Deciphering Interactions between Potential Inhibitors and the Plasmodium falciparum DHODH Enzyme: A Computational Perspective.

Malaria is a parasitic disease that, in its most severe form, can even lead to death. Insect-resistant vectors, insufficiently effective vaccines, and drugs that cannot stop parasitic infestations are making the fight against the disease increasingly difficult. It is known that the enzyme dihydroorotate dehydrogenase (DHODH) is of paramount importance for the synthesis of pyrimidine from the Plasmodium precursor, that is, for its growth and reproduction. Therefore, its blockade can lead to disruption of the parasite's life cycle in the vertebrate host. In this scenario, PfDHODH inhibitors have been considered candidates for a new therapy to stop the parasitic energy source. Given what is known, in this work, we applied molecular fractionation with conjugated caps (MFCC) in the framework of the quantum formalism of density functional theory (DFT) to evaluate the energies of the interactions between the enzyme and the different triazolopyrimidines (DSM483, DMS557, and DSM1), including a complex carrying the mutation C276F. From these results, it was possible to identify the main features of each system, focusing on the wild-type and mutant PfDHODH and examining the major amino acid residues that are part of the four complexes. Our analysis provides new information that can be used to develop new drugs that could prove to be more effective alternatives to present antimalarial drugs.

In Silico Evaluation of the Binding Energies of Androgen Receptor Agonists in Wild-Type and Mutational Models.

Anabolic androgenic steroids (AAS) are substances with androgenic and anabolic characteristics. Among the many side effects of hormone therapy with AAS, the following stand out: heart problems, adrenal gland disorders, aggressive behavior, increased risk of prostate cancer, problems related to lack of libido and impotence. Such substances vary in the relationship between androgenic activity, and the activation of the androgen receptor (AR) is of fundamental importance for the singularity of the action of each AAS. In this sense, our study evaluates the aspects that comprise the interactions of testosterone agonists (TES), dihydrotestosterone (DHT) and tetrahydrogestrinone (THG) in complex with the AR. In addition, we also evaluated the impact of ligand-receptor affinity differences in a mutation model. We apply computational techniques based on density functional theory (DFT) and use, as methodology, Molecular Fractionation with Conjugate Caps (MFCC). The energetic specificities present in the interaction between the analyzed complexes attest that the highest affinity with the AR receptor is found for AR-THG, followed by AR-DHT, AR-TES and AR-T877A-DHT, respectively. Our results also show the differences and equivalences between the different agonists, in addition to evaluating the difference between the DHT ligand in complex with the wild-type and mutant receptor, presenting the main amino acid residues that involve the interaction with the ligands. The computational methodology used proves to be an operative and sophisticated choice to help in the search for pharmacological agents for various therapies that have androgen as a target.

Investigation of protein-protein interactions and hotspot region on the NSP7-NSP8 binding site in NSP12 of SARS-CoV-2.

Background: The RNA-dependent RNA polymerase (RdRp) complex, essential in viral transcription and replication, is a key target for antiviral therapeutics. The core unit of RdRp comprises the nonstructural protein NSP12, with NSP7 and two copies of NSP8 (NSP81 and NSP82) binding to NSP12 to enhance its affinity for viral RNA and polymerase activity. Notably, the interfaces between these subunits are highly conserved, simplifying the design of molecules that can disrupt their interaction. Methods: We conducted a detailed quantum biochemical analysis to characterize the interactions within the NSP12-NSP7, NSP12-NSP81, and NSP12-NSP82 dimers. Our objective was to ascertain the contribution of individual amino acids to these protein-protein interactions, pinpointing hotspot regions crucial for complex stability. Results: The analysis revealed that the NSP12-NSP81 complex possessed the highest total interaction energy (TIE), with 14 pairs of residues demonstrating significant energetic contributions. In contrast, the NSP12-NSP7 complex exhibited substantial interactions in 8 residue pairs, while the NSP12-NSP82 complex had only one pair showing notable interaction. The study highlighted the importance of hydrogen bonds and π-alkyl interactions in maintaining these complexes. Intriguingly, introducing the RNA sequence with Remdesivir into the complex resulted in negligible alterations in both interaction energy and geometric configuration. Conclusion: Our comprehensive analysis of the RdRp complex at the protein-protein interface provides invaluable insights into interaction dynamics and energetics. These findings can guide the design of small molecules or peptide/peptidomimetic ligands to disrupt these critical interactions, offering a strategic pathway for developing effective antiviral drugs.

A reactive molecular dynamics study on the mechanical properties of a recently synthesized amorphous carbon monolayer converted into a nanotube/nanoscroll.

Recently, laser-assisted chemical vapor deposition has been used to synthesize a free-standing, continuous, and stable monolayer amorphous carbon (MAC). MAC is a pure carbon structure composed of randomly distributed five, six, seven, and eight atom rings, which is different from that of disordered graphene. More recently, amorphous MAC-based nanotubes (a-CNT) and nanoscrolls (a-CNS) were proposed. In this work, we have investigated (through fully atomistic reactive molecular dynamics simulations) the mechanical properties and sublimation points of pristine and a-CNT and a-CNS. The results showed that a-CNT and a-CNS have distinct elastic properties and fracture patterns compared to those of their pristine analogs. Both a-CNT and a-CNS presented a non-elastic regime before their total rupture, whereas the CNT and CNS underwent a direct conversion to fractured forms after a critical strain threshold. The critical strain values for the fracture of the a-CNT and a-CNS are about 30% and 25%, respectively, and they are lower than those of the corresponding CNT and CNS cases. Although less resilient to tension, the amorphous tubular structures have similar thermal stability in relation to the pristine cases with sublimation points of 5500 K, 6300 K, 5100 K, and 5900 K for a-CNT, CNT, a-CNS, and CNS, respectively. An interesting result is that the nanostructure behavior is substantially different depending on whether it is a nanotube or a nanoscroll, thus indicating that the topology plays an important role in defining its elastic properties.

Tuning Penta-Graphene Electronic Properties Through Engineered Line Defects.

Penta-graphene is a quasi-two-dimensional carbon allotrope consisting of a pentagonal lattice in which both sp2 and sp3-like carbons are present. Unlike graphene, penta-graphene exhibits a non-zero bandgap, which opens the possibility of its use in optoelectronic applications. However, as the observed bandgap is large, gap tuning strategies such as doping are required. In this work, density functional theory calculations are used to determine the effects of the different number of line defects of substitutional nitrogen or silicon atoms on the penta-graphene electronic behavior. Our results show that this doping can induce semiconductor, semimetallic, or metallic behavior depending on the doping atom and targeted hybridization (sp2 or sp3-like carbons). In particular, we observed that nitrogen doping of sp2-like carbons atoms can produce a bandgap modulation between semimetallic and semiconductor behavior. These results show that engineering line defects can be an effective way to tune penta-graphene electronic behavior.

Extraction of Two-Dimensional Aluminum Alloys from Decagonal Quasicrystals.

Atomically thin metallic alloys are receiving increased attention due to their prospective applications as interconnects/contacts in two-dimensional (2D) circuits, sensors, and catalysts, among others. In this work, we demonstrate an easily scalable technique for the synthesis of 2D metallic alloys from their 3D quasicrystalline precursors. We have used aluminum (Al)-based single-phase decagonal quasicrystal Al66Co17Cu17 alloy to extract the corresponding 2D alloy structure. The 2D layered Al alloy possesses 2-fold decagonal quasicrystalline symmetry and consists of two- or three-layer-thick sheets with a lateral dimension of microns. These 2D metallic layers were combined with the atomic layers of tungsten disulfide to form the stacked heterostructures, which is demonstrated to be a stable and efficient catalyst for hydrogen evolution reaction.

Deformation Mechanisms of Vertically Stacked WS2 /MoS2 Heterostructures: The Role of Interfaces.

The mechanical and optical properties generated due to the stacking of different atomically thin materials have made it possible to tune and engineer these materials for next-generation electronics. The understanding of the interlayer interactions in such stacked structures is of fundamental interest for structure and property correlation. Here, a combined approach of in situ Raman spectroscopy and mechanical straining along with molecular dynamics (MD) simulations has been used to probe one such interface, namely, the WS2/MoS2 heterostructure. Vertical heterostructures on poly(methyl methacrylate), when flexed, showed signs of decoupling at 1.2% strain. Theoretical calculations showed strain-induced stacking changes at 1.75% strain. The sliding characteristics of layers were also investigated using scanning probe microscopy based nanoscratch testing, and the results are further supported by MD simulations. The present study could be used to design future optoelectronic devices based on WS2/MoS2 heterostructures.

Lightweight Hexagonal Boron Nitride Foam for CO2 Absorption.

Weak van der Waals forces between inert hexagonal boron nitride (h-BN) nanosheets make it easy for them to slide over each other, resulting in an unstable structure in macroscopic dimensions. Creating interconnections between these inert nanosheets can remarkably enhance their mechanical properties. However, controlled design of such interconnections remains a fundamental problem for many applications of h-BN foams. In this work, a scalable in situ freeze-drying synthesis of low-density, lightweight 3D macroscopic structures made of h-BN nanosheets chemically connected by poly(vinyl alcohol) (PVA) molecules via chemical cross-link is demonstrated. Unlike pristine h-BN foam which disintegrates upon handling after freeze-drying, h-BN/PVA foams exhibit stable mechanical integrity in addition to high porosity and large surface area. Fully atomistic simulations are used to understand the interactions between h-BN nanosheets and PVA molecules. In addition, the h-BN/PVA foam is investigated as a possible CO2 absorption and as laser irradiation protection material.

Synthesis of Low-Density, Carbon-Doped, Porous Hexagonal Boron Nitride Solids.

Here, we report the scalable synthesis and characterization of low-density, porous, three-dimensional (3D) solids consisting of two-dimensional (2D) hexagonal boron nitride (h-BN) sheets. The structures are synthesized using bottom-up, low-temperature (∼300 °C), solid-state reaction of melamine and boric acid giving rise to porous and mechanically stable interconnected h-BN layers. A layered 3D structure forms due to the formation of h-BN, and significant improvements in the mechanical properties were observed over a range of temperatures, compared to graphene oxide or reduced graphene oxide foams. A theoretical model based on Density Functional Theory (DFT) is proposed for the formation of h-BN architectures. The material shows excellent, recyclable absorption capacity for oils and organic solvents.