RESUMO
INTRODUCTION: Molecular Dynamics (MD) simulations can support mechanism-based drug design. Indeed, MD simulations by capturing biomolecule motions at finite temperatures can reveal hidden binding sites, accurately predict drug-binding poses, and estimate the thermodynamics and kinetics, crucial information for drug discovery campaigns. Small-Guanosine Triphosphate Phosphohydrolases (GTPases) regulate a cascade of signaling events, that affect most cellular processes. Their deregulation is linked to several diseases, making them appealing drug targets. The broad roles of small-GTPases in cellular processes and the recent approval of a covalent KRas inhibitor as an anticancer agent renewed the interest in targeting small-GTPase with small molecules. AREA COVERED: This review emphasizes the role of MD simulations in elucidating small-GTPase mechanisms, assessing the impact of cancer-related variants, and discovering novel inhibitors. EXPERT OPINION: The application of MD simulations to small-GTPases exemplifies the role of MD simulations in the structure-based drug design process for challenging biomolecular targets. Furthermore, AI and machine learning-enhanced MD simulations, coupled with the upcoming power of quantum computing, are promising instruments to target elusive small-GTPases mutations and splice variants. This powerful synergy will aid in developing innovative therapeutic strategies associated to small-GTPases deregulation, which could potentially be used for personalized therapies and in a tissue-agnostic manner to treat tumors with mutations in small-GTPases.
RESUMO
Rho-GTPases proteins function as molecular switches alternating from an active to an inactive state upon Guanosine triphosphate (GTP) binding and hydrolysis to Guanosine diphosphate (GDP). Among them, Rac subfamily regulates cell dynamics, being overexpressed in distinct cancer types. Notably, these proteins are object of frequent cancer-associated mutations at Pro29 (P29S, P29L, and P29Q). To assess the impact of these mutations on Rac1 structure and function, we performed extensive all-atom molecular dynamics simulations on wild-type (wt) and oncogenic isoforms of this protein in GDP- and GTP-bound states. Our results unprecedentedly elucidate that P29Q/S-induced structural and dynamical perturbations of Rac1 core domain weaken the binding of the catalytic site Mg2+ ion, and reduce the GDP residence time within protein, enhancing the GDP/GTP exchange rate and Rac1 activity. This broadens our knowledge of the role of cancer-associated mutations on small GTPases mechanism supplying valuable information for future drug discovery efforts targeting specific Rac1 isoforms.
Assuntos
Neoplasias , Proteínas rho de Ligação ao GTP , Humanos , Proteínas rho de Ligação ao GTP/química , Mutação , Neoplasias/genética , Guanosina Trifosfato/química , Guanosina Trifosfato/metabolismo , Guanosina Difosfato/química , Guanosina Difosfato/metabolismo , Isoformas de Proteínas/metabolismoRESUMO
The nonstructural protein 12, known as RNA-dependent RNA polymerase (RdRp), is essential for both replication and repair of the viral genome. The RdRp of SARS-CoV-2 has been used as a promising candidate for drug development since the inception of the COVID-19 spread. In this work, we performed an in silico investigation on the insertion of the naturally modified pyrimidine nucleobase ddhCTP into the SARS-CoV-2 RdRp active site, in a comparative analysis with the natural one (CTP). The modification in ddhCTP involves the removal of the 3'-hydroxyl group that prevents the addition of subsequent nucleotides into the nascent strand, acting as an RNA chain terminator inhibitor. Quantum mechanical investigations helped to shed light on the mechanistic source of RdRp activity on the selected nucleobases, and comprehensive all-atom simulations provided insights about the structural rearrangements occurring in the active-site region when inorganic pyrophosphate (PPi) is formed. Subsequently, the intricate pathways for the release of PPi, the catalytic product of RdRp, were investigated using Umbrella Sampling simulations. The results are in line with the available experimental data and contribute to a more comprehensive point of view on such an important viral enzyme.
Assuntos
COVID-19 , Citidina Trifosfato , SARS-CoV-2 , Humanos , SARS-CoV-2/metabolismo , Replicação do RNA , RNA Viral , Antivirais/química , RNA Polimerase Dependente de RNA/metabolismoRESUMO
The novel coronavirus SARS-CoV-2 is the causative agent of the COVID-19 outbreak that is affecting the entire planet. As the pandemic is still spreading worldwide, with multiple mutations of the virus, it is of interest and of help to employ computational methods for identifying potential inhibitors of the enzymes responsible for viral replication. Attractive antiviral nucleotide analogue RNA-dependent RNA polymerase (RdRp) chain terminator inhibitors are investigated with this purpose. This study, based on molecular dynamics (MD) simulations, addresses the important aspects of the incorporation of an endogenously synthesized nucleoside triphosphate, ddhCTP, in comparison with the natural nucleobase cytidine triphosphate (CTP) in RdRp. The ddhCTP species is the product of the viperin antiviral protein as part of the innate immune response. The absence of the ribose 3'-OH in ddhCTP could have important implications in its inhibitory mechanism of RdRp. We built an in silico model of the RNA strand embedded in RdRp using experimental methods, starting from the cryo-electron microscopy structure and exploiting the information obtained by spectrometry on the RNA sequence. We determined that the model was stable during the MD simulation time. The obtained results provide deeper insights into the incorporation of nucleoside triphosphates, whose molecular mechanism by the RdRp active site still remains elusive.
Assuntos
COVID-19 , Citidina Trifosfato , RNA Polimerase Dependente de RNA , SARS-CoV-2 , Humanos , Antivirais/farmacologia , Antivirais/química , Microscopia Crioeletrônica , Citidina Trifosfato/química , Simulação de Dinâmica Molecular , Nucleosídeos , Nucleotídeos , Ribose , RNA Viral , RNA Polimerase Dependente de RNA/antagonistas & inibidores , RNA Polimerase Dependente de RNA/química , RNA Polimerase Dependente de RNA/metabolismo , SARS-CoV-2/química , SARS-CoV-2/metabolismoRESUMO
The inhibition mechanism of the main protease (Mpro) of SARS-CoV-2 by ebselen (EBS) and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3(2H)-one ring (EBS-OH) was studied by using a density functional level of theory. Preliminary molecular dynamics simulations on the apo form of Mpro were performed taking into account both the hydrogen donor and acceptor natures of the Nδ and Nε of His41, a member of the catalytic dyad. The potential energy surfaces for the formation of the Se-S covalent bond mediated by EBS and EBS-OH on Mpro are discussed in detail. The EBS-OH shows a distinctive behavior with respect to EBS in the formation of the noncovalent complex. Due to the presence of canonical H-bonds and noncanonical ones involving less electronegative atoms, such as sulfur and selenium, the influence on the energy barriers and reaction energy of the Minnesota hybrid meta-GGA functionals M06, M06-2X and M08HX, and the more recent range-separated hybrid functional wB97X were also considered. The knowledge of the inhibition mechanism of Mpro by the small protease inhibitors EBS or EBS-OH can enlarge the possibilities for designing more potent and selective inhibitor-based drugs to be used in combination with other antiviral therapies.
Assuntos
Antivirais/farmacologia , Tratamento Farmacológico da COVID-19 , Proteases 3C de Coronavírus/antagonistas & inibidores , Isoindóis/farmacologia , Compostos Organosselênicos/farmacologia , Inibidores de Proteases/farmacologia , Antivirais/uso terapêutico , Sítios de Ligação/efeitos dos fármacos , COVID-19/virologia , Domínio Catalítico/efeitos dos fármacos , Proteases 3C de Coronavírus/metabolismo , Desenho de Fármacos , Humanos , Isoindóis/química , Isoindóis/uso terapêutico , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Compostos Organosselênicos/química , Compostos Organosselênicos/uso terapêutico , Inibidores de Proteases/química , Inibidores de Proteases/uso terapêutico , SARS-CoV-2/efeitos dos fármacos , SARS-CoV-2/metabolismoRESUMO
The antioxidant capability of moracin C and iso-moracin C isomers against the OOH free radical was studied by applying density functional theory (DFT) and choosing the M05-2X exchange-correlation functional coupled with the all electron basis set, 6-311++G(d,p), for computations. Different reaction mechanisms [hydrogen atom transfer (HAT), single electron transfer (SET), and radical adduct formation (RAF)] were taken into account when considering water- and lipid-like environments. Rate constants were obtained by applying the conventional transition state theory (TST). The results show that, in water, scavenging activity mainly occurs through a radical addition mechanism for both isomers, while, in the lipid-like environment, the radical addition process is favored for iso-moracin C, while, redox- and non-redox-type reactions can equally occur for moracin C. The values of pKa relative to the deprotonation paths at physiological pH were predicted in aqueous solution.
RESUMO
Density functional theory was employed to highlight the antioxidant working mechanism of higenamine in aqueous and lipid-like environments. Different reaction mechanisms were considered for the reaction of higenamine with the â¢OOH radical. The pH values and the molar fraction at physiological pH were determined in aqueous solution. The results show that the preferred reaction mechanism was the hydrogen atom transfer from the catecholic ring. The computed kinetic constants revealed that, in order to obtain reliable results, it is important to consider all the species present in water solution derived from acid-base equilibria. From the present investigation, it emerges that at physiological pH (7.4), the scavenging activity of higenamine against the â¢OOH radical is higher than that of Trolox, chosen as a reference antioxidant. Furthermore, higenamine results to be more efficient for that purpose than melatonin and caffeine, whose protective action against oxidative stress is frequently associated with their reactive oxygen species (ROS) scavenging activity.
RESUMO
The primary processes that occur following direct irradiation of bio-macromolecules by ionizing radiation determine the multiscale responses that lead to biomolecular lesions. The so-called physical stage loosely describes processes of energy deposition and molecular ionization/excitation but remains largely elusive. We propose a new approach based on first principles density functional theory to simulate energy deposition in large and heterogeneous biomolecules by high-energy-transfer particles. Unlike traditional Monte Carlo approaches, our methodology does not rely on pre-parametrized sets of cross-sections, but captures excitation, ionization and low energy electron emission at the heart of complex biostructures. It furthermore gives access to valuable insights on ultrafast charge and hole dynamics on the femtosecond time scale. With this new tool, we reveal the mechanisms of ionization by swift ions in microscopic DNA models and solvated DNA comprising almost 750 atoms treated at the DFT level of description. We reveal a so-called ebb-and-flow ionization mechanism in which polarization of the irradiated moieties appears as a key feature. We also investigate where secondary electrons produced by irradiation localize on chemical moieties composing DNA. We compare irradiation of solvated DNA by light (H+, and He2+) vs. heavier (C6+) ions, highlighting the much higher probability of double ionization with the latter. Our methodology constitutes a stepping stone towards a greater understanding of the chemical stage and more generally towards the multiscale modelling of radiation damage in biology using first principles.
Assuntos
Simulação por Computador , DNA/química , DNA/efeitos da radiação , Modelos Químicos , Radiólise de ImpulsoRESUMO
The oxidative decarboxylation of the iron(II) α-hydroxy acid (mandelic acid) complex model, biomimetic of Rieske dioxygenase, has been investigated at the density functional level. The explored mechanism sheds light on the role of the α-hydroxyl group on the dioxygen activation. The potential energy surfaces have been explored in different electronic spin states. The rate-determining step of the process is the proton transfer. The oxidative decarboxylation preferentially takes place on the quintet state.
Assuntos
Materiais Biomiméticos/química , Compostos Ferrosos/química , Oxidantes/química , Estresse Oxidativo , Oxigênio/química , Teoria Quântica , Descarboxilação , Dioxigenases/metabolismo , Modelos MolecularesRESUMO
Background: Black salve, or sanguinarine, is a topical escharotic agent that has been used by patients for homeopathic ablation of epithelial dysplasia, including cervical intraepithelial neoplasia. Case Report: A 33-year-old female presented to the obstetric and gynecologic clinic for management of a missed abortion. At the time of presentation, she admitted to the use of topical black salve for treatment of cervical intraepithelial neoplasia 2 years prior. Speculum examination revealed a stenotic cervix that appeared flush against the vaginal cuff. Hysteroscopy performed 4 months later after the patient developed new oligomenorrhea revealed significant vaginal scarring with formation of a blind pouch that concealed the true cervix. Conclusion: Health care providers should be aware of homeopathic remedies trialed by patients on their own or as an alternative to recommended treatment. Such self-treatment may cause significant patient harm, such as scarring or deformity.
RESUMO
We report original analyses of attosecond electron dynamics of molecules subject to collisions by high energy charged particles based on Real-Time Time-Dependent-Density-Functional-Theory simulations coupled to Topological Analyses of the Electron Localization Function (TA-TD-ELF). We investigate irradiation of water and guanine. TA-TD-ELF enables qualitative and quantitative characterizations of bond breaking and formation, of charge migration within topological basins, or of electron attachment to the colliding particle. Whereas the Lewis-VSEPR structure of gas phase water is blown out within a few attoseconds after collision, that of guanine is far more robust and reconstitutes rapidly after impact even though the molecule remains electronically excited. This difference is accounted by the presence of the electron bath surrounding the impact point which enables energy relaxation within the molecule. Our approach should stimulate future studies to unravel the early steps following irradiation of various types of systems (isolated molecules, biomolecules, nanoclusters, solids, etc.) and is also readily applicable to irradiation by photons of various energies.