible pathway to derive GSH resistant anticancer agents. The cellular studies show that all the three complexes show good blood compatibility (haemolysis <3%) and induce cellular death through caspase activation via the mitochondrial pathway. They have anti-angiogenic activity and prevent the healing of treated cells.
We report a supramolecular approach for preparation of photostable NIR nanovesicles based on a cyanine dye derivative as a photoacoustic (PA) contrast agent for high-performance nano-imaging.
The incidence of melanoma has increased over the past several decades. Despite improved case mortality, overall deaths from melanoma have increased because of the large increase in incidence. Although we have a better understanding of the pathogenesis of melanoma and improved early diagnostic capabilities, the burden of disease and societal costs remain high. This article provides an update on the epidemiology of cutaneous melanoma worldwide and the common risk factors including heritable and modifiable risks, emphasizing the importance of education, early detection, and prevention in reducing the disease burden.
Schiff bases are condensation products of primary amines with carbonyl compounds gaining importance day by day in present scenario. Schiff bases are the compounds carrying imine or azomethine (–C=N–) functional group and are found to be a versatile pharmacophore for design and development of various bioactive lead compounds. Schiff bases exhibit useful biological activities such anti-inflammatory, analgesic, antimicrobial, anticonvulsant, antitubercular, anticancer, antioxidant, anthelmintic, antiglycation, and antidepressant activities. Schiff bases are also used as catalysts, pigments and dyes, intermediates in organic synthesis, polymer stabilizers, and corrosion inhibitors. The present review summarizes information on the diverse biological activities and also highlights the recently synthesized numerous Schiff bases as potential bioactive core.
The review reports a short biography of the Italian naturalized chemist Hugo Schiff and an outline on the synthesis and use of his most popular discovery: the imines, very well known and popular as Schiff Bases. Recent developments on their "metallo-imines" variants have been described. The applications of Schiff bases in organic synthesis as partner in Staudinger and hetero Diels-Alder reactions, as "privileged" ligands in the organometallic complexes and as biological active Schiff intermediates/targets have been reported as well.
In the title compound, C15H14N2O4·H2O, the dihedral angle between the two aromatic rings is 33.3 (5)°. The methoxy group is twisted slightly away from the attached benzene ring [C—O—C—C = 13.8 (9)°]. An intramolecular O—H⋯N hydrogen bond is observed. In the crystal structure, the molecules are linked into a two-dimensional network parallel to the (010) plane by intermolecular N—H⋯O, O—H⋯O and C—H⋯O hydrogen bonds
In the title compound, C(15)H(15)N(3)O(3)·H(2)O, the hydazide Schiff base mol-ecule shows an E conformation around the C=N bond. An intra-molecular O-H⋯N hydrogen bond makes an S(6) ring motif. The dihedral angle between the substituted phenyl rings is 23.40 (11)°. The water mol-ecule mediates linking of neighbouring mol-ecules through O-H⋯(O,O) hydrogen bonds into infinite chains along the a axis, which are further connected together through N-H⋯O hydrogen bonds, forming a two-dimensional network parallel to (001). C-H⋯O inter-actions aso occur.
Calculations of traditional HF and DFT based reactivity descriptors are reported for the isomeric benzofused thieno[3,2-b]furans in order to get insight into the factors determining the nature of their interactions with electrophiles. Global reactivity descriptors such as ionization energy, molecular hardness, electrophilicity, frontier molecular orbital energies and shapes, the condensed Fukui functions, total energies were determined and used to identify the differences in the stability and reactivity of benzofused thieno[3,2-b]furans. Additionally the bond order uniformity analysis, local ionization energy and electrostatic potential energy surfaces revealed structural differences of isomeric thieno[3,2-b]furans. Calculated values lead to the conclusion that heterocyclic system in thieno[3,2-b]benzofuran is more aromatic and stable than in isomeric benzothieno[3,2-b]furan. Theoretical results are in complete agreement with the experimental results and show exceptional reactivity of C(2) atom for both isomers.
The available data on the van der Waals radii of atoms in molecules and crystals are summarized. The nature of the continuous variation in interatomic distances from van der Waals to covalent values and the mechanisms of transformations between these types of chemical bonding are discussed.
The age-specific mortality rates and total deaths from specific cancers have not been documented for the various regions and subpopulations of India. We therefore assessed the cause of death in 2001-03 in homes in small areas that were chosen to be representative of all the parts of India.
At least 130 trained physicians independently assigned causes to 122,429 deaths, which occurred in 1·1 million homes in 6671 small areas that were randomly selected to be representative of all of India, based on a structured non-medical surveyor's field report.
7137 of 122,429 study deaths were due to cancer, corresponding to 556,400 national cancer deaths in India in 2010. 395,400 (71%) cancer deaths occurred in people aged 30-69 years (200,100 men and 195,300 women). At 30-69 years, the three most common fatal cancers were oral (including lip and pharynx, 45,800 [22·9%]), stomach (25,200 [12·6%]), and lung (including trachea and larynx, 22,900 [11·4%]) in men, and cervical (33,400 [17·1%]), stomach (27,500 [14·1%]), and breast (19,900 [10·2%]) in women. Tobacco-related cancers represented 42·0% (84,000) of male and 18·3% (35,700) of female cancer deaths and there were twice as many deaths from oral cancers as lung cancers. Age-standardised cancer mortality rates per 100,000 were similar in rural (men 95·6 [99% CI 89·6-101·7] and women 96·6 [90·7-102·6]) and urban areas (men 102·4 [92·7-112·1] and women 91·2 [81·9-100·5]), but varied greatly between the states, and were two times higher in the least educated than in the most educated adults (men, illiterate 106·6 [97·4-115·7] vs most educated 45·7 [37·8-53·6]; women, illiterate 106·7 [99·9-113·6] vs most educated 43·4 [30·7-56·1]). Cervical cancer was far less common in Muslim than in Hindu women (study deaths 24, age-standardised mortality ratio 0·68 [0·64-0·71] vs 340, 1·06 [1·05-1·08]).
Prevention of tobacco-related and cervical cancers and earlier detection of treatable cancers would reduce cancer deaths in India, particularly in the rural areas that are underserved by cancer services. The substantial variation in cancer rates in India suggests other risk factors or causative agents that remain to be discovered.
Bill & Melinda Gates Foundation and US National Institutes of Health.
ABSTRACT:
A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats.
We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion.
Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.
The purpose of this study was to analyze the physical properties and chemical compositions of a new experimental cement (NEC) and compare them with mineral trioxide aggregate (MTA); pH, working time, setting time, dimensional changes following setting, flow, film thickness, and chemical composition of NEC and MTA were assessed. For chemical compositions, all specimens were imaged and analyzed by scanning electron microscopy and electron probe microanalysis (EPMA). The physical properties were performed according to ISO 6876:2001. Working time, pH, and dimensional changes of NEC and MTA showed similar results. Shorter setting time was obtained with the NEC compared with MTA (p < 0.05). The NEC showed more flow than MTA. In addition, the film thickness of the NEC was considerably less than the MTA (p < 0.01 and p < 0.001, respectively). EPMA investigations indicated that lime (CaO) was the dominant compound in NEC and MTA; however, other compounds were significantly different. It was concluded that the chemical composition of NEC is different compare with MTA; it can be concluded that the NEC exhibits acceptable physical properties.
The drug discovery process has been deeply transformed recently by the use of computational ligand-based or structure-based methods, helping the lead compounds identification and optimization, and finally the delivery of new drug candidates more quickly and at lower cost. Structure-based computational methods for drug discovery mainly involve ligand-protein docking and rapid binding free energy estimation, both of which require force field parameterization for many drug candidates. Here, we present a fast force field generation tool, called SwissParam, able to generate, for arbitrary small organic molecule, topologies, and parameters based on the Merck molecular force field, but in a functional form that is compatible with the CHARMM force field. Output files can be used with CHARMM or GROMACS. The topologies and parameters generated by SwissParam are used by the docking software EADock2 and EADock DSS to describe the small molecules to be docked, whereas the protein is described by the CHARMM force field, and allow them to reach success rates ranging from 56 to 78%. We have also developed a rapid binding free energy estimation approach, using SwissParam for ligands and CHARMM22/27 for proteins, which requires only a short minimization to reproduce the experimental binding free energy of 214 ligand-protein complexes involving 62 different proteins, with a standard error of 2.0 kcal mol(-1), and a correlation coefficient of 0.74. Together, these results demonstrate the relevance of using SwissParam topologies and parameters to describe small organic molecules in computer-aided drug design applications, together with a CHARMM22/27 description of the target protein. SwissParam is available free of charge for academic users at www.swissparam.ch.
In the title compound, C15H14N2O4 center dot H2O, the dihedral angle between the two aromatic rings is 33.3 (5)degrees. The methoxy group is twisted slightly away from the attached benzene ring [C-O-C-C = 13.8 (9)degrees]. An intramolecular O-H center dot center dot center dot N hydrogen bond is observed. In the crystal structure, the molecules are linked into a two-dimensional network parallel to the (010) plane by intermolecular N-H center dot center dot center dot O, O-H center dot center dot center dot O and C-H center dot center dot center dot O hydrogen bonds.
The aim of this in vitro study was to evaluate five commonly used soft lining materials, Viscogel (VG), Ufi Gel P (UGP), Softliner (S), Coe-Soft (CS), and Molloplast-B (MB) in terms of cytotoxicity by MTT assay, using L929 mouse fibroblasts. Sixteen disk-shaped specimens from each material were prepared (according to the manufacturer's instructions) in stainless steel mold (10 mm diameter and 1.5 mm thick). The specimens were incubated for 24, 48, 72, and 96 h in Dulbecco's Modified Eagle Medium Ham's F12 (DMEM/F12) and following each incubation interval, cytotoxicity of the extracts to cultured mouse fibroblasts (L929) were measured by MTT assay. Data were statistically analyzed by two-way analysis of variance (ANOVA), and Duncan's test, at a significance level of p < 0.05. Group CS revealed significantly high cytotoxic effect at all incubation periods (p < 0.05). Although no cytotoxic effect for Group S was found at 24, 48, 72 h periods, it has been raised at 96-h incubation period (p > 0.05). Group VG, UGP, S (except at 96 h period), and Group MB demonstrated high cell survival rates at incubation periods.
A series of phenoxyimine compounds were designed and synthesized by the condensation of different substituted salicylaldehyde and aniline at the molar ratio of 1:1 in one step reaction. All synthesized compounds were characterized by analytical and spectroscopic techniques. All compounds were screened for cytotoxicity activities against different cancer cell lines. Compound 3 exhibits significant cytotoxic activity with an IC50 value of 1.099 µM, 1.132 µM against COLO-205 (Colorectal adenocarcinoma) and A-549 (Lung carcinoma) cell line respectively, while compound 4 exhibits noteworthy cytotoxic activity with an IC50 value of 0.52 µM against MDA-MB-231(Breast adenocarcinoma). Similarly, other compounds also exhibited good cytotoxicity properties. Furthermore, the phenoxyimine compounds showed the greatest antioxidant activity against DPPH radicals. The nontoxic activity was confirmed by cytocompatibility assay on L929 normal cell line and hemolysis assay on human red blood cells. Additionally, in silico molecular docking of all compounds were carried out against EGFR, HER-2 and VEGF. Compound 3 having minimum binding energy ΔGb = -8.81 kcal/mol, ΔGb = -10.49 kcal /mol, ΔGb = -9.99 kcal /mol, was bound into the active pocket of EGFR, HER-2 and VEGF respectively.
In Search of new microtubule-targeting compounds and to identify a promising Eg5 inhibitory agents, a series of 2-((7-chloroquinolin-4-yl) amino) benzohydrazide Schiff bases molecules (6 a-r) were synthesized using appropriate synthetic method. The synthesized compounds were characterized by using FTIR, Proton NMR, Carbon NMR and mass spectral analysis. All eighteen compounds were evaluated for their Eg5 inhibitory activity. Among the evaluated compounds, only seven compounds are shown inhibitory activity. The results of Steady state ATPase reveled that compounds 6b, 6l and 6p exhibited promising inhibitory activity with IC50 Values of 2.720 ± 0.69, 2.676 ± 0.53 and 2.408 ± 0.46 respectively. Malachite Green Assay results reveled that 6q compound showed better inhibitory activity with IC50 Value of 0.095 ± 0.27. In vitro antioxidant capacity of the synthesized compounds was investigated. A molecular docking studies were performed to evaluate interaction in to binding site of kinesin spindle protein, these interaction influencing may support Eg5 inhibitory activity. The drug like parameters of the eighteen synthesized compounds were also computed using Qikprop software. In conclusion, some of 2-((7-chloroquinolin-4-yl) amino) benzohydrazide Schiff base compounds represent promising drug like agents for discovery of effective anticancer molecules.
The structure-activity-relationships (SAR) were studied on two series of 2-(thienyl-2-yl or 3-yl)-4-furyl-6-aryl pyridine derivatives as anti-cancer drugs by DFT method at B 3 LYP/6-31G* level of theory.The structural and electronic properties of these compounds such as HOMO, LUMO, electronic energies, were calculated to gain insight about their role in modulating the anticancer activity. SAR study revealed that when CH 3 or Cl is present in para-position of phenyl ring, enhanced biological activity. Also, the structures of4-(5-chlorofuran-2-yl)-2-(thiophen-3yl) and 4-(5-chlorofuran-2-yl)-2-(thieophen-2-yl) moieties were important for cytotoxic effect. Finally, HOMO and LUMO energy values show clue about the biological activity profile of these compounds.
An organic crystal 4-amino pyridinium nicotinate (4APNA) single crystal has been grown by a slow evaporation method. The crystallinity and structural orientation of as-grown 4APNA compound was thoroughly studied using single-crystal X-ray diffraction and powder X-ray diffraction (XRD) and found to be a monoclinic crystal system with P21/c space group. Various functional groups in the grown crystal have been identified using Fourier-transform infrared (FTIR) spectra. The suitability of the crystal for optical applications was analyzed through Ultraviolet-Visible-near-IR Spectroscopy (UV-Vis-NIR) studies. Theoretical calculations were carried out using density functional theory (DFT) to define optical geometry using B3LYP with a 6-311G (d, p) basis set and the results have been compared with experimental data. The intermolecular interactions that exist inside the crystal have been investigated by Hirshfeld surface evaluation.
The title compound (E)-4-Bromo-N'-(2,4-dihydroxy-benzylidene) benzohydrazide (4BDBH) a novel hydrazone Schiff base compound was synthesized effectively by condensation of 4-bromobenzoic hydrazide and 2,4-dihydroxy benzaldehyde. Structural investigation by single crystal XRD reveals that 4BDBH crystallizes in monoclinic system with space group P21/c. The crystal structure of 4BDBH is stabilized by an intramolecular OH⋯N and intermolecular CH⋯O, NH⋯O, CH⋯Br, CH⋯π and π⋯π interactions. Vibrational spectroscopic studies were performed by utilizing FT–IR and FT–Raman spectral analysis along with DFT/B3LYP/6-311G(d,p) method using GAUSSIAN 09 software. This structure has also been confirmed by FT–IR and FT–Raman spectroscopy. Furthermore, the first order hyperpolarizability, MEP, HOMO– LUMO and Global chemical reactivity descriptors of 4BDBH were studied extensively. The results of the optimized molecular structure are presented and compared with that of the experimental X-ray diffraction values.
Our increasing understanding of cancer biology has led to the development of molecularly targeted anticancer drugs. The full potential of these agents has not, however, been realised, owing to the presence of de novo (intrinsic) resistance, often resulting from compensatory signalling pathways, or the development of acquired resistance in cancer cells via clonal evolution under the selective pressures of treatment. Combinations of targeted treatments can circumvent some mechanisms of resistance to yield a clinical benefit. We explore the challenges in identifying the best drug combinations and the best combination strategies, as well as the complexities of delivering these treatments to patients. Recognizing treatment-induced toxicity and the inability to use continuous pharmacodynamically effective doses of many targeted treatments necessitates creative intermittent scheduling. Serial tumour profiling and the use of parallel co-clinical trials can contribute to understanding mechanisms of resistance, and will guide the development of adaptive clinical trial designs that can accommodate hypothesis testing, in order to realize the full potential of combination therapies.
The title compound, (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid is characterized by means of X-ray crystallography, spectroscopic methods and quantum chemical calculations. The title compound crystallizes in centrosymmetric space group P21/c. Moreover, the crystal structure is primarily stabilized through intramolecular N-H⋯O and O-H⋯O and intermolecular N-H⋯O and C-H⋯O interactions along with carbonyl⋯carbonyl and C-H⋯C contacts. These intermolecular interactions are analysed and quantified by using Hirshfeld surface analysis, PIXEL energy, NBO, AIM and DFT calculations. The overall lattice energies of the title and parent compounds suggest that the title compound is stabilized by a 4.5 kcal mol-1 higher energy than the parent compound. The additional stabilization force comes from the methoxy substitution on the title molecule, which is evident since the methoxy group is involved in the intermolecular C-H⋯O interaction as an acceptor. The vibrational modes of the interacting groups are investigated using both experimental and theoretical FT-IR and FT-Raman spectra. The experimental and theoretical UV-Vis spectra agree well. The time dependent DFT spectra show that the ligand-to-ligand charge transfer is responsible for the intense absorbance of the compound.
A series of novel acylhydrazone derivatives were designed, synthesized and evaluated for their potential cytotoxic effects against human cancer cell lines. The preliminary results indicated that some of the obtained compounds (such as 8b, 13c) exhibited good to moderate cytotoxic activities against human HepG2, Huh-7, and BCG-823 cell lines. Especially, compounds 8c and 8e presented obviously selective cytotoxic activities against Huh-7 in vitro (8c, IC50=7.74±2.18μg/mL; 8e, IC50=4.46±1.05μg/mL) compared to 5-FU (IC50=10.41±3.41μg/mL). The highly potential compounds to induce apoptosis in HepG2 cells were analyzed by flow cytometry, and the apoptotic effects of compounds 8b and 13c were further evaluated using Annexin V-FITC/propidium iodide dual staining assay.
Calculations of traditional HF and DFT based reactivity descriptors are reported for the isomeric benzofused thieno[3,2-b]furans in order to get insight into the factors determining the nature of their interactions with electrophiles. Global reactivity descriptors such as ionization energy, molecular hardness, electrophilicity, frontier molecular orbital energies and shapes, the condensed Fukui functions, total energies were determined and used to identify the differences in the stability and reactivity of benzofused thieno[3,2-b]furans. Additionally the bond order uniformity analysis, local ionization energy and electrostatic potential energy surfaces revealed structural differences of isomeric thieno[3,2-b]furans. Calculated values lead to the conclusion that heterocyclic system in thieno[3,2-b]benzofuran is more aromatic and stable than in isomeric benzothieno[3,2-b]furan. Theoretical results are in complete agreement with the experimental results and show exceptional reactivity of C(2) atom for both isomers.
Mn(II) complexes derived from a set of acylhydrazones were synthesised and characterized by elemental analyzes, IR, UV–vis and X-band EPR spectral studies as well as conductivity and magnetic susceptibility measurements. In the reported complexes, the hydrazones exist either in the keto or enolate form, as evidenced by IR spectral data. Crystal structures of two complexes are well established using single crystal X-ray diffraction studies. In both of these complexes two equivalent monoanionic ligands are coordinated in a meridional fashion using cis pyridyl, trans azomethine nitrogen and cis enolate oxygen atoms positioned very nearly perpendicular to each other. EPR spectra in DMF solutions at 77 K show hyperfine sextets and in some of the complexes the low intensity forbidden lines lying between each of the two hyperfine lines are also observed.
The molecular structure of a new Schiff base, 2-[4-hydroxy benzylidene]-amino naphthalene (HBAN) has been examined by HF and B3LYP/6-311++G(d,p) calculations. The X-ray structure was determined in order to establish the conformation of the molecule. The compound, C17H13NO, crystallizes in the orthorhombic, P212121 space group with the cell dimension, a=6.2867(2), b=10.2108(3), c=19.2950(6) Å, α=β=γ=90° and z=4. The asymmetric unit contains a molecule of a Schiff base. A strong intermolecular OH⋯N and a weak CH⋯O hydrogen bonds stabilized the crystal structure. The vibrational spectra of HBAN have been calculated using density functional theoretical computation and compared with the experimental. The study is extended to the HOMO-LUMO analysis to calculate the energy gap (Δ), Ionization potential (I), Electron Affinity (A), Global Hardness (η), Chemical Potential (μ) and Global Electrophilicity (w). The calculated HOMO and LUMO energy reveals that the charge transfer occurs within the molecule.
A series of imino and amino derivatives of 4-hydroxycoumarins were synthesised and evaluated for antioxidant potential, through different in vitro models such as (DPPH) free radical-scavenging activity, linoleic acid emulsion model system, reducing power assay and phosphomolybdenum method. Also, antimicrobial activity of obtained coumarins was evaluated against 13 bacteria and eight fungi. All prepared compounds possessed good antioxidant activity and among them a p-nitrophenol derivative with IC50 at 25.9μM possessed radical-scavenging activity which was comparable to BHT. Observed data for antibacterial activity indicated strong activity of all tested amino derivatives, while imines showed better antifungal properties.
Five Ni(II) complexes of aroyl hydrazone ligands with 2,6-diacetyl pyridine monooxime are reported. X-ray crystal structure of the Ni(II) salicyloylhydrazone complex is also reported. In these complexes Ni(II) is in a distorted octahedral N4O2 coordination environment, with each of the two ligands coordinating through the pyridine nitrogen, imino-hydrazone nitrogen and the deprotonated oxygen of the hydrazone moiety. The iminooxime group remain uncoordinated in both the ligands and the planes containing the CH3–CN–OH groups are orthogonal to the adjacent pyridine rings. On excitation at 375 nm, the ligands as well as the Ni(II) complexes, show luminescence. However, the Ni(II) complexes have much lower quantum yield of emission than the free ligands.
Intermolecular van der Waals radii of the nonmetallic elements have been assembled into a list of "recommended" values for volume calculations. These values have been arrived at by selecting from the most reliable X-ray diffraction data those which could be reconciled with crystal density at 0°K. (to give reasonable packing density), gas kinetic collision cross section, critical density, and liquid state properties. A qualitative understanding of the nature of van der Waals radii is provided by correlation with the de Broglie wave length of the outermost valence electron. Tentative values for the van der Waals radii of metallic elements - in metal organic compounds - are proposed. The paper concludes with a list of increments for the volume of molecules impenetrable to thermal collision, the so-called van der Waals volume, and of the corresponding increments in area per molecule.
In this chapter we review the development of small molecule inhibitors that act on targets involved in the causation and progression of human cancer. Considerable success has been achieved with drugs like imatinib and erlotinib that demonstrate the clinical utility of the molecular targeted approach. However, the success rate for cancer drugs in clinical development is only 1 in 20. We review the technologies that are being implemented to improve the success rate and increase the speed of preclinical oncology drug development. Topics covered include the selection and validation of drug targets, with emphasis on the genetics and biology of the disease, as well as on “druggability”; the generation of chemical “leads”, including various high-throughput screening approaches; the use of structure-based drug design, particularly using X-ray crystallography; the value of chemical biology approaches; and the importance of biomarkers for patient selection and rational drug development. The integrated use of these technologies is illustrated using selected case histories. The chapter concludes with a look into the future and an assessment of the likely progress towards the development of bespoke cancer medicine. This chapter is followed by a companion chapter in which we review the clinical development of targeted molecular therapeutics.
This paper provides an overview of the title paper by Miertus, Scrocco and Tomasi, including the impact that it has had on
the theoretical description of solvation by means of continuum models.
The methanolic fresh leaf extracts of Macaranga gigantea, Macaranga pruinosa, Macaranga tanarius and Macaranga triloba were screened for their antioxidant properties (AOP), tyrosinase inhibition and antibacterial activities. Total phenolic content (TPC), 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging, ferric-ion reducing power (FRAP), ferrous-ion chelating (FIC) and lipid peroxidation inhibition (LPI) activities were used to evaluate the AOP. Modified 3,4-dihydroxy-L-phenylalanine (L-DOPA) method was used to determine tyrosinase inhibition activity, whereas antibacterial activity was determined using the disc-diffusion technique. TPC screening of the same species from different collection sites showed no significant difference between sites. M.triloba showed the highest ascorbic acid equivalent antioxidant activity (AEAC), FRAP and LPI values. M. tanarius, which showed the lowest TPC, AEAC, FRAP and LPI activities, exhibited the best FIC activity. M. pruinosa showed the best tyrosinase inhibition activity, whereas M. triloba showed the best antibacterial activity against Gram-positive bacteria species, with minimal inhibition dosage (MID) values as low as 10 μg/disc.
In this study, the molecular structure and spectroscopic properties of title compound were characterized by X-ray diffraction, FT-IR and UV-vis spectroscopies. These properties of title compound were also investigated from calculative point of view. The X-ray diffraction and FT-IR analyses reveal the existence of keto form in the solid state. UV-vis spectra were recorded in different organic solvents. The results show that title compound exists in both keto and enol forms in DMSO, EtOH but it exists in enol form in benzene. In addition, the title compound in DMSO showed new absorption band at 436 nm due to the high ionizing effect of this solvent. The geometry optimization of title compound in gas phase was performed using DFT method with B3LYP applying 6-311G(d,p) basis set. TD-DFT calculations starting from optimized geometry were carried out in gas phase to calculate excitation energies of title compound. The non-linear optical properties were computed with the same level of theory and title compound showed a good second order nonlinear optical property. In addition, thermodynamic properties were obtained in the range of 100-500 K.
Gefitinib is a small molecule tyrosine kinase inhibitor of epidermal growth factor receptor (EGFR). Since 2004, it was clear that a substantial proportion of non-small-cell lung cancers (NSCLC) obtaining objective response when treated with gefitinib harbour activating mutations in the EGFR gene. Consequently, EGFR mutation has been widely studied, together with other molecular characteristics, as a potential predictive factor for gefitinib efficacy. As of August 2010, four East Asian randomized phase III trials comparing gefitinib to platinum-based chemotherapy in patients with advanced non-small-cell lung cancer (NSCLC) eligible for first-line treatment have been reported or published. Two of these trials were conducted without a molecular selection in patients with clinical characteristics (adenocarcinoma histology, never or light smoking) characterized by higher prevalence of EGFR mutation. In patients selected for the presence of tumor harbouring EGFR mutation, the administration of first-line gefitinib, as compared to standard chemotherapy, was associated with longer progression-free survival, higher objective response rate, a more favourable toxicity profile and better quality of life. The relevant improvement in progression-free survival with first-line administration of gefitinib has been confirmed in the other two randomized trials, dedicated to cases with EGFR mutation. In July 2009, European Medicines Agency granted marketing authorization for gefitinib for the treatment of locally advanced or metastatic NSCLC with sensitizing mutations of the EGFR gene, across all lines of therapy. Gefitinib currently represents the best first-line treatment option for this molecularly selected subgroup of patients.
Cytotoxic chemotherapy remains the mainstay of treatment for triple-negative breast cancer (TNBC) despite the promise of new targeted and biologic agents. Many studies have shown significant benefit of chemotherapy in the neoadjuvant, adjuvant, and metastatic treatment of TNBC. Neoadjuvant chemotherapy studies have consistently reported higher response rates in TNBC than non-TNBC, and pathologic complete response has been shown to predict improved long-term outcomes for TNBC. Although the specific adjuvant regimens that may be most effective for TNBC are still being determined, third-generation chemotherapy regimens using dose dense or metronomic polychemotherapy are among the most effective tools presently available. The role of specific chemotherapy agents in the treatment of TNBC remains incompletely defined and warrants careful review to ensure that the most effective therapy is delivered while minimizing unnecessary toxicity. Platinum agents have seen renewed interest in TNBC based on a growing body of preclinical and clinical data suggesting encouraging activity. Taxanes and anthracyclines are active in TNBC and remain important agents but have not shown specific benefit over non-TNBC. Capecitabine has limited reported data in TNBC, but some reports suggest differential activity in TNBC compared with hormone receptor-positive breast cancer. TNBC is itself a heterogeneous group in which subgroups such as BRCA1 mutation carriers may have particular sensitivity to platinum agents and relatively less sensitivity to taxanes. Therefore, the identification of additional molecular biomarkers to predict response to specific chemotherapy is required to further improve treatment strategies with the current menu of chemotherapy options and future combinations with targeted therapies.
A series of 4-(morpholin-4-yl)-N'-(arylidene)benzohydrazides were synthesized using appropriate synthetic route. Antimycobacterial activity of the synthesized compounds (5a-5j) was carried out and percentage reduction in relative light units (RLU) was calculated using luciferase reporter phages (LRP) assay. Percentage reduction in relative light units (RLU) for isoniazid was also calculated. The test compounds showed significant antitubercular activity against Mycobacterium tuberculosis H37Rv and clinical isolates: S, H, R, and E resistant M. tuberculosis, when tested in vitro. Quantitative structure-activity relationship (QSAR) investigation with 2D-QSAR analysis was applied to find a correlation between different experimental or calculated physicochemical parameters of the compounds studied and 3D-QSAR analysis and to indicate the exact steric and electronic requirements in the ranges at various positions around pharmacophore. In general Schiff bases exhibit antimycobacterial activity and morpholine ring is important for antimicrobial activity. So we have synthesized 10 different 4-(morpholin-4-yl)-N'-(arylidene)benzohydrazides. The structures of new compounds were characterized by TLC, FTIR, (1)H NMR, mass spectral data and elemental analysis. Amongst the compounds tested 5d and 5c were found to be the most potent, while 5i, 5e, and 5j were found to have an average activity against M. tuberculosis H37Rv and 5a, 5f, 5h, 5g, and 5b were found to have a greater activity against clinical isolates: S, H, R, and E resistant M. tuberculosis as compared to M. tuberculosis H37Rv.
We have developed a new and simple flow cytometric method to detect damaged red blood cells (RBCs) using anti-Hb in hypotonic solution. We studied a total of 200 patients, including 62 patients with schistocytosis, 8 postsplenectomy patients, and 108 healthy controls. Peripheral blood (2 microl) was stained with phycoerythrin-conjugated (PE) antihemoglobin antibody (anti-Hb) in 0.6% (w/v) NaCl solution, and analyzed by flow cytometry omitting the washing step. The proportion of RBCs stained by anti-Hb was 0.55% (SD +/-0.23%) in normal controls and was significantly higher in patients with schistocytosis (2.95+/-2.95%, p <0.001). Six of 108 blood samples from normal controls and 60 of 62 samples from schistocytosis patients showed > or =1.01% stained RBCs (ie, values > mean+2SD of normal controls). The number of schistocytes counted by microscopic examination correlated with the proportion of RBCs stained by anti-Hb (r = 0.637, p <0.001). The proportions of stained RBCs in blood samples with malaria, spherocytosis, and elliptocytosis were also significantly higher than in normal controls. However, the results in postsplenectomy and iron-deficiency anemia (IDA) patients were not significantly different from the normal controls; the number of schistocytes in postsplenectomy patients was not related to the proportion of RBCs stained by anti-Hb. Based on these findings, flow cytometry of damaged RBCs using anti-Hb in hypotonic solution is a simple, sensitive, and accurate method to detect active hemolysis.
We present a method, termed AutoLigand, for the prediction of ligand-binding sites in proteins of known structure. The method searches the space surrounding the protein and finds the contiguous envelope with the specified volume of atoms, which has the largest possible interaction energy with the protein. It uses a full atomic representation, with atom types for carbon, hydrogen, oxygen, nitrogen and sulfur (and others, if desired), and is designed to minimize the need for artificial geometry. Testing on a set of 187 diverse protein-ligand complexes has shown that the method is successful in predicting the location and approximate volume of the binding site in 73% of cases. Additional testing was performed on a set of 96 protein-ligand complexes with crystallographic structures of apo and holo forms, and AutoLigand was able to predict the binding site in 80% of the apo structures.
Global Cancer Observatory: Cancer Today
- Ferlay