Nanomarker for Early Detection of Alzheimer’s Disease Combining Ab initio DFT Simulations and Molecular Docking Approach

Schopf, Patrícia Ferreira; Zanella, Ivana; Cordeiro, M. Natália D. S.; Ruso, Juan M.; González-Durruthy, Michael; Martins, Mirkos Ortiz

doi:10.3390/biophysica1020007

Cited by 5 publications

(3 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…After the fragmentation of each amino acid, to calculate the interaction energy between the receptor and the ligand, two methods were applied: density functional theory (DFT) formalism [ 34 ] and the generalized gradient approximation (GGA) functional B97D, computed by Gaussian 16 software package. It has been previously suggested that this GGA-type density functional is an accurate and efficient QM method [ 35 ], especially when dispersion forces are an important element, often valid for large systems.…”

Section: Methodsmentioning

confidence: 99%

Antiviral Activity and Molecular Dynamics Simulation of Hops Compounds against Oropouche Virus (Peribunyaviridae)

Mandova,

Saivish,

Menezes

et al. 2023

Pharmaceutics

View full text Add to dashboard Cite

The Oropouche virus (OROV) is a member of the family Peribunyaviridae (order Bunyavirales) and the cause of a dengue-like febrile illness transmitted mainly by biting midges and mosquitoes. In this study, we aimed to explore acylphloroglucinols and xanthohumol from hops (Humulus lupulus L.) as a promising alternative for antiviral therapies. The evaluation of the inhibitory potential of hops compounds on the viral cycle of OROV was performed through two complementary approaches. The first approach applies cell-based assay post-inoculation experiments to explore the inhibitory potential on the latest steps of the viral cycle, such as genome translation, replication, virion assembly, and virion release from the cells. The second part covers in silico methods evaluating the ability of those compounds to inhibit the activity of the endonuclease domain, which is essential for transcription, binding, and cleaving RNA. In conclusion, the beta acids showed strongest inhibitory potential in post-treatment assay (EC50 = 26.7 µg/mL). Xanthohumol had the highest affinity for OROV endonuclease followed by colupulone and cohumulone. This result contrasts with that observed for docking and MM/PBSA analysis, where cohumulone was found to have a higher affinity. Finally, among the three tested ligands, Lys92 and Arg33 exhibited the highest affinity with the protein.

show abstract

Section: Methodsmentioning

confidence: 99%

Antiviral Activity and Molecular Dynamics Simulation of Hops Compounds against Oropouche Virus (Peribunyaviridae)

Mandova,

Saivish,

Menezes

et al. 2023

Pharmaceutics

View full text Add to dashboard Cite

show abstract

“…For instance, Schopf and co-workers reported the DFT simulation combined with molecular docking approach for the detection of AD biomarkers. 37 They considered the tau protein as an AD biomarker and studied its interaction with theoretically modeled ligands. Apart from that, to the best of our knowledge, there is hardly any study that reported the design of a biosensor capable of detecting AD fingerprint VOCs for early diagnosis.…”

Section: Introductionmentioning

confidence: 99%

“…There are very few computational studies that dealt with the early diagnosis of AD. For instance, Schopf and co-workers reported the DFT simulation combined with molecular docking approach for the detection of AD biomarkers . They considered the tau protein as an AD biomarker and studied its interaction with theoretically modeled ligands.…”

Section: Introductionmentioning

confidence: 99%

First-Principles Approach for Assessing the Detection of Alzheimer’s Biomarkers Using Titanium Carbide MXenes

Kumar,

Bae,

Lee

et al. 2024

ACS Appl. Nano Mater.

View full text Add to dashboard Cite

Alzheimer's disease (AD) is considered the most common neurodegenerative condition and is the main cause of dementia. AD progresses rapidly and is the major cause of death in the elderly population; thus, an early diagnosis is of vital importance. Medical research has successfully characterized a set of volatile organic compounds (VOCs) present in exhaled patient's breath to be considered as fingerprints of AD. The present work, for the first time, aims at computationally designing highly efficient nano-biosensors capable of detecting the VOC biomarkers. We apply density functional theory (DFT) to study the adsorption properties of three representative VOCs, namely, 2,3-dimethylheptane (23-DMH), butylated hydroxytoluene (BHT), and pivalic acid (PVA), versus four interfering air molecules (i.e., N 2 , O 2 , CO 2 , and H 2 O) on four different MXenes (i.e., thick Ti 3 C 2 T x and thin Ti 2 CT x MXenes, T x = O or S). All the molecules are found to exhibit physisorption interactions on the studied MXenes. Nevertheless, the energetic analysis shows clear selective adsorption of BHT on Ti 3 C 2 O 2 with an adsorption energy of −1.513 eV, which is desirable for practical sensing applications. Furthermore, distinct from all other VOCs and interfering air molecules, BHT oxidizes to the O passivation layer of MXenes with a charge transfer of +0.421e and induces magnetization of 0.467 μ B to transform the surface to become ferromagnetic. These changes are very promising to rectify the current−voltage characteristics and yield a high sensor response. We further performed thermodynamic analysis through the Langmuir adsorption model, which ensures the excellent adsorption performance of Ti 3 C 2 O 2 over a broad range of BHT concentrations at ambient temperature. Therefore, Ti 3 C 2 O 2 could be considered as highly sensitive and selective nano-biosensors toward the fingerprint VOCs of AD.

show abstract

Discovery and Design of Radiopharmaceuticals by In silico Methods

Salahinejad

Winkler

Shiri

2022

CRP

View full text Add to dashboard Cite

There has been impressive growth in the use of radiopharmaceuticals for therapy, selective toxic payload delivery, and noninvasive diagnostic imaging of disease. The increasing timeframes and costs involved in the discovery and development of new radiopharmaceuticals have driven the development of more efficient strategies for this process. Computer-aided drug design (CADD) methods and machine learning (ML) have become more effective over the last two decades for drug and materials discovery and optimization They are now fast, flexible, and sufficiently accurate to accelerate the discovery of new molecules and materials. Radiopharmaceuticals have also started to benefit from rapid developments in computational methods. Here we review the types of computational molecular design techniques that have been used for radiopharmaceuticals design. We also provide a thorough examination of success stories in the design of radiopharmaceuticals, and the strengths and weaknesses of the computational methods. We begin by providing a brief overview of therapeutic and diagnostic radiopharmaceuticals and the steps involved in radiopharmaceuticals design and development. We then review the computational design methods used in radiopharmaceutical studies – molecular mechanics, quantum mechanics, molecular dynamics, molecular docking, pharmacophore modelling, and data-driven ML. Finally, the difficulties and opportunities presented by radiopharmaceutical modelling are highlighted. The review emphasizes the potential of computational design methods to accelerate the production of these very useful clinical radiopharmaceutical agents and aims to raise awareness among radiopharmaceutical researchers about computational modelling and simulation methods that can be of benefit to this field.

show abstract

Nanomarker for Early Detection of Alzheimer’s Disease Combining Ab initio DFT Simulations and Molecular Docking Approach

Cited by 5 publications

References 26 publications

Antiviral Activity and Molecular Dynamics Simulation of Hops Compounds against Oropouche Virus (Peribunyaviridae)

Antiviral Activity and Molecular Dynamics Simulation of Hops Compounds against Oropouche Virus (Peribunyaviridae)

First-Principles Approach for Assessing the Detection of Alzheimer’s Biomarkers Using Titanium Carbide MXenes

Discovery and Design of Radiopharmaceuticals by In silico Methods

Contact Info

Product

Resources

About