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1.
Chembiochem ; 25(13): e202400224, 2024 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-38668376

RESUMO

Neurodegenerative diseases (NDDs) refer to a complex heterogeneous group of diseases which are associated with the accumulation of amyloid fibrils or plaques in the brain leading to progressive loss of neuronal functions. Alzheimer's disease is one of the major NDD responsible for 60-80 % of all dementia cases. Currently, there are no curative or disease-reversing/modifying molecules for many of the NDDs except a few such as donepezil, rivastigmine, galantamine, carbidopa and levodopa which treat the disease-associated symptoms. Similarly, there are very few FDA-approved tracers such as flortaucipir (Tauvid) for tau fibril imaging and florbetaben (Neuraceq), flutemetamol (Vizamyl), and florbetapir (Amyvid) for amyloid imaging available for diagnosis. Recent advances in the cryogenic electron microscopy reported distinctly different microstructures for tau fibrils associated with different tauopathies highlighting the possibility to develop tauopathy-specific imaging agents and therapeutics. In addition, it is important to identify the proteins that are associated with disease development and progression to know about their 3D structure to develop various diagnostics, therapeutics and theranostic agents. The current article discusses in detail the disease-associated amyloid and non-amyloid proteins along with their structural insights. We comprehensively discussed various novel proteins associated with NDDs and their implications in disease pathology. In addition, we document various emerging chemical compounds developed for diagnosis and therapy of different NDDs with special emphasis on theranostic agents for better management of NDDs.


Assuntos
Doenças Neurodegenerativas , Humanos , Doenças Neurodegenerativas/tratamento farmacológico , Doenças Neurodegenerativas/metabolismo , Proteínas tau/metabolismo , Proteínas tau/antagonistas & inibidores , Amiloide/metabolismo , Amiloide/antagonistas & inibidores , Amiloide/química , Proteínas Amiloidogênicas/metabolismo , Proteínas Amiloidogênicas/química , Proteínas Amiloidogênicas/antagonistas & inibidores , Nanomedicina Teranóstica , Animais
2.
Phys Chem Chem Phys ; 24(34): 20371-20380, 2022 Aug 31.
Artigo em Inglês | MEDLINE | ID: mdl-35983778

RESUMO

New variants of SARS-CoV-2 are being reported worldwide. The World Health Organization has reported Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.1.529) as the variants of concern. There are speculations that the variants might evade the host immune responses induced by currently available vaccines and develop resistance to drugs under consideration. The first step of viral infection in COVID-19 occurs through the interaction of the spike protein's receptor-binding domain (RBD) with the peptidase domain of the human ACE-2 (hACE-2) receptor. This study aims to get a molecular-level understanding of the mechanism behind the increased infection rate in the alpha variant. We have computationally studied the spike protein interaction in both the wild-type and B.1.1.7 variant with the hACE-2 receptor using molecular dynamics and MM-GBSA based binding free energy calculations. The binding free energy difference shows that the mutant variant of the spike protein has increased binding affinity for the hACE-2 receptor (i.e. ΔG(N501Y,A570D) is in the range -7.2 to -7.6 kcal mol-1) and the results were validated using Density functional theory. We demonstrate that with the use of state-of-the-art computational approaches, we can, in advance, predict the virulent nature of variants of SARS-CoV-2 and alert the world healthcare system.


Assuntos
COVID-19 , SARS-CoV-2 , Humanos , Glicoproteína da Espícula de Coronavírus/genética , Virulência
3.
Phys Chem Chem Phys ; 24(42): 26316, 2022 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-36281630

RESUMO

Correction for 'Computational investigation of the increased virulence and pathogenesis of SARS-CoV-2 lineage B.1.1.7' by N. Arul Murugan et al., Phys. Chem. Chem. Phys., 2022, 24, 20371-20380, https://doi.org/10.1039/D2CP00469K.

4.
Biochemistry ; 60(26): 2084-2097, 2021 07 06.
Artigo em Inglês | MEDLINE | ID: mdl-34142803

RESUMO

The discovery of small molecules that exhibit turn-on far-red or near-infrared (NIR) fluorescence upon DNA binding and understanding how they bind DNA are important for imaging and bioanalytical applications. Here we report the DNA-bound structure and the DNA binding mechanism of quinone cyanine dithiazole (QCy-DT), a recently reported AT-specific turn-on NIR fluorescent probe for double-stranded DNA. The nuclear magnetic resonance (NMR)-derived structure showed minor groove binding but no specific ligand-DNA interactions, consistent with an endothermic and entropy-driven binding mechanism deduced from isothermal titration calorimetry. Minor groove binding is typically fast because it minimally perturbs the DNA structure. However, QCy-DT exhibited unusually slow DNA binding. The cyanine-based probe is capable of cis-trans isomerization due to overlapping methine bridges, with 16 possible slowly interconverting cis/trans isomers. Using NMR, density functional theory, and free energy calculations, we show that the DNA-free and DNA-bound environments of QCy-DT prefer distinctly different isomers, indicating that the origin of the slow kinetics is a cis-trans isomerization and that the minor groove preferentially selects an otherwise unstable cis/trans isomer of QCy-DT. Flux analysis showed the conformational selection pathway to be the dominating DNA binding mechanism at low DNA concentrations, which switches to the induced fit pathway at high DNA concentrations. This report of cis/trans isomerization of a ligand, upon binding the DNA minor groove, expands the prevailing understanding of unique discriminatory powers of the minor groove and has an important bearing on using polymethine cyanine dyes to probe the kinetics of molecular interactions.


Assuntos
Benzotiazóis/química , DNA/química , Corantes Fluorescentes/química , Benzotiazóis/metabolismo , DNA/metabolismo , Teoria da Densidade Funcional , Corantes Fluorescentes/metabolismo , Isomerismo , Ligantes , Modelos Químicos , Simulação de Acoplamento Molecular , Conformação de Ácido Nucleico , Termodinâmica
5.
Chembiochem ; 22(23): 3348-3357, 2021 12 02.
Artigo em Inglês | MEDLINE | ID: mdl-34546619

RESUMO

Alzheimer's disease is characterized by the accumulation of amyloid beta (Aß) and Tau aggregates in the brain, which induces various pathological events resulting in neurodegeneration. There have been continuous efforts to develop modulators of the Aß and Tau aggregation process to halt or modify disease progression. A few small-molecule-based inhibitors that target both Aß and Tau pathology have been reported. Here, we report the screening of a targeted library of small molecules to modulate Aß and Tau aggregation together with their in vitro, in silico and cellular studies. In vitro ThT fluorescence assay, dot blot assay, gel electrophoresis and transmission electron microscopy (TEM) results have shown that thiophene-based lead molecules effectively modulate Aß aggregation and inhibit Tau aggregation. In silico studies performed by employing molecular docking, molecular dynamics and binding-free energy calculations have helped in understanding the mechanism of interaction of the lead thiophene compounds with Aß and Tau fibril targets. In cellulo studies revealed that the lead candidate is biocompatible and effectively ameliorates neuronal cells from Aß and Tau-mediated amyloid toxicity.


Assuntos
Doença de Alzheimer/tratamento farmacológico , Peptídeos beta-Amiloides/antagonistas & inibidores , Fármacos Neuroprotetores/farmacologia , Bibliotecas de Moléculas Pequenas/farmacologia , Tiofenos/farmacologia , Proteínas tau/antagonistas & inibidores , Doença de Alzheimer/metabolismo , Peptídeos beta-Amiloides/metabolismo , Linhagem Celular , Avaliação Pré-Clínica de Medicamentos , Humanos , Fármacos Neuroprotetores/química , Agregados Proteicos/efeitos dos fármacos , Bibliotecas de Moléculas Pequenas/química , Tiofenos/química , Proteínas tau/metabolismo
6.
Adv Exp Med Biol ; 1322: 261-284, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34258744

RESUMO

Three types of chemical entities, namely, small organic molecules (organics), peptides, and biologics, are mainly used as drug candidates for the treatment of various diseases. Even though the peptide drugs are known since 1920 in association with the clinical use of insulin, only a limited number of peptides are currently used for therapeutics due to various disadvantages associated with them such as limited serum and blood stability, oral bioavailability, and permeability. Since, through chemical modifications and structure tuning, many of these limitations can be overcome, peptide-based drugs are gaining attention in pharmaceutical research. As of today, there are more than 60 peptide-based drugs approved by FDA, and over 150 peptides are in the advanced clinical studies. In this book chapter, the peptide-based lead compounds and drugs available for treating various viral diseases and their advantages and disadvantages when compared to small molecules drugs are discussed.


Assuntos
Produtos Biológicos , Viroses , Antivirais/uso terapêutico , Humanos , Insulina , Peptídeos , Viroses/tratamento farmacológico
7.
J Chem Inf Model ; 60(8): 3854-3863, 2020 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-32786232

RESUMO

Monoamine oxidase B (MAO-B) is a potential biomarker for Parkinson's disease (PD), a neurodegenerative disease associated with the loss of motor activities in human subjects. The disease state is associated with dopamine deprival, and so the inhibitors of MAO-B can serve as therapeutic drugs for PD. Since the expression level of MAO-B directly correlates to the disease progress, the distribution and population of this enzyme can be employed to monitor disease development. One of the approaches available for estimating the population is two-photon imaging. The ligands used for two-photon imaging should have high binding affinity and binding specificity toward MAO-B along with significant two-photon absorption cross sections when they are bound to the target. In this article, we study using a multiscale modeling approach, the binding affinity and spectroscopic properties (one- and two-photon absorption) of three (Flu1, Flu2, Flu3) of the currently available probes for monitoring the MAO-B level. We report that the binding affinity of the probes can be explained using the molecular size and binding cavity volume. The experimentally determined one-photon absorption spectrum is well reproduced by the employed QM/MM approaches, and the most accurate spectral shifts, on passing from one probe to another, are obtained at the coupled-cluster (CC2) level of theory. An important conclusion from this study is also the demonstration that intrinsic molecular two-photon absorption strengths (δ2PA) increase in the order δ2PA (Flu1) > δ2PA (Flu2) > δ2PA (Flu3). This is in contrast with experimental data, which predict similar values of two-photon absorption cross sections for Flu1 and Flu3. We demontrate, based on the results of electronic-structure calculations for Flu1 that this discrepancy cannot be explained by an explicit account for neighboring residues (which could lead to charge transfer between a probe and neighboring aromatic amino acids thus boosting δ2PA). In summary, we show that the employed multiscale approach not only can optimize two-photon absorption properties and verify binding affinity, but it can also help in detailed analyses of experimental data.


Assuntos
Doenças Neurodegenerativas , Doença de Parkinson , Biomarcadores , Humanos , Monoaminoxidase , Inibidores da Monoaminoxidase , Doença de Parkinson/diagnóstico
8.
Eur J Nucl Med Mol Imaging ; 46(6): 1369-1382, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30919054

RESUMO

PURPOSE: Several tracers have been designed for tracking the abnormal accumulation of tau pathology in vivo. Recently, concerns have been raised about the sources of off-target binding for these tracers; inconclusive data propose binding for some tracers to monoamine oxidase B (MAO-B). METHODS: Molecular docking and dynamics simulations were used to estimate the affinity and free energy for the binding of several tau tracers (FDDNP, THK523, THK5105, THK5317, THK5351, T807 [aka AV-1451, flortaucipir], T808, PBB3, RO-948, MK-6240, JNJ-311 and PI-2620) to MAO-B. These values were then compared with those for safinamide (MAO-B inhibitor). PET imaging was used with the tau tracer [18F]THK5317 and the MAO-B tracer [11C]DED in five patients with Alzheimer's disease to investigate the MAO-B binding component of this first generation tau tracer in vivo. RESULTS: The computational modelling studies identified a binding site for all the tau tracers on MAO-B; this was the same site as that for safinamide. The binding affinity and free energy of binding for the tau tracers to MAO-B was substantial and in a similar range to those for safinamide. The most recently developed tau tracers MK-6240, JNJ-311 and PI-2620 appeared, in silico, to have the lowest relative affinity for MAO-B. The in vivo investigations found that the regional distribution of binding for [18F]THK5317 was different from that for [11C]DED, although areas of suspected off-target [18F]THK5317 binding were detected. The binding relationship between [18F]THK5317 and [11C]DED depended on the availability of the MAO-B enzyme. CONCLUSIONS: The developed tau tracers show in silico and in vivo evidence of cross-interaction with MAO-B; the MAO-B component of the tracer binding was dependent on the regional concentration of the enzyme.


Assuntos
Doença de Alzheimer/diagnóstico por imagem , Monoaminoxidase/metabolismo , Tomografia por Emissão de Pósitrons , Compostos Radiofarmacêuticos/análise , Idoso , Alanina/análogos & derivados , Alanina/análise , Benzilaminas/análise , Sítios de Ligação , Encéfalo/diagnóstico por imagem , Biologia Computacional , Simulação por Computador , Feminino , Humanos , Ligantes , Imageamento por Ressonância Magnética , Masculino , Pessoa de Meia-Idade , Simulação de Acoplamento Molecular , Ligação Proteica , Conformação Proteica , Estudos Retrospectivos , Proteínas tau/metabolismo
9.
J Chem Inf Model ; 59(10): 4100-4115, 2019 10 28.
Artigo em Inglês | MEDLINE | ID: mdl-31553614

RESUMO

Sirtuins are a family of nicotinamide adenine dinucleotide (NAD+)-dependent enzymes, which undergo robust deacetylase activity, resulting in the production of nicotinamide. It is well known that nicotinamide, which is one of the products, can also act as an inhibitor for further deacetylation process by forming NAD+ again. Hence, the removal of nicotinamide from sirtuins is a demanding process, and the mechanistic understanding of the process remains elusive. In this investigation, we have made an attempt to unravel the unbinding pathways of nicotinamide from SIRT1, SIRT2, and SIRT3 (SIRT1-3) using Random Acceleration Molecular Dynamics (RAMD) Simulations, and we have successfully identified various unbinding channels. The selectivity of the egression channel is determined by using a thorough analysis of the frequency of egression trajectories. Similarly, various inhibitors have been docked with the active sites of SIRT1-3, and their egression pathways have been investigated to understand whether they follow the same egression pathway as that of nicotinamide. The residues that are responsible for the unbinding pathways have been determined from the analysis of RAMD trajectories. From these results, it is clear that phenylalanine and histidine residues play major roles in the egression of inhibitors. Additionally, the key residues Leu, Pro, Met, Phe, Tyr, and Ile are found to control the release by acting as gateway residues. The role of these residues from different egression channels has been studied by carrying out mutations with alanine residue. This is the first report on sirtuins, which demonstrates the novel unbinding pathways for nicotinamide/inhibitors. This work provides new insights for developing more promising SIRT1-3 inhibitors.


Assuntos
Simulação de Dinâmica Molecular , Sirtuínas/química , Catálise , Descoberta de Drogas , Modelos Moleculares , Ligação Proteica , Conformação Proteica , Sirtuínas/antagonistas & inibidores , Software
10.
Chembiochem ; 18(8): 755-763, 2017 04 18.
Artigo em Inglês | MEDLINE | ID: mdl-28150905

RESUMO

The thrombin-binding aptamer (TBA), which shows anticoagulant properties, is one of the most studied G-quadruplex-forming aptamers. In this study, we investigated the impact of different chemical modifications such as a three-carbon spacer (spacer-C3 ), unlocked nucleic acid (UNA) and 3'-amino-modified UNA (amino-UNA) on the structural dynamics and stability of TBA. All three modifications were incorporated at three different loop positions (T3, T7, T12) of the TBA G-quadruplex structure to result in a series of TBA variants and their stability was studied by thermal denaturation; folding was studied by circular dichroism spectroscopy and thrombin clotting time. The results showed that spacer-C3 introduction at the T7 loop position (TBA-SP7) significantly improved stability and thrombin clotting time while maintaining a similar binding affinity as TBA to thrombin. Detailed molecular modelling experiments provided novel insights into the experimental observations, further supporting the efficacy of TBA-SP7. The results of this study could provide valuable information for future designs of TBA analogues with superior thrombin inhibition properties.


Assuntos
Aptâmeros de Nucleotídeos/química , Aptâmeros de Nucleotídeos/síntese química , Quadruplex G , Coagulação Sanguínea , Modelos Químicos , Simulação de Dinâmica Molecular , Estrutura Molecular , Processos Estocásticos
11.
Biomacromolecules ; 18(11): 3581-3590, 2017 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-28856890

RESUMO

Ambidextrous supergelators are developed through structure-gelation screening of rationally designed cyclic dipeptides (CDPs). The organo- and hydrogels of CDPs were thoroughly characterized by their minimal gelation concentration (MGC) for organic and aqueous solvents, thermal stability (Tg), and viscoelastic properties. Intermolecular hydrogen bonding, the major driving force for gelation was evaluated using temperature-dependent nuclear magnetic resonance (NMR) spectroscopy. The contribution of attractive van der Waals interaction of tBoc group in driving CDP gelation was ascertained using ß-cyclodextrin (ß-CD)-adamantane carboxylic acid (AC)-based host-guest gelation and 1H NMR studies. The self-assembled fibrous network of CDPs in organic and aqueous solvents responsible for the molecular gelation was elucidated using field emission scanning electron microscopy (FESEM) analysis. Among the CDPs studied CDP-2 found to be supergelator with MGC of 0.3 wt % and form in situ hydrogels under simulated physiological conditions. The in situ gelation property was evaluated by the incorporation of curcumin, as a model study to demonstrate the drug delivery application. Furthermore, supergelator CDP-2 was found to exhibit in cellulo cytocompatibility. Moreover, density functional theory (DFT) calculations were carried out to propose the microscopic structure for the self-assembly of CDP compounds and intermolecular N-H···O hydrogen bonding interactions appear to stabilize the fibrous network. The hydrophobic interactions among the tert-butyloxycarbonyl (tBoc) groups and π-π stacking interactions between phenyl rings contribute to the further stabilization of self-assembled 2D fibrous networks of CDPs. Overall, the present study highlights the in situ gelation property of CDP-based supergelators and their potential for biomedical and regenerative medicine applications.


Assuntos
Dipeptídeos/química , Hidrogéis/química , Solventes/química , Dicroísmo Circular , Dipeptídeos/síntese química , Hidrogéis/síntese química , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Microscopia de Força Atômica , Água/química
12.
J Phys Chem A ; 120(36): 7175-82, 2016 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-27556901

RESUMO

We study the linear and nonlinear optical properties of a well-known acid-base indicator, bromophenol blue (BPB), in aqueous solution by employing static and integrated approaches. In the static approach, optical properties have been calculated using time-dependent density functional theory (TD-DFT) on the fully relaxed geometries of the neutral and different unprotonated forms of BPB. Moreover, both closed and open forms of BPB were considered. In the integrated approach, the optical properties have been computed over many snapshots extracted from molecular dynamics simulation using a hybrid time-dependent density functional theory/molecular mechanics approach. The static approach suggests closed neutral ⇒ anionic interconversion as the dominant mechanism for the red shift in the absorption spectra of BPB due to a change from acidic to basic pH. It is found by employing an integrated approach that the two interconversions, namely open neutral ⇒ anionic and open neutral ⇒ dianionic, can contribute to the pH-dependent shift in the absorption spectra of BPB. Even though both static and integrated approaches reproduce the pH-dependent red shift in the absorption spectra of BPB, the latter one is suitable to determine both the spectra and spectral broadening. Finally, the computed static first hyperpolarizability for various protonated and deprotonated forms of BPB reveals that this molecule can be used as a nonlinear optical probe for pH sensing in addition to its highly exploited use as an optical probe.

13.
Mol Pharm ; 12(9): 3312-22, 2015 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-26281017

RESUMO

The extraordinary ligand binding properties of albumin makes it a key player in the pharmacokinetics and pharmacodynamics of many vital drugs. Albumin is highly susceptible for nonenzymatic glycation mediated structural modifications, and there is a need to determine structural and functional impact of specific AGEs modifications. The present study was aimed toward determining the AGE mediated structure and function changes, primarily looking into the effect on binding affinity of drugs in the two major drug binding sites of albumin. The impact of the two most predominant AGEs modifications, i.e., carboxyethyllysine (CEL) and argpyrimidine (Arg-P), was studied on the basis of the combination of in vitro and in silico experiments. In vitro studies were carried out by AGEs modification of bovine serum albumin (BSA) for the formation of Arg-P and CEL followed by drug interaction studies. In silico studies involved molecular dynamics (MD) simulations and docking studies for native and AGEs modified BSAs. In particular the side chain modification was specifically carried out for the residues in the drug binding sites, i.e., Arg-194, Arg-196, Arg-198, and Arg-217, and Lys-204 (site I) and Arg-409 and Lys-413 (site II). The equilibrated structures of native BSA (n-BSA) and glycated BSA (G-BSA) as obtained from MD were used for drug binding studies using molecular docking approach. It was evident from the results of both in vitro and in silico drug interaction studies that AGEs modification results in the reduced drug binding affinity for tolbutamide (TLB) and ibuprofen (IBP) in sites I and II. Moreover, the AGEs modification mediated conformational changes resulted in the shallow binding pockets with reduced accessibility for drugs.


Assuntos
Produtos Finais de Glicação Avançada/química , Lisina/análogos & derivados , Ornitina/análogos & derivados , Pirimidinas/química , Soroalbumina Bovina/química , Soroalbumina Bovina/metabolismo , Animais , Sítios de Ligação , Bovinos , Dicroísmo Circular , Produtos Finais de Glicação Avançada/metabolismo , Glicosilação , Lisina/química , Lisina/metabolismo , Simulação de Dinâmica Molecular , Ornitina/química , Ornitina/metabolismo , Ligação Proteica , Conformação Proteica , Pirimidinas/metabolismo
14.
J Phys Chem A ; 119(21): 5145-52, 2015 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-25418554

RESUMO

This study demonstrates that a hybrid density functional theory/molecular mechanics approach can be successfully combined with time-dependent wavepacket approach to predict the shape of optical bands for molecules in solutions, including vibrational fine structure. A key step in this treatment is the estimation of the inhomogeneous broadening based on the hybrid approach, where the polarization between solute and atomically decomposed solvent is taken into account in a self-consistent manner. The potential of this approach is shown by predicting optical absorption bands for three heterocyclic ketoimine difluoroborates in solution.


Assuntos
Boratos/química , Compostos Heterocíclicos/química , Modelos Químicos , Simulação de Dinâmica Molecular , Soluções/química , Análise Espectral , Clorofórmio/química , Dimetilformamida/química , Solventes/química , Vibração , Análise de Ondaletas
15.
J Phys Chem A ; 118(10): 1879-86, 2014 Mar 13.
Artigo em Inglês | MEDLINE | ID: mdl-24547982

RESUMO

Black carbon soot (BS) is considered to be the second most contributing organic matter next to carbon dioxide for the global warming effect. There is, however, so far no consensus on the quantitative warming effect due to the increased distribution of black carbon in the atmosphere. A recent report (Science 2012, 337, 1078) suggests that due to BS there is only a few percentage enhancement in absorption of BS-immersed aerosols. To get proper interpretation of the available experimental data, it becomes essential to obtain details of the microscopic origin of the absorption and scattering processes of the aerosol clusters due to the presence of soot. However, so far, due to the large spatial scale and the need for a quantum mechanical description of the particles involved in the absorption and scattering, this quest has posed an insurmountable challenge. In the present work we propose the use of a multiscale integrated approach based on molecular dynamics and a quantum mechanical-molecular mechanical method to model the optical property of molecules immersed in nanosized aerosol particles. We choose fluoranthene (FA) with varying cis-pinonic acid (CPA) impurity concentration as an illustrative example of application. We observe that normally FA tends to be on the surface of the nanoaerosols but in the presence of CPA impurities its spatial location changes to a core aggregate to some extent. We find that the absorption maximum is only slightly red-shifted in the presence of increased CPA concentrations and that the oscillator strengths are not altered significantly. The comparable values for the oscillator strengths of all the low energy excitations suggest that the absorption enhancement of the aerosol due to BS will not be substantial, which is in line with the recent experimental report in Science.

16.
J Biomol Struct Dyn ; : 1-13, 2024 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-38212976

RESUMO

The robust structural nature of human serum albumin (HSA) is responsible for its multifarious functional property. The site specific glycation of HSA due to hyperglycaemia (excess glucose) causes structural changes which have an impact on the functioning of the protein. This work investigates the effects of glucose-mediated glycation in the altered inter-domain motion, distorted binding site conformation and modified hydration patterns, Trp214 orientation, and secondary structure transition using simulation approach. Here we have observed an increase of turns in the helices of glycated HSA, which modulates the open-close conformation of Sudlow I & II. The secondary structure changes of glycated HSA indicate plausible reduction in the alpha helical content in the helices which participates in ligand binding. It also affects geometrical features of drug binding sites (Sudlow I and II) such as volume and hydration. We found that glycation disturbs domain specific mobility patterns of HSA, a substantial feature for albumin drug binding ability which is also correlated with changes in the local environment of Trp214.Communicated by Ramaswamy H. Sarma.

17.
J Mater Chem B ; 12(18): 4441-4450, 2024 May 08.
Artigo em Inglês | MEDLINE | ID: mdl-38639071

RESUMO

In this study, we report a small molecule optical marker BI-CyG derived from the structural engineering of a cyanine scaffold. The developed probe offers suitable advantages over existing cyanine-based albumin specific probes in terms of its excitation and emission wavelengths, which are 760 and 830-832 nm, respectively. Structural tuning of the cyanine architecture leading to extended π-conjugation and resulting in a suitable bathochromic shift in the emission wavelength of the probe is represented in this study. The probe besides emitting in the NIR region, also possesses the desirable characteristics of being a potential target selective optical marker, as established from various biophysical studies. Molecular modelling and simulation studies provided critical insights into the binding of the probe in the protein microenvironment, which was further supported by experimental studies. The probe displayed intracellular albumin selectivity and was utilized for demonstrating alteration in albumin levels in pathological states such as hyperglycemia in hepatic cells. The present study also sheds some light on using BI-CyG as an imaging probe and on the role of metformin as a suitable drug for balancing hyperglycemia-induced reduced intra-hepatic albumin levels. The study, thus, attempts to highlight the structural derivatization of cyanine to afford a potential probe for serum albumin and its deployment to image altering albumin levels in an induced pathological condition, hyperglycemia.


Assuntos
Albuminas , Carbocianinas , Hiperglicemia , Animais , Humanos , Albuminas/química , Albuminas/metabolismo , Carbocianinas/química , Corantes Fluorescentes/química , Corantes Fluorescentes/síntese química , Hiperglicemia/metabolismo , Sondas Moleculares/química , Estrutura Molecular , Imagem Óptica
18.
GigaByte ; 2024: gigabyte114, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38525218

RESUMO

Molecular Property Diagnostic Suite (MPDS) was conceived and developed as an open-source disease-specific web portal based on Galaxy. MPDSCOVID-19 was developed for COVID-19 as a one-stop solution for drug discovery research. Galaxy platforms enable the creation of customized workflows connecting various modules in the web server. The architecture of MPDSCOVID-19 effectively employs Galaxy v22.04 features, which are ported on CentOS 7.8 and Python 3.7. MPDSCOVID-19 provides significant updates and the addition of several new tools updated after six years. Tools developed by our group in Perl/Python and open-source tools are collated and integrated into MPDSCOVID-19 using XML scripts. Our MPDS suite aims to facilitate transparent and open innovation. This approach significantly helps bring inclusiveness in the community while promoting free access and participation in software development. Availability & Implementation: The MPDSCOVID-19 portal can be accessed at https://mpds.neist.res.in:8085/.

19.
J Am Chem Soc ; 135(36): 13590-7, 2013 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-23951997

RESUMO

Along with the growing evidence that relates membrane abnormalities to various diseases, biological membranes have been acknowledged as targets for therapy. Any such abnormality in the membrane structure alters the membrane potential which in principle can be captured by measuring properties of specific optical probes. There exists by now many molecular probes with absorption and fluorescence properties that are sensitive to local membrane structure and to the membrane potential. To suggest new high-performance optical probes for membrane-potential imaging it is important to understand in detail the membrane-induced structural changes in the probe, the membrane association dynamics of the probe, and its membrane-specific optical properties. To contribute to this effort, we here study an optical probe, N-acetylaladanamide (NAAA), in the presence of a POPC lipid bilayer using a multiscale integrated approach to assess the probe structure, dynamics, and optical properties in its membrane-bound status and in water solvent. We find that the probe eventually assimilates into the membrane with a specific orientation where the hydrophobic part of the probe is buried inside the lipid bilayer, while the hydrophilic part is exposed to the water solvent. The computed absorption maximum is red-shifted when compared to the gas phase. The computations of the two-photon absorption and second harmonic generation cross sections of the NAAA probe in its membrane-bound state which is of its first kind in the literature suggest that this probe can be used for imaging the membrane potential using nonlinear optical microscopy.


Assuntos
2-Naftilamina/análogos & derivados , Acetamidas/química , Simulação de Dinâmica Molecular , Fibras Ópticas , Fosfatidilcolinas/química , 2-Naftilamina/química , Modelos Moleculares , Fenômenos Ópticos , Teoria Quântica
20.
Chemphyschem ; 14(16): 3731-9, 2013 Nov 11.
Artigo em Inglês | MEDLINE | ID: mdl-24106066

RESUMO

In this study, we report on the influence of solvent on the two-photon absorption (2PA) spectra of Reichardt's dye (RD). The measurement of 2PA cross-sections is performed for three solvents (chloroform, dimethyl formamide, and dimethyl sulfoxide) using the Z-scan technique. The key finding of this study is the observation that the cross-section, corresponding to the 2PA of the intramolecular charge-transfer state, diminishes substantially upon increasing the solvent polarity. To unravel the solvent dependence of the 2PA cross-section, the electronic structure of RD is determined using a hybrid quantum mechanics/molecular mechanics (QM/MM) approach, in which polarization between the solute and solvent is taken into account by using a self-consistent scheme in the solvent polarization. The two-state approximation proves to be adequate for the studied system, and allowed the observed solvent-polarity-induced decrease of the 2PA cross-section to be related to the decrease of the transition moment and the increase in the excitation energy.


Assuntos
Modelos Moleculares , Fótons , Compostos de Piridínio/química , Teoria Quântica , Solventes/química
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