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1.
Molecules ; 29(8)2024 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-38675678

RESUMO

Bromodomain 4 and 9 (BRD4 and BRD9) have been regarded as important targets of drug designs in regard to the treatment of multiple diseases. In our current study, molecular dynamics (MD) simulations, deep learning (DL) and binding free energy calculations are integrated to probe the binding modes of three inhibitors (H1B, JQ1 and TVU) to BRD4 and BRD9. The MD trajectory-based DL successfully identify significant functional function domains, such as BC-loop and ZA-loop. The information from the post-processing analysis of MD simulations indicates that inhibitor binding highly influences the structural flexibility and dynamic behavior of BRD4 and BRD9. The results of the MM-GBSA calculations not only suggest that the binding ability of H1B, JQ1 and TVU to BRD9 are stronger than to BRD4, but they also verify that van der Walls interactions are the primary forces responsible for inhibitor binding. The hot spots of BRD4 and BRD9 revealed by residue-based free energy estimation provide target sites of drug design in regard to BRD4 and BRD9. This work is anticipated to provide useful theoretical aids for the development of selective inhibitors over BRD family members.


Assuntos
Proteínas que Contêm Bromodomínio , Proteínas de Ciclo Celular , Aprendizado Profundo , Simulação de Dinâmica Molecular , Ligação Proteica , Fatores de Transcrição , Fatores de Transcrição/antagonistas & inibidores , Fatores de Transcrição/metabolismo , Fatores de Transcrição/química , Proteínas de Ciclo Celular/antagonistas & inibidores , Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/metabolismo , Humanos , Sítios de Ligação , Termodinâmica , Triazóis/química , Triazóis/farmacologia , Azepinas/química , Azepinas/farmacologia , Proteínas Nucleares/metabolismo , Proteínas Nucleares/antagonistas & inibidores , Proteínas Nucleares/química , Simulação de Acoplamento Molecular
2.
Biotechnol J ; 19(2): e2300437, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38403464

RESUMO

Psoriasis is a common immune-mediated skin condition characterized by aberrant keratinocytes and cell proliferation. The purpose of this study was to explore the FDA-approved drugs by 3D-QSAR pharmacophore model and evaluate their efficiency by in-silico, in vitro, and in vivo psoriasis animal model. A 3D-QSAR pharmacophore model was developed by utilizing HypoGen algorithm using the structural features of 48 diaryl derivatives with diverse molecular patterns. The model was validated by a test set of 27 compounds, by cost analysis method, and Fischer's randomization test. The correlation coefficient of the best model (Hypo2) was 0.9601 for the training set while it was 0.805 for the test set. The selected model was taken as a 3D query for the virtual screening of over 3000 FDA-approved drugs. Compounds mapped with the pharmacophore model were further screened through molecular docking. The hits that showed the best docking results were screened through in silico skin toxicity approach. Top five hits were selected for the MD simulation studies. Based on MD simulations results, the best two hit molecules, that is, ebastine (Ebs) and mebeverine (Mbv) were selected for in vitro and in vivo antioxidant studies performed in mice. TNF-α and COX pro-inflammatory mediators, biochemical assays, histopathological analyses, and immunohistochemistry observations confirmed the anti-inflammatory response of the selected drugs. Based on these findings, it appeared that Ebs can effectively treat psoriasis-like skin lesions and down-regulate inflammatory responses which was consistent with docking predictions and could potentially be employed for further research on inflammation-related skin illnesses such as psoriasis.


Assuntos
Farmacóforo , Psoríase , Animais , Camundongos , Simulação de Acoplamento Molecular , Relação Quantitativa Estrutura-Atividade , Simulação por Computador , Psoríase/tratamento farmacológico , Simulação de Dinâmica Molecular
3.
Comput Biol Med ; 171: 108037, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38377716

RESUMO

The development of deep learning models for predicting toxicological endpoints has shown great promise, but one of the challenges in the field is the accuracy and interpretability of these models. The bioactive conformation of a compound plays a critical role for it to bind in the target. It is a big issue to figure out the bioactive conformation in deep learning without the co-crystal structure or highly precise molecular simulations. In this study, we developed a deep learning framework of Multi-Conformation Point Network (MCPNET) to construct classification and regression models, respectively, based on electrostatic potential distributions on vdW surfaces around multiple conformations of the compound using a dataset of compounds with developmental toxicity in zebrafish embryo. MCPNET applied 3D multi-conformational surface point cloud to extract the molecular features for model training, which may be critical for capturing the structural diversity of compounds. The models achieved an accuracy of 85 % on the classification task and R2 of 0.66 on the regression task, outperforming traditional machine learning models and other deep learning models. The key feature of our model is its interpretability with the component visualization to identify the factors contributing to the prediction and to understand the compound action mechanism. MCPNET may predict the conformation quietly close to the bioactive conformation of a compound by attention-based multi-conformation pooling mechanism. Our results demonstrated the potential of deep learning based on 3D molecular representations in accurately predicting developmental toxicity. The source code is publicly available at https://github.com/Superlit-CC/MCPNET.


Assuntos
Aprendizado Profundo , Animais , Peixe-Zebra , Aprendizado de Máquina , Conformação Molecular , Software
4.
Exp Eye Res ; 240: 109807, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38278468

RESUMO

Subretinal fluid (SRF) accumulates between photoreceptor outer segments and retinal pigment epithelium during rhegmatogenous retinal detachment. Biomolecular components such as lipids originate from cells surrounding the SRF. Knowledge of the composition of these molecules in SRF potentially provides mechanistic insight into the physiologic transfer of lipids between retinal tissue compartments. Using mass spectrometry and tandem mass spectrometry analysis on an electrospray ionization quadrupole-time-of-flight mass spectrometer, we identified a total of 115 lipid molecular species of 11 subclasses and 9 classes in two samples from two patients with rhegmatogenous retinal detachment. These included 47 glycerophosphocholines, 6 glycerophosphoethanolamines, 1 glycerophosphoinositol, 18 sphingomyelins, 9 cholesteryl esters, free cholesterol, 3 ceramides, 22 triacylglycerols and 8 free fatty acids. Glycerophosphocholines were of the highest intensity. By minimizing the formation of different adduct forms or clustering ions of different adducts, we determined the relative intensity of lipid molecular species within the same subclasses. The profiles were compared with those of retinal cells available in the published literature. The glycerophosphocholine profile of SRF was similar to that of cone outer segments, suggesting that outer segment degradation products are constitutively released into the interphotoreceptor matrix, appearing in SRF during detachment. This hypothesis was supported by the retinal distributions of corresponding lipid synthases' mRNA expression obtained from an online resource based on publicly available single-cell sequencing data. In contrast, based on lipid profiles and relevant gene expression in this study, the sources of free cholesterol and cholesteryl esters in SRF appeared more ambiguous, possibly reflecting that outer retina takes up plasma lipoproteins. Further studies to identify and quantify lipids in SRF will help better understand etiology of diseases relevant to outer retina.


Assuntos
Descolamento Retiniano , Humanos , Descolamento Retiniano/metabolismo , Líquido Sub-Retiniano/metabolismo , Ésteres do Colesterol/metabolismo , Lipidômica , Retina/metabolismo
5.
Mini Rev Med Chem ; 2024 Jan 23.
Artigo em Inglês | MEDLINE | ID: mdl-38265367

RESUMO

Rational predictions on binding kinetics parameters of drugs to targets play significant roles in future drug designs. Full conformational samplings of targets are requisite for accurate predictions of binding kinetic parameters. In this review, we mainly focus on the applications of enhanced sampling technologies in calculations of binding kinetics parameters and residence time of drugs. The methods involved in molecular dynamics simulations are applied to not only probe conformational changes of targets but also reveal calculations of residence time that is significant for drug efficiency. For this review, special attention are paid to accelerated molecular dynamics (aMD) and Gaussian aMD (GaMD) simulations that have been adopted to predict the association or disassociation rate constant. We also expect that this review can provide useful information for future drug design.

6.
Artigo em Inglês | MEDLINE | ID: mdl-38206777

RESUMO

Ultrasound imaging offers a non-invasive, radiation-free method for visualizing internal tissues and organs, with deep penetration capabilities. This has established it as a crucial tool for physicians in diagnosing internal tissue pathologies and monitoring human conditions. Nonetheless, conventional ultrasound probes are often characterized by their rigidity and bulkiness. Designing a transducer that can seamlessly adapt to the contours and dynamics of soft, curved human skin presents significant technical hurdles. We present a novel flexible and stretchable ultrasound transducer (FSUT) designed for adaptability to large-curvature surfaces while preserving superior imaging quality. Central to this breakthrough is the innovative use of screen-printed silver nanowires (AgNWs) coupled with a composite elastic substrate, together ensuring robust and stable electrical and mechanical connections. Standard tensile and fatigue tests verify its durability. The mechanical, electrical and acoustic properties of FSUTs are characterised using standard methods, with large tensile strains (≥110%), high flexibility (R ≥1.4 mm) and light weight (≤1.58 g) to meet the needs of wearable devices. Center frequency and -6dB bandwidth are approximately 5.3MHz and 66.47%, respectively. Images of the commercial anechoic cyst phantom yielded an axial and lateral resolution (depths of 10 mm to 70 mm) of approximately 0.31mm and 0.46mm, 0.34mm and 0.84mm respectively. The complex curved surface imaging capabilities of FSUT were tested on agar-gelatin-based breast cyst phantoms under different curvatures. Finally, ultrasound images of the thyroid, brachial and carotid arteries were also obtained from volunteer wearing FSUT.

7.
J Biomol Struct Dyn ; 42(7): 3363-3381, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-37216340

RESUMO

Point mutations play a vital role in the conformational transformation of HRAS. In this work, Gaussian accelerated molecular dynamics (GaMD) simulations followed by constructions of free energy landscapes (FELs) were adopted to explore the effect of mutations D33K, A59T and L120A on conformation states of the GDP-bound HRAS. The results from the post-processing analyses on GaMD trajectories suggest that mutations alter the flexibility and motion modes of the switch domains from HRAS. The analyses from FELs show that mutations induce more disordered states of the switch domains and affect interactions of GDP with HRAS, implying that mutations yield a vital effect on the binding of HRAS to effectors. The GDP-residue interaction network revealed by our current work indicates that salt bridges and hydrogen bonding interactions (HBIs) play key roles in the binding of GDP to HRAS. Furthermore, instability in the interactions of magnesium ions and GDP with the switch SI leads to the extreme disorder of the switch domains. This study is expected to provide the energetic basis and molecular mechanism for further understanding the function of HRAS.Communicated by Ramaswamy H. Sarma.


Assuntos
Simulação de Dinâmica Molecular , Mutação Puntual , Entropia , Mutação
8.
bioRxiv ; 2023 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-38106085

RESUMO

Resting-state functional connectivity (RSFC) is widely used to predict phenotypic traits in individuals. Large sample sizes can significantly improve prediction accuracies. However, for studies of certain clinical populations or focused neuroscience inquiries, small-scale datasets often remain a necessity. We have previously proposed a "meta-matching" approach to translate prediction models from large datasets to predict new phenotypes in small datasets. We demonstrated large improvement of meta-matching over classical kernel ridge regression (KRR) when translating models from a single source dataset (UK Biobank) to the Human Connectome Project Young Adults (HCP-YA) dataset. In the current study, we propose two meta-matching variants ("meta-matching with dataset stacking" and "multilayer meta-matching") to translate models from multiple source datasets across disparate sample sizes to predict new phenotypes in small target datasets. We evaluate both approaches by translating models trained from five source datasets (with sample sizes ranging from 862 participants to 36,834 participants) to predict phenotypes in the HCP-YA and HCP-Aging datasets. We find that multilayer meta-matching modestly outperforms meta-matching with dataset stacking. Both meta-matching variants perform better than the original "meta-matching with stacking" approach trained only on the UK Biobank. All meta-matching variants outperform classical KRR and transfer learning by a large margin. In fact, KRR is better than classical transfer learning when less than 50 participants are available for finetuning, suggesting the difficulty of classical transfer learning in the very small sample regime. The multilayer meta-matching model is publicly available at GITHUB_LINK.

9.
J Biomol Struct Dyn ; : 1-20, 2023 Dec 19.
Artigo em Inglês | MEDLINE | ID: mdl-38112295

RESUMO

Cyclin dependent kinases (CDKs) play an important role in cell cycle regulation and their dysfunction is associated with many cancers. That is why CDKs have been attractive targets for the treatment of cancer. Glioblastoma is a cancer caused by the aberrant expression of CDK4/6, so exploring the mechanism of the selection of CDK4/6 toward inhibitors relative to the other family members CDK1/2 is essential. In this work, multiple replica molecular dynamics (MRMD) simulations, principal component analysis (PCA), free energy landscapes (FELs), molecular mechanics Poisson-Boltzmann/Generalized Born surface area (MM-PB/GBSA) and other methods were integrated to decipher the selectively binding mechanism of the inhibitor N1J to CDK4/6 and CDK1/2. Molecular electrostatic potential (MESP) analysis provides an explanation for the N1J selectivity. Residue-based free energy decomposition reveals that most of the hot residues are located at the same location of CDKs proteins, but the different types of residues in different proteins cause changes in binding energy, which is considered as a potential developmental direction to improve the selectivity of inhibitors to CDK4/6. These results provide insights into the source of inhibitor and CDK4/6 selectivity for the future development of more selective inhibitors.Communicated by Ramaswamy H. Sarma.

10.
Phys Chem Chem Phys ; 25(41): 28479-28496, 2023 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-37846774

RESUMO

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to spread globally, and rapid viral evolution and the emergence of new variants pose challenges to pandemic control. During infection, the spike protein of SARS-CoV-2 interacts with the human ACE2 protein via its receptor binding domain (RBD), and it is known that engineered forms of ACE2 can compete with wild-type (WT) ACE2 for binding to inhibit infection. Here, we conducted multiple replica molecular dynamics (MRMD) simulations to study the mechanisms of the engineered ACE2 variants 3N39 and 3N94 and provide directions for optimization. Our findings reveal that engineered ACE2 is notably more efficacious in systems that show weaker binding to WT ACE2 (i.e., WT and BA.1 RBD), but also faces immune escape as the virus evolves. Moreover, by modifying residue types near the binding interface, engineered ACE2 alters the electrostatic potential distribution and reconfigures the hydrogen bonding network, which results in modified binding to the RBD. However, this structural rearrangement does not occur in all RBD variants. In addition, we identified potentially engineerable beneficial residues and potentially engineerable detrimental residues in both ACE2 and RBD. Functional conservation can thus enable the optimization of these residues and improve the binding competitiveness of engineered ACE2, which therefore provides additional immune escape prevention. Finally, we conclude that these findings have implications for understanding the mechanisms responsible for engineered ACE2 and can help us to develop engineered ACE2 proteins that show superior performance.


Assuntos
Enzima de Conversão de Angiotensina 2 , Simulação de Dinâmica Molecular , Humanos , Sítios de Ligação , Ligação Competitiva , Pandemias , SARS-CoV-2/genética , Ligação Proteica , Mutação
11.
Materials (Basel) ; 16(20)2023 Oct 19.
Artigo em Inglês | MEDLINE | ID: mdl-37895753

RESUMO

The disposal of glass fiber-reinforced plastic (GFRP) waste has become an urgent issue in both the engineering and environmental fields. In this study, the feasibility of reusing mechanically recycled GFRP in concrete was evaluated. Secondary screening of the recycled material was conducted to obtain different types of products, and the recycled GFRP (rGFRP) was characterized. Subsequently, the effect of rGFRP on concrete performance was evaluated using different dosages (0%, 1%, 3%, 5%) of rGFRP powder and rGFRP cluster (with different sizes and fiber contents) to replace fine aggregate in concrete preparation. The experimental results indicated that the addition of rGFRP powder has no significant impact on the mechanical properties of concrete, while the addition of a small amount of rGFRP cluster slightly improves the compressive strength and splitting tensile strength of concrete. Additionally, the short fibers in rGFRP improve the failure mode of concrete, and increased fiber content and longer fiber length demonstrate a more pronounced reinforcing effect. The challenges and potential directions for future research in the realm of reusing rGFRP in concrete are discussed at the end. A systematic process for reusing GFRP waste in concrete is proposed to address the primary challenges and provide guidance for its practical engineering application.

12.
J Biomol Struct Dyn ; : 1-18, 2023 Sep 23.
Artigo em Inglês | MEDLINE | ID: mdl-37740650

RESUMO

The pseudokinase domain (JH2) of the protein tyrosine kinase (Janus kinase 2, JAK2) regulates the activity of a tyrosine kinase domain (JH1) in JAK2, which is further affected by mutations in the JH2. In this work, Gaussian accelerated molecular dynamics (GaMD) simulations followed by construction of free energy landscapes (FELs) and principal component analysis (PCA) were performed to study effect of two mutations V617F and V617F/E596A on the conformations of the ATP-bound JH2. The dynamic analyses reveal that mutations affect the structural flexibility and correlated motions of the JH2, meanwhile also change the dynamics behavior of the P-loop and αC-helix of the JH2. The information from FELs unveils that mutations induce less energy states than the free JH2 and the WT one. The analyses of interaction networks uncover that mutations affect the salt bridge interactions of ATP with K581, K677 and R715 and alter hydrogen bonding interactions (HBIs) of ATP with the JH2. The changes in conformations of the JH2 and ATP-JH2 interaction networks caused by mutations in turn generate effect on the activity regulations of the JH2 on the JH1. This work is expected to provide significant theoretical helps for deeply understanding the function of the JH2 and drug design toward JAK2.Communicated by Ramaswamy H. Sarma.

13.
Accid Anal Prev ; 192: 107237, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-37544041

RESUMO

The service states of tunnel lighting will directly affect the lighting conditions, which affect traffic safety. Therefore, it is imperative to evaluate and predict traffic safety accurately in different lighting states. In this research, three hundred experimental scenarios of the service states of tunnel lighting were designed and implemented to evaluate the impact of different service states of tunnel lighting on traffic safety. The evaluation was achieved through a visual identification experiment in a physical tunnel. The experimental results show higher simulated vehicle speeds pose a greater threat to traffic safety. The severity of lighting attenuation contributes to an increased risk to traffic safety. An increase in the number of luminaires failure also poses a greater threat to traffic safety. The newly proposed traffic safety factor was employed to evaluate traffic safety quantitatively in road tunnels. To improve the accuracy and comprehensiveness of the traffic safety factor prediction in different lighting service states, an advanced neural network prediction system was developed. The prediction system was constructed using the Sparrow Search Algorithm (SSA) to optimize Extreme Learning Machine (ELM) neural network, and the dataset from the experiment was used for the prediction model. The SSA-ELM neural network model is a reliable model that can predict the traffic safety factor comprehensively and accurately. The recommended threshold value for the traffic safety factor is 0.6. When the value falls below 0.6, it shows that the service states of tunnel lighting pose a threat to traffic safety in the tunnel. These findings can provide insights into the safe and energy-efficient maintenance of road tunnels.


Assuntos
Acidentes de Trânsito , Iluminação , Humanos , Acidentes de Trânsito/prevenção & controle , Segurança , Algoritmos , Redes Neurais de Computação
14.
J Org Chem ; 88(15): 10448-10459, 2023 Aug 04.
Artigo em Inglês | MEDLINE | ID: mdl-37458429

RESUMO

An efficient radical cascade cyclization of unactivated alkenes toward the synthesis of a series of ring-fused quinazolinones has been developed in moderate to excellent yields using commercially available ethers, alkanes, and alcohols, respectively, under a base-free condition in a short time without a transition metal as catalyst. Notably, the transformations can be carried out with the advantages of a broad substrate scope and high atomic economy. Density functional theory calculations and wavefunction analyses were performed to elucidate the radical reaction mechanism.

15.
bioRxiv ; 2023 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-37292775

RESUMO

Internalizing and externalizing traits are two distinct classes of behaviors in psychiatry. However, whether shared or unique brain network features predict internalizing and externalizing behaviors in children and adults remain poorly understood. Using a sample of 2262 children from the Adolescent Brain Cognitive Development (ABCD) study and 752 adults from the Human Connectome Project (HCP), we show that network features predicting internalizing and externalizing behavior are, at least in part, dissociable in children, but not in adults. In ABCD children, traits within internalizing and externalizing behavioral categories are predicted by more similar network features concatenated across task and resting states than those between different categories. We did not observe this pattern in HCP adults. Distinct network features predict internalizing and externalizing behaviors in ABCD children and HCP adults. These data reveal shared and unique brain network features accounting for individual variation within broad internalizing and externalizing categories across developmental stages.

16.
Angew Chem Int Ed Engl ; 62(35): e202306380, 2023 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-37307027

RESUMO

A highly chemoselective earth-abundant transition metal copper catalyzed asymmetric hydrogenation of C=O bonds of exocyclic α,ß-unsaturated pentanones was realized using H2 . The desired products were obtained with up to 99 % yield and 96 % ee (enantiomeric excess) (99 % ee, after recrystallization). The corresponding chiral exocyclic allylic pentanol products can be converted into several bioactive molecules. The hydrogenation mechanism was investigated via deuterium-labelling experiments and control experiments, which indicate that the keto-enol isomerization rate of the substrate is faster than that of the hydrogenation and also show that the Cu-H complex can only catalyze chemoselectively the asymmetric reduction of the carbonyl group. Computational results indicate that the multiple attractive dispersion interactions (MADI effect) between the catalyst with bulky substituents and substrate play important roles which stabilize the transition states and reduce the generation of by-products.

17.
Molecules ; 28(12)2023 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-37375328

RESUMO

ß-amyloid cleaving enzyme 1 (BACE1) is regarded as an important target of drug design toward the treatment of Alzheimer's disease (AD). In this study, three separate molecular dynamics (MD) simulations and calculations of binding free energies were carried out to comparatively determine the identification mechanism of BACE1 for three inhibitors, 60W, 954 and 60X. The analyses of MD trajectories indicated that the presence of three inhibitors influences the structural stability, flexibility and internal dynamics of BACE1. Binding free energies calculated by using solvated interaction energy (SIE) and molecular mechanics generalized Born surface area (MM-GBSA) methods reveal that the hydrophobic interactions provide decisive forces for inhibitor-BACE1 binding. The calculations of residue-based free energy decomposition suggest that the sidechains of residues L91, D93, S96, V130, Q134, W137, F169 and I179 play key roles in inhibitor-BACE1 binding, which provides a direction for future drug design toward the treatment of AD.


Assuntos
Doença de Alzheimer , Simulação de Dinâmica Molecular , Humanos , Peptídeos beta-Amiloides/metabolismo , Secretases da Proteína Precursora do Amiloide , Ácido Aspártico Endopeptidases , Entropia , Doença de Alzheimer/metabolismo , Simulação de Acoplamento Molecular
18.
Molecules ; 28(12)2023 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-37375347

RESUMO

The heat shock protein (HSP90) has been an import target of drug design in the treatment of human disease. An exploration of the conformational changes in HSP90 can provide useful information for the development of efficient inhibitors targeting HSP90. In this work, multiple independent all-atom molecular dynamics (AAMD) simulations followed by calculations of the molecular mechanics generalized Born surface area (MM-GBSA) were performed to explore the binding mechanism of three inhibitors (W8Y, W8V, and W8S) to HSP90. The dynamics analyses verified that the presence of inhibitors impacts the structural flexibility, correlated movements, and dynamics behavior of HSP90. The results of the MM-GBSA calculations suggest that the selection of GB models and empirical parameters has important influences on the predicted results and verify that van der Waals interactions are the main forces that determine inhibitor-HSP90 binding. The contributions of separate residues to the inhibitor-HSP90 binding process indicate that hydrogen-bonding interactions (HBIs) and hydrophobic interactions play important roles in HSP90-inhibitor identifications. Moreover, residues L34, N37, D40, A41, D79, I82, G83, M84, F124, and T171 are recognized as hot spots of inhibitor-HSP90 binding and provide significant target sites of for the design of drugs related to HSP90. This study aims to contribute to the development of efficient inhibitors that target HSP90 by providing an energy-based and theoretical foundation.


Assuntos
Desenho de Fármacos , Simulação de Dinâmica Molecular , Humanos , Entropia , Ligação Proteica , Proteínas de Choque Térmico , Sítios de Ligação
19.
J Enzyme Inhib Med Chem ; 38(1): 2195995, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37057639

RESUMO

Mutations highly affect the structural flexibility of two switch domains in M-RAS considered an important target of anticancer drug design. Gaussian accelerated molecular dynamics (GaMD) simulations were applied to probe the effect of mutations P40D, D41E, and P40D/D41E/L51R on the conformational transition of the switch domains from the GTP-bound M-RAS. The analyses of free energy landscapes (FELs) not only reveal that three mutations induce less energetic states than the wild-type (WT) M-RAS but also verify that the switch domains are extremely disordered. Principal component analysis (PCA) and dynamics analysis suggest that three mutations greatly affect collective motions and structural flexibility of the switch domains that mostly overlap with binding regions of M-RAS to its effectors, which in turn disturbs the activity of M-RAS. The analyses of the interaction network between GTP and M-RAS show that the high instability in hydrogen bonding interactions (HBIs) of GTP with residue 41 and Y42 in the switch domain I drives the disordered states of the switch domains. This work is expected to provide a molecular mechanism for deeply understanding the function of M-RAS and future drug design towards the treatment of cancers.


Assuntos
Simulação de Dinâmica Molecular , Proteínas ras , Proteínas ras/genética , Proteínas ras/química , Proteínas ras/metabolismo , Conformação Proteica , Guanosina Trifosfato/química , Guanosina Trifosfato/metabolismo , Mutação
20.
Neuroimage ; 274: 120115, 2023 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-37088322

RESUMO

There is significant interest in using neuroimaging data to predict behavior. The predictive models are often interpreted by the computation of feature importance, which quantifies the predictive relevance of an imaging feature. Tian and Zalesky (2021) suggest that feature importance estimates exhibit low split-half reliability, as well as a trade-off between prediction accuracy and feature importance reliability across parcellation resolutions. However, it is unclear whether the trade-off between prediction accuracy and feature importance reliability is universal. Here, we demonstrate that, with a sufficient sample size, feature importance (operationalized as Haufe-transformed weights) can achieve fair to excellent split-half reliability. With a sample size of 2600 participants, Haufe-transformed weights achieve average intra-class correlation coefficients of 0.75, 0.57 and 0.53 for cognitive, personality and mental health measures respectively. Haufe-transformed weights are much more reliable than original regression weights and univariate FC-behavior correlations. Original regression weights are not reliable even with 2600 participants. Intriguingly, feature importance reliability is strongly positively correlated with prediction accuracy across phenotypes. Within a particular behavioral domain, there is no clear relationship between prediction performance and feature importance reliability across regression models. Furthermore, we show mathematically that feature importance reliability is necessary, but not sufficient, for low feature importance error. In the case of linear models, lower feature importance error is mathematically related to lower prediction error. Therefore, higher feature importance reliability might yield lower feature importance error and higher prediction accuracy. Finally, we discuss how our theoretical results relate with the reliability of imaging features and behavioral measures. Overall, the current study provides empirical and theoretical insights into the relationship between prediction accuracy and feature importance reliability.


Assuntos
Modelos Teóricos , Reprodutibilidade dos Testes , Modelos Lineares , Fenótipo , Tamanho da Amostra
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