Paulo A. Netz
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View article: Computational modeling of oxytocin-receptors interactions with the common marmoset Callithrix jacchus Pro8OT variant
Computational modeling of oxytocin-receptors interactions with the common marmoset Callithrix jacchus Pro8OT variant Open
The oxytocinergic system plays a crucial role in regulating physiological and behavioral processes, making it a key component of neurobiology in both humans and animals. This study utilizes computational modeling to explore the interaction…
View article: An Amyloidogenic Fragment of the Spike Protein from SARS-CoV-2 Virus Stimulates the Aggregation and Toxicity of Parkinson’s Disease Protein Alpha-Synuclein
An Amyloidogenic Fragment of the Spike Protein from SARS-CoV-2 Virus Stimulates the Aggregation and Toxicity of Parkinson’s Disease Protein Alpha-Synuclein Open
Emerging evidence suggests that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may have long-term deleterious effects on the central nervous system and even contribute to post-COVID neurological syndromes. Inter…
View article: Applying Molecular Dynamics Simulations to Unveil the Anisotropic Growth Mechanism of Gold Nanorods: Advances and Perspectives
Applying Molecular Dynamics Simulations to Unveil the Anisotropic Growth Mechanism of Gold Nanorods: Advances and Perspectives Open
The unique properties of gold nanorods (AuNRs), combined with their relatively straightforward production, good yields, and satisfactory control over size and shape, have sparked considerable interest in their potential applications. Howev…
View article: Computational Investigations on Inhibitors of Mycobacterium tuberculosis Shikimate Kinase: Machine Learning, Docking, Molecular Dynamics and Free Energy Calculations
Computational Investigations on Inhibitors of Mycobacterium tuberculosis Shikimate Kinase: Machine Learning, Docking, Molecular Dynamics and Free Energy Calculations Open
Shikimate kinase emerges as an intriguing macromolecular target for the development of novel pharmaceutical agents for the treatment of tuberculosis. This study aimed to develop a neural network (NN) for the discovery of potential inhibito…
View article: EXPLORANDO O MECANISMO DE DEGRADAÇÃO ENZIMÁTICA DO POLIURETANO (PU) POR MEIO DAS POLIURETANASES ESTERASES A E B (PueA E PueB): UMA ABORDAGEM INTEGRADA DE DOCKING, DINÂMICA MOLECULAR (MD) E QM/MM
EXPLORANDO O MECANISMO DE DEGRADAÇÃO ENZIMÁTICA DO POLIURETANO (PU) POR MEIO DAS POLIURETANASES ESTERASES A E B (PueA E PueB): UMA ABORDAGEM INTEGRADA DE DOCKING, DINÂMICA MOLECULAR (MD) E QM/MM Open
EXPLORING THE MECHANISM OF ENZYMATIC DEGRADATION OF POLYURETHANE (PU) BY MEANS OF POLYURETHANASE ESTERASES A AND B (PueA AND PueB): AN INTEGRATED APPROACH OF DOCKING, MOLECULAR DYNAMICS (MD) AND QM/MM. The continuous global production of p…
View article: CCDC 2173258: Experimental Crystal Structure Determination
CCDC 2173258: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: Exploring Bachelard’s Epistemological Obstacles in Physical Chemistry Textbooks: The Case of Thermodynamics Concepts
Exploring Bachelard’s Epistemological Obstacles in Physical Chemistry Textbooks: The Case of Thermodynamics Concepts Open
Background : Although textbooks are used at all education levels, they are not free from errors, mistakes, and misconceptions. In the literature, many works have investigated textbooks in various ways, with particular emphasis on the influ…
View article: CCDC 2183731: Experimental Crystal Structure Determination
CCDC 2183731: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 2179076: Experimental Crystal Structure Determination
CCDC 2179076: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 2212745: Experimental Crystal Structure Determination
CCDC 2212745: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 2183730: Experimental Crystal Structure Determination
CCDC 2183730: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 2179077: Experimental Crystal Structure Determination
CCDC 2179077: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: A Family of Bisnaphthyl C<sub>2</sub>-Symmetric and Asymmetric Clefts: Synthesis, Solid-State Structure, and Calculation of the Interplanar Angle
A Family of Bisnaphthyl C<sub>2</sub>-Symmetric and Asymmetric Clefts: Synthesis, Solid-State Structure, and Calculation of the Interplanar Angle Open
The synthesis of a new family of naphthalenoid C2-symmetric clefts has been realized through a four-step synthetic sequence giving three C2-symmetric clefts and a rare nonsymmetric example. Subsequently, stereoselecti…
View article: Antioxidant and Anticancer Potential of the New Cu(II) Complexes Bearing Imine-Phenolate Ligands with Pendant Amine N-Donor Groups
Antioxidant and Anticancer Potential of the New Cu(II) Complexes Bearing Imine-Phenolate Ligands with Pendant Amine N-Donor Groups Open
Cu(II) complexes bearing NNO-donor Schiff base ligands (2a, b) have been synthesized and characterized. The single crystal X-ray analysis of the 2a complex revealed that a mononuclear and a dinuclear complex co-crystallize in the solid sta…
View article: A new family of rigid C2-symmetric cleft molecules as potential medicinal chemistry scaffolds
A new family of rigid C2-symmetric cleft molecules as potential medicinal chemistry scaffolds Open
The discovery of new scaffolds that selectively interact with biomolecules is vital in the development of new medicinal and chemical biology tools, therapeutics and sensors. Their binding and specificity is reliant on several well establis…
View article: A new family of rigid C2-symmetric cleft molecules as potential medicinal chemistry scaffolds
A new family of rigid C2-symmetric cleft molecules as potential medicinal chemistry scaffolds Open
The discovery of new scaffolds that selectively interact with biomolecules (e.g. DNA) supports the development of new medicinal and chemical biology tools, such as novel therapeutics and sensors. Whilst their binding and specificity is dep…
View article: Molecular evolution and structural analyses of the spike glycoprotein from Brazilian SARS-CoV-2 genomes: the impact of selected mutations
Molecular evolution and structural analyses of the spike glycoprotein from Brazilian SARS-CoV-2 genomes: the impact of selected mutations Open
The COVID-19 pandemic caused by SARS-CoV-2 has reached by February 2022 more than 380 million cases and 5.5 million deaths worldwide since its beginning in late 2019, leading to enhanced concern in the scientific community and the general …
View article: Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2)
Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2) Open
Covid-19 is a viral disease caused by the virus SARS-CoV-2 that spread worldwide and caused more than 4.3 million deaths. Moreover, SARS-CoV-2 still continues to evolve, and specifically the E484K, N501Y, and South Africa triple (K417N + E…
View article: Determination of the interaction between the receptor binding domain of 2019-nCoV spike protein, TMPRSS2, cathepsin B and cathepsin L, and glycosidic and aglycon forms of some flavonols
Determination of the interaction between the receptor binding domain of 2019-nCoV spike protein, TMPRSS2, cathepsin B and cathepsin L, and glycosidic and aglycon forms of some flavonols Open
The novel coronavirus (COVID-19, SARS-CoV-2) is a rapidly spreading disease with a high mortality. In this research, the interactions between specific flavonols and the 2019-nCoV receptor binding domain (RBD), transmembrane protease, serin…
View article: <i>In silico</i> analysis of the interactions of certain flavonoids with the receptor-binding domain of 2019 novel coronavirus and cellular proteases and their pharmacokinetic properties
<i>In silico</i> analysis of the interactions of certain flavonoids with the receptor-binding domain of 2019 novel coronavirus and cellular proteases and their pharmacokinetic properties Open
Coronavirus Disease 2019 (COVID-19) has infected more than thirty five million people worldwide and caused nearly 1 million deaths as of October 2020. The microorganism causing COVID-19 was named as Severe Acute Respiratory Syndrome Corona…
View article: How Does the Novel Coronavirus Interact with the Human ACE2 Enzyme? A Thermodynamic Answer
How Does the Novel Coronavirus Interact with the Human ACE2 Enzyme? A Thermodynamic Answer Open
The SARS-CoV-2 coronavirus pandemic is certainly the most important public health concern today. Until now there are no vaccines or treatments available, despite intensive international efforts. One of the targets for new drugs is the Coro…
View article: How Does the Novel Coronavirus Interact with the Human ACE2 Enzyme? A Thermodynamic Answer
How Does the Novel Coronavirus Interact with the Human ACE2 Enzyme? A Thermodynamic Answer Open
The SARS-CoV-2 coronavirus pandemic is certainly the most important public health concern today. Until now there are no vaccines or treatments available, despite intensive international efforts. One of the targets for new drugs is the Coro…
View article: How Does the Novel Coronavirus Interact with the Human ACE2 Enzyme? A Thermodynamic Answer
How Does the Novel Coronavirus Interact with the Human ACE2 Enzyme? A Thermodynamic Answer Open
The SARS-CoV-2 coronavirus pandemic is certainly the most important public health concern today. Until now there are no vaccines or treatments available, despite intensive international efforts. One of the targets for new drugs is the Coro…
View article: Dynamical aspects of supercooled TIP3P–water in the grooves of DNA
Dynamical aspects of supercooled TIP3P–water in the grooves of DNA Open
We investigate by molecular dynamics simulations the mobility of the water located at the DNA minor and major grooves. We employ the TIP3P water model, and our system is analyzed for a range of temperatures 190–300 K. For high temperatures…
View article: Tianeptine Esters Derivatives: A Study of Protein-Drug Interaction Performed by Fluorescence Quenching and Molecular Docking
Tianeptine Esters Derivatives: A Study of Protein-Drug Interaction Performed by Fluorescence Quenching and Molecular Docking Open
The nature of binding between bovine serum albumin (BSA) and the antidepressant tianeptine and a new series of esters derivatives were studied in this paper. The interactions with BSA were investigated by UV-Vis and fluorescence spectrosco…
View article: Tianeptine Esters Derivatives: A Study of Protein-Drug Interaction Performed by Fluorescence Quenching and Molecular Docking
Tianeptine Esters Derivatives: A Study of Protein-Drug Interaction Performed by Fluorescence Quenching and Molecular Docking Open
The nature of binding between bovine serum albumin (BSA) and the antidepressant tianeptine and a new series of esters derivatives were studied in this paper.The interactions with BSA were investigated by UV-Vis and fluorescence spectroscop…
View article: Novos métodos de simulação em ácidos nucleicos
Novos métodos de simulação em ácidos nucleicos Open
Apesar da inegável importância dos ácidos nucleicos (DNA e RNA) para a genética, bioquímica, biologia molecular e farmacologia, eles tem sido muito menos estudados que as proteínas, mediante métodos computacionais.O grande tamanho das molé…
View article: Structure and mobility of water confined in AlPO4-54 nanotubes
Structure and mobility of water confined in AlPO4-54 nanotubes Open
We performed molecular dynamics simulations of water confined within AlPO4-54 nanotubes. AlPO4-54 is an artificial material made of AlO4 and of PO4 in tetrahedra arranged in a periodic structure forming pores of approximately 1.3 nm in dia…
View article: Ru-Catalyzed Estragole Isomerization under Homogeneous and Ionic Liquid Biphasic Conditions
Ru-Catalyzed Estragole Isomerization under Homogeneous and Ionic Liquid Biphasic Conditions Open
The isomerization of estragole to trans-anethole is an important reaction and is industrially performed using an excess of NaOH or KOH in ethanol at high temperatures with very low selectivity. Simple Ru-based transition-metal compl…
View article: Investigation of the Interaction of 2-(2'-Hydroxyphenyl)-benzoxazoles and their Derivatives with B-DNA by Docking and Molecular Dynamics
Investigation of the Interaction of 2-(2'-Hydroxyphenyl)-benzoxazoles and their Derivatives with B-DNA by Docking and Molecular Dynamics Open
In this work we carried out a study covering conformational analysis, docking calculations and molecular dynamics (MD) simulations of six excited state intramolecular proton transfer (ESIPT)-fluorescent 2-(2'-hydroxyphenyl)-benzoxazoles, i…