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1.
Inorg Chem ; 58(11): 7615-7627, 2019 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-31074996

RESUMO

Despite significant advances in the development of highly efficient and robust oxygen evolution reaction (OER) electrocatalysts to replace noble-metal catalysts, commercializing OER catalysts with high catalytic activity for sustainable development still remains a great challenge. Especially, transition-metal Fe-based OER catalysts, despite their earth-abundant, cost-efficient, and environmentally benign superiorities over Co- and Ni-based materials, have received relatively insufficient attention because of their poor apparent OER activities. Herein, by rational design, we report Ni-modified pyrite (FeS2) spheres with yolk-shell structure that could serve as pre-electrocatalyst precursors to induce a highly active nickel-iron oxyhydroxide via in situ electrochemical topological transformation under the OER process. Notably, as confirmed by the results of X-ray absorption spectroscopy, X-ray photoelectron spectroscopy, and density functional theory (DFT) calculations, Ni doping could effectively regulate the intrinsic electronic structure of FeS2 to realize a semiconductor-to-semimetal transition, which endows FeS2 with dramatically improved conductivity and water adsorption ability, providing prequisites for subsequent topological transformation. Moreover, systematic post-characterizations further reveal that the optimal Ni-FeS2-0.5 sample completely converts to amorphous Ni-doped FeOOH via an in situ electrochemical transformation with yolk-shell structure well-preserved under the OER conditions. The electronic structure modulation combined with electrochemical topotactic transformation strategies well stimulate the reactive Fe sites in Ni-FeS2-0.5, which show impressively low overpotentials of 250 and 326 mV to drive the current densities ( j) of 10 and 100 mA cm-2, respectively, and a Tafel slope as small as 34 mV dec-1 for the OER process. When assembled as a water electrolyzer for the overall water splitting, Ni-FeS2-0.5 can display a low voltage of 1.55 V to drive a current density of 10 mA cm-2, outperforming most of the transition-metal-based bifunctional electrocatalysts to date. This work may provide new insight into the rational design of other high-performance Fe-based OER electrocatalysts and inspire the exploration of cost-effective, ecofriendly electrocatalysts to meet the demand for future sustainable development.

2.
J Nanosci Nanotechnol ; 18(8): 5404-5413, 2018 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-29458592

RESUMO

In this paper, authors report the synthesis of nanocrystalline hierarchical zeolite ZSM-5 and its application as a heterogeneous catalyst in the alkylation of phenol with cyclohexene. The catalyst was synthesized by vacuum-concentration coupled hydrothermal technique in the presence of two templates. This synthetic route could successfully introduce pores of higher hierarchy in the zeolite ZSM-5 structure. Hierarchical ZSM-5 could catalyse effectively the industrially important reaction of cyclohexene with phenol. We ascribe the high efficiency of the catalyst to its conducive structural features such as nanoscale size, high surface area, presence of hierarchy of pores and existence of Lewis sites along with Brønsted acid sites. The effect of various reaction parameters like duration, catalyst amount, reactant mole ratio and temperature were assessed. Under optimum reaction conditions, the catalyst showed up to 65% selectivity towards the major product, cyclohexyl phenyl ether. There was no discernible decline in percent conversion or selectivity even when the catalyst was re-used for up to four runs. Kinetic studies were done through regression analysis and a mechanistic route based on LHHW model was suggested.

3.
Mol Divers ; 21(3): 533-546, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28444482

RESUMO

1,4-Dihydropyridines are well-known calcium channel blockers, but variations in the substituents attached to the ring have resulted in their role reversal making them calcium channel activators in some cases. We describe the microwave-assisted eco-friendly approach for the synthesis of pyranopyrazole-1,4-dihydropyridines, a new class of 1,4-DHPs, under solvent-free conditions in good yield, and screen them for various in silico, in vitro and in vivo activities. The in vivo experimentation results show that the compounds possess positive inotropic effect, and the docking results validate their good binding with calcium channels. Compounds 7c, 7g and 7i appear to be the most effective positive inotropes, even at low doses, and bind with the calcium channels even more strongly than Bay K 8644, a well-known calcium channel activator. The chronotropic effect for the new compounds was also studied. The target and off-target affinity profiling supported the in vivo results and revealed that the hybridized pyranopyrazole dihydropyridine scaffold has delivered new moderate hits, to be optimized, for the cytochrome P450 3A4 enzymes, opening avenues for combined pharmacological activity through standard structural modification.


Assuntos
Agonistas dos Canais de Cálcio/administração & dosagem , Agonistas dos Canais de Cálcio/síntese química , Di-Hidropiridinas/administração & dosagem , Di-Hidropiridinas/síntese química , Animais , Pressão Sanguínea/efeitos dos fármacos , Agonistas dos Canais de Cálcio/química , Agonistas dos Canais de Cálcio/farmacologia , Di-Hidropiridinas/química , Di-Hidropiridinas/farmacologia , Relação Dose-Resposta a Droga , Frequência Cardíaca/efeitos dos fármacos , Camundongos , Micro-Ondas , Modelos Moleculares , Simulação de Acoplamento Molecular , Estrutura Molecular
4.
J Nanosci Nanotechnol ; 17(2): 1329-337, 2017 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-29683627

RESUMO

The current paper reports the application of nanocrystalline form of zeolite ZSM-5 in lieu of Friedel Crafts catalysts in the benzylation of anisole using benzyl alcohol. There are many problems associated with the use and disposal of conventional catalysts due to their toxicity, corrosiveness and non-recyclability. Nanocrystalline zeolites can be a less polluting alternative to the conventional Friedel Crafts catalysts. Nanocrystalline ZSM-5 was synthesized by a facile method and was characterized using SEM, XRD and FTIR. The prepared nanocrystalline zeolite was then evaluated for its efficiency and selectivity in liquid phase benzylation of anisole. Optimum conditions of reaction time, temperature, quantity of catalyst and mole ratio of reactants were obtained. Kinetic studies were done to propose a mechanistic model for the catalyzed reaction. Results of this study suggest that the synthesized nanocrystals of zeolites are efficient, selective, stable, consistent and reusable catalysts. This catalyst thus holds the possibility of being a better alternative to homogeneous catalysts, from environmental and economic perspectives.

5.
J Biomol Struct Dyn ; 41(12): 5465-5480, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-35735269

RESUMO

Cancer remains a serious health concern representing one of the leading causes of deaths worldwide. The enzyme human carbonic anhydrase IX (hCA IX) is found to be over-expressed in many cancer types and its selective inhibition over its cytosolic off-target isoform, human carbonic anhydrase II (hCA II), represents a potential area of research in the development of novel anticancer compounds. This work is concerned with the use of various in silico tools for the identification of natural product based molecules that can selectively inhibit hCA IX over hCA II. MM-GBSA assisted structure-based virtual screening against hCA IX was performed for nearly 225,000 natural products imported from the ZINC15 database. The obtained hits were checked for their potency by considering acetazolamide, the bound inhibitor of hCA IX, as the reference molecule, and 121 molecules were identified as potent hCA IX inhibitors. After ensuring their potency, cross-docking, followed by MM-GBSA calculations of the hits with hCA II, was performed, and their selectivity was assessed by considering the hCA IX selective compound SLC-0111 as the reference molecule, and 50 natural products were identified as potent as well as selective hCA IX inhibitors. Molecules with the quinoline scaffold showed the highest selectivity, and their selectivity was attributed to the strong electrostatic interactions of the zinc binding group (ZBG) with the active site Zn(II) ion. Furthermore, the stability of the binding modes of the top hCA IX selective hits was ensured by performing molecular dynamics (MD) simulations, which clearly proved that one of the short-listed molecules is truly selective, as it does not interact with the active site Zn(II) ion of hCA II, but interacts strongly with this ion in hCA IX. Bonding pose metadynamics studies revealed that the ligand moves to a more stable binding site from the one predicted by the docking studies and shows stronger interaction with the protein and Zn(II) at this binding site. The ligand is not likely to have issues with bioavailability. As a result, this ligand can be taken for bioassay testing and subsequently used as a feasible therapeutic treatment for a variety of cancer types. Communicated by Ramaswamy H. Sarma.


Assuntos
Simulação de Dinâmica Molecular , Neoplasias , Humanos , Anidrase Carbônica IX , Estrutura Molecular , Relação Estrutura-Atividade , Simulação de Acoplamento Molecular , Ligantes , Neoplasias/tratamento farmacológico , Inibidores da Anidrase Carbônica/farmacologia , Inibidores da Anidrase Carbônica/química
6.
J Biomol Struct Dyn ; : 1-16, 2023 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-37301606

RESUMO

Interaction of the minor groove binder, Hoechst 33258, with the Dickerson-Drew DNA dodecamer sequence has been investigated using docking, MM/QM, MM/GBSA and molecular dynamics computations to study the modes of binding and the interactions responsible for the binding. Besides the original Hoechst 33258 ligand (HT), a total of 12 ionization and stereochemical states for the ligand are obtained at the physiological pH and have been docked into B-DNA. These states have one or the other or both benzimidazole rings in protonated states, apart from the piperazine nitrogen, which has a quaternary nitrogen in all the states. Most of these states are found to exhibit good docking scores and free energy of binding with B-DNA. The best docked state has been taken further for molecular dynamics simulations and compared with the original HT. This state is protonated at both benzimidazole rings besides the piperazine ring and hence has very highly negative coulombic interaction energy. In both cases, there are strong coulombic interactions, but these are offset by the almost equally unfavorable solvation energies. Thus, the nonpolar forces, particularly van der Waals contacts, dominate the interaction, and the polar interactions highlight subtle changes in the binding energies, leading to more highly protonated states having more negative binding energies.Communicated by Ramaswamy H. Sarma.

7.
Anal Methods ; 15(32): 4000-4009, 2023 Aug 17.
Artigo em Inglês | MEDLINE | ID: mdl-37545382

RESUMO

A new rhodamine based fluorescent and colorimetric chemosensor S1 was synthesized for the selective recognition of Cr3+, a trivalent metal ion. The interaction of S1 toward different metal ions has been studied via fluorescence and UV-visible spectroscopy. The studies revealed that the fluorescence and colorimetric changes of chemosensor S1 are prominent for Cr3+ over other competitive metal ions. Moreover, the chemosensor S1 exhibits 1 : 1 complex formation with Cr3+ as apparent from the Job's plot and the Benesi-Hildebrand (B-H) plot. Density functional theory (DFT) studies also revealed that the Cr3+ ion is coordinated to three atoms of S1, which validates the formation of a complex between S1 and Cr3+. The limit of detection (LOD) of chemosensor S1 for Cr3+ was 0.21 µM. Furthermore, to explore the recyclability of S1, ethylenediaminetetraacetic acid (EDTA) was added to the S1-Cr3+ solution. On the addition of EDTA to the solution of S1-Cr3+, the reversibility of the complex was observed, and a colorimetric variation was also observed on the addition of Cr3+ and EDTA to S1 which mimics the "INHIBIT "molecular logic gate. Chemosensor S1 also demonstrated practical utility through detection of Cr3+ in the solid state.

8.
J Mol Graph Model ; 111: 108099, 2022 03.
Artigo em Inglês | MEDLINE | ID: mdl-34871980

RESUMO

This paper examines the alterations in the properties of II-VI Quantum Dots (QDs) when these are coated with a shell made of another material of the same family and investigates the structural, electronic and magnetic properties of doped CdS/ZnS core/shell QDs. The core/shell QDs have been constructed by building the shell over the bare core QD and it is found that this construction of a shell over the bare QD can bring about dramatic changes in its optical properties. On changing the shell by varying either the cation or the anion, substantial variations are brought about in the band gap and electrophilicity. The trend of Fermi energies is more negative for core/shell QDs than for the QDs without a shell, and the value is almost the same for core/shell QDs with the same core. Swapping of the core and the shell materials brings greater stability in the case of shells of the wider band gap materials. Binding energy data demonstrates that the CdS/ZnS, CdSe/ZnSe, CdSe/CdS core/shell systems are more stable than ZnS/CdS, ZnSe/CdSe, CdS/CdSe core/shell systems, respectively. An augmentation in the properties is found on doping the QD with transition metal ions. The binding energies are found to be functions of the kind of dopant as well as the spin multiplicity and account for the stability of one spin state over the other at a specific site of the QD. The most fascinating property that plays a decisive role in the extant work is the introduction of magnetism in core/shell QDs as a result of the entry of unpaired electrons within the CdS/ZnS QDs on doping with transition metal ions. The deviation of the observed magnetic moments from the expected values increases as the dopant is varied from Mn2+ to Fe2+ to Co2+ to Ni2+ to Cu2+. Hirshfeld charge analysis shows that the doped ion accepts negative charge from the sulfide ions in the core, with the smallest charge transfer seen in the case of Hg2+ ions. As we move from Mn2+ to Hg2+, the trend followed for the Hirshfeld charges indicates that the overall charge on the core is lower and that on the shell is higher for all the doped cases in comparison to the undoped CdS/ZnS core/shell QD. The band gap values reveal that the Fe2+ doped CdS/ZnS core/shell structures have the smallest band gaps. Hence, we expect that this paper will help researchers to develop a strategy to produce QDs of the anticipated properties for various applications, and transition metal ions can be successfully employed for modification of various magnetoelectronic properties of the host semiconductor for future applications in nanotechnology.


Assuntos
Pontos Quânticos , Elementos de Transição , Sulfetos , Compostos de Zinco
9.
J Biomol Struct Dyn ; 40(10): 4516-4531, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-33317405

RESUMO

Human carbonic anhydrase IX (hCA IX) is a promising target for the development of potential anticancer agents. In the current study, pharmacophore and 3D-QSAR models have been developed using SLC-0111 derivatives. The developed models have been further utilized for the virtual screening process to develop potent hCA IX inhibitors. Thirteen different models have been developed by employing various combinations of training and test set molecules. Based on this, a model, AADDR.135, comprising two H-bond acceptors, two H-bond donors and one aromatic ring, has been found as the best QSAR model. The proposed model exhibits high robustness (R2 = 0.9789), with good predictive ability (Q2 = 0.6872). An external library of drug-like compounds (∼10000 molecules) imported from the ZINC15 database has been screened over the model AADDR.135. In total, 1601 compounds were obtained as hits. Molecular docking studies and molecular dynamics simulations have been performed on the obtained hits and, based on these computations, two unique molecules have been identified as potential hCA IX inhibitors. These show higher binding energies compared to the parent molecule and its most potent analogue.Communicated by Ramaswamy H. Sarma.


Assuntos
Simulação de Dinâmica Molecular , Relação Quantitativa Estrutura-Atividade , Anidrase Carbônica IX/química , Humanos , Simulação de Acoplamento Molecular
10.
J Biomol Struct Dyn ; 40(21): 11229-11238, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34323658

RESUMO

We have investigated the active site of E. coli MurB using the Quantum Mechanics/Molecular Mechanics (QM/MM) methodology. The docking of three novel series of 4-thiazolidinone derivatives has been performed using two methods: rigid docking and flexible docking (Induced Fit Docking: IFD). The results have been compared to understand the conformational aspects of the enzyme. The docking results from rigid docking show that the ligands with highly negative ΔGbind have poor docking scores. In addition, the value of the regression coefficient (R) obtained on correlating the ΔGbind and the experimental pMIC values is insignificant. On keeping the protein flexible, there is a remarkable improvement in both the docking score and ΔGbind, along with a good value of R (0.64). Two important residues, Tyr254 and Try190 are found to be highly displaced during the flexible docking and hence their role in effective ligand binding has been confirmed. Thus, comparing the two methodologies, IFD has emerged as the more appropriate one for studying the E. coli MurB enzyme. To further substantiate the findings, MD studies over a time period of 20 ns have been performed on the IFD-LIII j and Rigid/XP-LIII j complexes and the results shows the former complex to be more stable, with lower average RMSD and higher average ΔGbind.Communicated by Ramaswamy H. Sarma.


Assuntos
Escherichia coli , Simulação de Dinâmica Molecular , Ligantes , Simulação de Acoplamento Molecular , Ligação Proteica , Domínio Catalítico
11.
J Biomol Struct Dyn ; 39(2): 502-517, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31900046

RESUMO

Histone deacetylases (HDACs) are a widely popular class of epigenetic regulators, second only in importance to DNA methyltransferases. They are responsible for deacetylating the lysine residues of a wide range of proteins, both nuclear and cytoplasmic. Therefore, deregulated HDAC activity is implicated in disruption of important biological functions leading to cancerous, neuropathological, infectious and inflammatory diseased states. The current therapeutic strategies aimed at combating HDAC related pathologies consist of pan HDAC inhibitors that target multiple HDAC isoforms. Many side-effects of such therapeutics have been reported due to off-target effects. Hence, efforts need to be focused towards developing therapeutics targeting single isoforms. This work aims at recognizing structural features, both of receptors and inhibitors, that would help achieve selective inhibition of HDAC isoforms. Protein alignment studies have been carried out to define the receptor structure differences that can be exploited for this purpose. Binding modes of highly isoform selective inhibitors have been established through molecular docking studies to characterize the receptor-ligand interactions responsible for selective inhibition. This information is represented with the help of pharmacophore models.


Assuntos
Inibidores de Histona Desacetilases , Histona Desacetilases , Inibidores de Histona Desacetilases/farmacologia , Ligantes , Simulação de Acoplamento Molecular , Isoformas de Proteínas
12.
Phytochemistry ; 192: 112964, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34598043

RESUMO

Polyphenolic compounds are known to exhibit potent antioxidant properties owing to the presence of various phenolic groups. The present study reports the antioxidant potentials of six retrochalcones, namely echinatin, and licochalcone A, B, C, D and E, isolated from the root of the Glycyrrhiza species, toward various reactive oxygen and nitrogen species. Different mechanistic pathways, viz. hydrogen atom transfer (HAT), single electron transfer (SET), single electron transfer followed by proton transfer (SET-PT), and sequential proton loss electron transfer (SPLET), have been considered. In addition, two other pathways, i.e. sequential double proton loss electron transfer (SdPLET) and sequential proton loss hydrogen atom transfer (SPLHAT), which are significant for the scavenging of reactive species by the mono-deprotonated forms of retrochalcones, have also been considered. All the calculations were performed using density functional theory at the B3LYP/6-311++G** level in the gas phase and in aqueous solution. The results suggest the predominance of the HAT mechanism in the gas phase, while in aqueous solution, the SPLET mechanism is thermodynamically favored. The possibility of SdPLET increases at higher pH.


Assuntos
Antioxidantes , Glycyrrhiza , Fenóis , Prótons , Termodinâmica
13.
J Biomol Struct Dyn ; 39(2): 656-671, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31906796

RESUMO

Currently, the growing incidence of drug resistance toward tuberculosis intensified the need for discovery of novel targets and their inhibitors. The enzyme MurB which is involved in one of the steps for peptidoglycan biosynthesis is an effective target that can produce drugs having lesser side-effects. Recently the only crystal structure of Mycobacterium Tuberculosis MurB has been deposited and, therefore, in the present study, we have used this as a target for virtual screening of drug-like molecules from the ZINC Database. We have also designed a complete workflow for the process which resulted in 12 hit compounds that have good docking scores, ΔGbind, and Glide energy. The hits obtained have also been found to share structural features with some known antibiotics such as Amoxicillin. Furthermore, MD simulations on the top most hit L1 displayed its stable binding with the enzyme. Thus, this study has proved helpful in proposing novel inhibitors for MurB enzyme that can be tested against various TB strains.


Assuntos
Simulação de Dinâmica Molecular , Mycobacterium tuberculosis , Sítios de Ligação , Inibidores Enzimáticos/farmacologia , Simulação de Acoplamento Molecular , Oxirredutases , Ligação Proteica
14.
J Mol Graph Model ; 101: 107754, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-32966915

RESUMO

Phosgene derivatives and chloromethyl chloroformate are chlorinated organic compounds, which are toxic in nature and are used as chemical warfare agents and for the synthesis of other organic compounds. In this work, the different modes of adsorption of these toxic molecules on pristine graphene and Fe4-decorated graphene have been studied. It has been found that physisorption of these adsorbates occurs on pristine graphene, but when graphene is decorated with a Fe4-cluster, dissociative adsorption takes place and the adsorption energy and charge transfer increase. After Fe4-cluster decoration, the surface exhibits magnetic character and its band gap decreases. The magnetic properties of the surface, before and after adsorption, have been studied using density of states (DOS)/partial density of states (PDOS) and electron density difference plots and it is found that the band gap increases after adsorption of the adsorbates.


Assuntos
Grafite , Fosgênio , Adsorção
15.
Comput Biol Med ; 123: 103850, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32658783

RESUMO

Histone deacetylases (HDACs) play important roles in various biological processes, but are also notorious for their over-expression in numerous cancers and neurological disorders. Therefore, the development of isoform selective HDAC inhibitors is crucial in order to prevent any side effects of pan inhibition. This work focuses on identifying novel inhibitors for the selective inhibition of HDAC8, an isoform implicated in fatal diseases like T-cell lymphoma, colon cancer and childhood neuroblastoma. Virtual screening of the 'In-trials' subset of ZINC database has been carried out with the help of two pharmacophore models signifying potent and selective HDAC8 inhibition. A detailed molecular docking strategy, followed by molecular dynamics simulations and post-scoring with MM-GBSA calculations, has led to the identification of six promising molecules that have excellent binding with the HDAC8 active site. In order to establish the selectivity profile of these molecules, their binding to off-target HDAC isoforms has also been evaluated. Substitution analyses of the proposed inhibitors suggest that aromatic substituents that access the adjacent hydrophobic pocket of the HDAC8 active site have the potential to further enhance the HDAC8 selectivity.


Assuntos
Histona Desacetilases , Simulação de Dinâmica Molecular , Domínio Catalítico , Inibidores de Histona Desacetilases/farmacologia , Histona Desacetilases/metabolismo , Simulação de Acoplamento Molecular
16.
Free Radic Res ; 54(10): 777-786, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-33183109

RESUMO

The antioxidant properties of echinatin (Ech), isolated from liquorice, have recently been reported. It is well known that the free radical species can be deactivated by phenolic antioxidants via different mechanistic pathways. In this work, the scavenging of eighteen different reactive oxygen species (ROS) has been considered, focussing on three main working mechanisms, namely hydrogen atom transfer (HAT), single electron transfer followed by proton transfer (SET-PT) and sequential proton loss electron transfer (SPLET). The investigations have been performed in different dielectric media, viz. gas phase, benzene, methanol and aqueous solution, using density functional theory (DFT) calculations at the M05-2X/6-311++G** level. Various molecular descriptors have been elucidated for Ech as well as the ROS and compared with the reference antioxidant molecule, trolox. In addition, the redox potentials and the equilibrium constants have been calculated to discuss the feasibility of the overall scavenging process. The results demonstrate that the 4-OH group is the first site for H-atom donation, followed by 4'-OH. Further, it has been found that HAT would be the most favourable mechanism in the gas phase. The SPLET mechanism is thermodynamically favoured in polar media like water and methanol, while in the case of non-polar solvents like benzene, the two mechanisms are observed to be competitive.


Assuntos
Antioxidantes/metabolismo , Chalconas/metabolismo , Polaridade Celular , Humanos , Estrutura Molecular , Espécies Reativas de Oxigênio , Solventes , Termodinâmica
17.
J Biomol Struct Dyn ; 38(1): 48-65, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-30633630

RESUMO

Histone deacetylase 8 (HDAC8) has emerged as an important therapeutic target due to its involvement in various cancerous and neurodegenerative disease states. Since pan HDAC inhibition has been linked to various side effects, the need of the hour is to develop inhibitors truly selective for one isoform. This work attempts to explore the structural basis of selective HDAC8 inhibition by docking, pharmacophore and 3 D QSAR studies of 53 highly potent and highly selective triazol-based hydroxamic acid inhibitors. The binding modes of these novel inhibitors have been explored via Glide XP (Extra Precision) and induced-fit docking (IFD) strategies. The IFD poses of highly active and selective inhibitors showed conformational changes in active site residues like Trp141, Phe152 and Phe208, which were further verified by molecular dynamics simulations. A new CH-π interaction, which is atypical of HDAC inhibitors, was also observed in case of some highly selective inhibitors. Two pharmacophore models have been proposed; one highlights the structural basis of potency of these inhibitors and the other focuses on the selectivity. The corresponding QSAR models, obtained from alignment of the inhibitors as per the proposed pharmacophore models, are highly statistically significant. These models highlight the importance of size of the hydrophobic and aromatic groups present in the inhibitors and their contribution to activity of the inhibitors. The ADMET properties of the ligand library have also been analyzed and the predicted descriptors have been correlated with activity using principal components analysis to gain insight into the effect of pharmacokinetic properties on the activity.Communicated by Ramaswamy H. Sarma.


Assuntos
Inibidores de Histona Desacetilases/química , Histona Desacetilases/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Relação Quantitativa Estrutura-Atividade , Proteínas Repressoras/química , Sítios de Ligação , Domínio Catalítico , Relação Dose-Resposta a Droga , Desenho de Fármacos , Inibidores de Histona Desacetilases/farmacologia , Humanos , Interações Hidrofóbicas e Hidrofílicas , Ligantes , Estrutura Molecular , Ligação Proteica , Proteínas Repressoras/antagonistas & inibidores
18.
Biophys Chem ; 265: 106439, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32738591

RESUMO

Human carbonic anhydrase IX (hCA IX) is over-expressed in many tumor types and serves as an important target for the discovery of novel anticancer agents. However, development of compounds that can selectively inhibit hCA IX over its widespread cytosolic isoform human carbonic anhydrase II (hCA II) is a major challenge. This work focuses on recognizing the structural features of the hCA IX receptor that could help in achieving its selective inhibition. Tools such as protein structure alignment, rigid as well as flexible docking, QM/MM calculations and molecular dynamics simulations on SLC-0111, a selective hCA IX inhibitor, in complexation with each receptor, have been used to differentiate the receptor-ligand interactions in the two complexes. It is found that the ligand shows better binding to hCA IX due to stronger coordination to the Zn (II) ion. The ligand provides bidentate coordination through its negatively charged nitrogen and an oxygen of the sulfonamide zinc binding group. Binding energy calculations show that the potency of this ligand is due to the hydrophobic contacts, whereas the selectivity is due to the electrostatic interactions. Molecular docking and binding energy calculations for three different series of SLC-0111 analogs have identified a few molecules that show high potency and selectivity toward hCA IX. It is found that both hydrophobic and polar contacts contribute to the potency and selectivity of the ligands.


Assuntos
Antígenos de Neoplasias/metabolismo , Anidrase Carbônica II/metabolismo , Anidrase Carbônica IX/metabolismo , Teoria Quântica , Inibidores da Anidrase Carbônica/farmacologia , Domínio Catalítico , Humanos , Interações Hidrofóbicas e Hidrofílicas , Simulação de Acoplamento Molecular , Compostos de Fenilureia/farmacologia , Ligação Proteica , Reprodutibilidade dos Testes , Eletricidade Estática , Sulfonamidas/farmacologia , Triazinas/farmacologia
19.
J Mater Sci Mater Med ; 20 Suppl 1: S123-30, 2009 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-18568389

RESUMO

In this work, polysorbate surfactants with same functional groups but with varying molecular masses (Tween-80, Tween-40 and Tween-20) in different concentrations (0.1% to 20% w/w) were used to study the effect of the length of the surfactant chain on the luminescence of the entrapped TOPO-capped CdSe nanocrystals. Various phospholipids with different functional headgroups such as ethylene glycol (-PEG) and amine (-NH2) were used to improve biocompatibility and provide sites for bioconjugation respectively. It is understood that that the hydrophobic ends of the surfactant binds with the water repelling groups of the cap layer, thus modifying the CdSe cap layer and making it soluble in aqueous media. It was observed that the PL emission intensity of CdSe increases with increase in concentration of Tween-series surfactant unlike in the case of thiol-coated CdSe nanoparticles. However, higher PL intensity was obtained in the case of stoichiometric CdSe with Tween-40 corresponding to 20% w/w. The efficient PL sustainability of water-soluble CdSe QD's can be attributed to the simpler chain structure of Tween-40 surfactant resulting in better passivation of the micelle.


Assuntos
Materiais Biocompatíveis/síntese química , Compostos de Cádmio/química , Luminescência , Pontos Quânticos , Compostos de Selênio/química , Absorciometria de Fóton , Materiais Biocompatíveis/química , Eficiência , Micelas , Modelos Biológicos , Compostos Organofosforados/química , Polissorbatos/farmacologia , Solubilidade , Tensoativos/farmacologia , Água/química , Água/farmacologia
20.
Medchemcomm ; 10(3): 351-368, 2019 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-30996856

RESUMO

Isatin (1H-indole-2,3-dione) and its derivatives represent an important class of heterocyclic compounds that can be used as precursors for drug synthesis. Since its discovery, a lot of research work has been done regarding the synthesis, chemical properties, and biological and industrial applications of isatin. In this review, we have reported several novel methods for the synthesis of N-, C2-, and C3-substituted and spiro derivatives of isatin. The isatin moiety also shows important chemical reactions such as oxidation, ring expansion, Friedel-Crafts reaction and aldol condensation. These reactions, in turn, produce several biologically viable compounds like 2-oxindoles, tryptanthrin, indirubins, and many more. We have also summarized some recently reported biological activities exhibited by isatin derivatives, like anti-cancer, anti-bacterial, anti-diabetic and others. Special attention has been paid to their anti-cancer activity, and various anti-cancer targets such as histone deacetylase, carbonic anhydrase, tyrosine kinase, and tubulin have been discussed in detail. Other applications of isatin derivatives, such as in the dye industry and in corrosion prevention, have also been discussed.

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