Natural 2',4-Dihydroxy-4',6'-dimethoxy Chalcone Isolated from Chromolaena tacotana Inhibits Breast Cancer Cell Growth through Autophagy and Mitochondrial Apoptosis.

Breast cancer (BC) is one of the most common cancers among women. Effective treatment requires precise tailoring to the genetic makeup of the cancer for improved efficacy. Numerous research studies have concentrated on natural compounds and their anti-breast cancer properties to improve the existing treatment options. Chromolaena tacotana (Klatt) R.M. King and H. Rob (Ch. tacotana) is a notable source of bioactive hydroxy-methylated flavonoids. However, the specific anti-BC mechanisms of these flavonoids, particularly those present in the plant's inflorescences, remain partly undefined. This study focuses on assessing a chalcone derivative extracted from Ch. tacotana inflorescences for its potential to concurrently activate regulated autophagy and intrinsic apoptosis in luminal A and triple-negative BC cells. We determined the chemical composition of the chalcone using ultraviolet (UV) and nuclear magnetic resonance (NMR) spectroscopy. Its selective cytotoxicity against BC cell lines was assessed using the MTT assay. Flow cytometry and Western blot analysis were employed to examine the modulation of proteins governing autophagy and the intrinsic apoptosis pathway. Additionally, in silico simulations were conducted to predict interactions between chalcone and various anti-apoptotic proteins, including the mTOR protein. Chalcone was identified as 2',4-dihydroxy-4',6'-dimethoxy-chalcone (DDC). This compound demonstrated a selective inhibition of BC cell proliferation and triggered autophagy and intrinsic apoptosis. It induced cell cycle arrest in the G0/G1 phase and altered mitochondrial outer membrane potential (∆ψm). The study detected the activation of autophagic LC3-II and mitochondrial pro-apoptotic proteins in both BC cell lines. The regulation of Bcl-XL and Bcl-2 proteins varied according to the BC subtype, yet they showed promising molecular interactions with DDC. Among the examined pro-survival proteins, mTOR and Mcl-1 exhibited the most favorable binding energies and were downregulated in BC cell lines. Further research is needed to fully understand the molecular dynamics involved in the activation and interaction of autophagy and apoptosis pathways in cancer cells in response to potential anticancer agents, like the hydroxy-methylated flavonoids from Ch. tacotana.

A Novel Tri-Hydroxy-Methylated Chalcone Isolated from Chromolaena tacotana with Anti-Cancer Potential Targeting Pro-Survival Proteins.

Chromolaena tacotana (Klatt) R. M. King and H. Rob (Ch. tacotana) contains bioactive flavonoids that may have antioxidant and/or anti-cancer properties. This study investigated the potential anti-cancer properties of a newly identified chalcone isolated from the inflorescences of the plant Chromolaena tacotana (Klatt) R. M. King and H. Rob (Ch. tacotana). The chalcone structure was determined using HPLC/MS (QTOF), UV, and NMR spectroscopy. The compound cytotoxicity and selectivity were evaluated on prostate, cervical, and breast cancer cell lines using the MTT assay. Apoptosis and autophagy induction were assessed through flow cytometry by detecting annexin V/7-AAD, active Casp3/7, and LC3B proteins. These results were supported by Western blot analysis. Mitochondrial effects on membrane potential, as well as levels of pro- and anti-apoptotic proteins were analyzed using flow cytometry, fluorescent microscopy, and Western blot analysis specifically on a triple-negative breast cancer (TNBC) cell line. Furthermore, molecular docking (MD) and molecular dynamics (MD) simulations were performed to evaluate the interaction between the compounds and pro-survival proteins. The compound identified as 2',3,4-trihydroxy-4',6'-dimethoxy chalcone inhibited the cancer cell line proliferation and induced apoptosis and autophagy. MDA-MB-231, a TNBC cell line, exhibited the highest sensitivity to the compound with good selectivity. This activity was associated with the regulation of mitochondrial membrane potential, activation of the pro-apoptotic proteins, and reduction of anti-apoptotic proteins, thereby triggering the intrinsic apoptotic pathway. The chalcone consistently interacted with anti-apoptotic proteins, particularly the Bcl-2 protein, throughout the simulation period. However, there was a noticeable conformational shift observed with the negative autophagy regulator mTOR protein. Future studies should focus on the molecular mechanisms underlying the anti-cancer potential of the new chalcone and other flavonoids from Ch. tacotana, particularly against predominant cancer cell types.

An Immunoinformatics Approach for SARS-CoV-2 in Latam Populations and Multi-Epitope Vaccine Candidate Directed towards the World's Population.

The coronavirus pandemic is a major public health crisis affecting global health systems with dire socioeconomic consequences, especially in vulnerable regions such as Latin America (LATAM). There is an urgent need for a vaccine to help control contagion, reduce mortality and alleviate social costs. In this study, we propose a rational multi-epitope candidate vaccine against SARS-CoV-2. Using bioinformatics, we constructed a library of potential vaccine peptides, based on the affinity of the most common major human histocompatibility complex (HLA) I and II molecules in the LATAM population to predict immunological complexes among antigenic, non-toxic and non-allergenic peptides extracted from the conserved regions of 92 proteomes. Although HLA-C, had the greatest antigenic peptide capacity from SARS-CoV-2, HLA-B and HLA-A, could be more relevant based on COVID-19 risk of infection in LATAM countries. We also used three-dimensional structures of SARS-CoV-2 proteins to identify potential regions for antibody production. The best HLA-I and II predictions (with increased coverage in common alleles and regions evoking B lymphocyte responses) were grouped into an optimized final multi-epitope construct containing the adjuvants Beta defensin-3, TpD, and PADRE, which are recognized for invoking a safe and specific immune response. Finally, we used Molecular Dynamics to identify the multi-epitope construct which may be a stable target for TLR-4/MD-2. This would prove to be safe and provide the physicochemical requirements for conducting experimental tests around the world.

Dynamic Effects of CYP2D6 Genetic Variants in a Set of Poor Metaboliser Patients with Infiltrating Ductal Cancer Under Treatment with Tamoxifen.

Breast cancer is a group of multigenic diseases. It is the most common cancer diagnosed among women worldwide and is often treated with tamoxifen. Tamoxifen is catalysed by cytochrome P450 2D6 (CYP2D6), and inter-individual variations in the enzyme due to single nucleotide polymorphisms (SNPs) could alter enzyme activity. We evaluated SNPs in patients from Colombia in South America who were receiving tamoxifen treatment for breast cancer. Allelic diversity in the CYP2D6 gene was found in the studied population, with two patients displaying the poor-metaboliser phenotype. Molecular dynamics and trajectory analyses were performed for CYP2D6 from these two patients, comparing it with the common allelic form (CYP2D6*1). Although we found no significant structural change in the protein, its dynamics differ significantly from those of CYP2D6*1, the effect of such differential dynamics resulting in an inefficient enzyme with serious implications for tamoxifen-treated patients, increasing the risk of disease relapse and ineffective treatment.

HSO3Cl: a prototype molecule for studying OH-stretching overtone induced photodissociation.

Vibrationally induced photodissociation in sulfurochloridic acid (HSO3Cl) is found to be a viable process to form SO3 and HCl from excitations of the OH-stretching overtone starting at νOH = 4. Reactive molecular dynamics simulations on a fully-dimensional potential energy surface fitted to MP2 calculations show that hydrogen transfer and HCl elimination compete with one another on the nanosecond time scale. Excitation with 5 and 6 quanta in the OH-stretch direct elimination of HCl is a dominant process on the several hundred picosecond time scale. At longer times, HCl formation is preceded by intramolecular hydrogen transfer and concomitant excitation of torsional degrees of freedom. As HSO3Cl is a suitable proxy for H2SO4, which is relevant for weather and climate in the upper atmosphere, it is concluded that vibrationally induced photodissociation is a possible mechanism for H2SO4 decomposition. Final state energy distributions for different internal degrees of freedom are predicted which should be observable in laboratory measurements.

Competitive reaction pathways in vibrationally induced photodissociation of H2SO4.

Vibrationally induced photodissociation of sulfuric acid into H2O + SO3 is investigated based on reactive molecular dynamics (MD) simulations. Multisurface adiabatic reactive MD simulations allow us to follow both, H-transfer and water elimination after excitation of the ν9 OH-stretching mode. Analysis of several thousand trajectories finds that the H2O and SO3 fragments have distinct final state distributions with respect to translational, rotational, and vibrational degrees of freedom. Rotational distributions peak at quantum numbers j ≤ 5 for water and j ≈ 60 for SO3. The final state distributions should be useful in identifying products in forthcoming experiments. Based on the MD trajectories, a kinetic scheme has been developed which is able to explain most of the trajectory data and suggests that IVR is very rapid. Typical lifetimes of the excited complex range from several 10 picoseconds to hundreds of nanoseconds, depending on the excitation level. Including temperature and pressure profiles characteristic for the stratosphere in the kinetic model shows that excitations higher than ν9 = 4 can significantly contribute to the photolysis rate. This extends and specifies earlier work in that multi-level modeling is required to understand the significance of vibrationally induced decomposition pathways of sulfuric acid in the middle atmosphere.

Multisurface Adiabatic Reactive Molecular Dynamics.

Adiabatic reactive molecular dynamics (ARMD) simulation method is a surface-crossing algorithm for modeling chemical reactions in classical molecular dynamics simulations using empirical force fields. As the ARMD Hamiltonian is time dependent during crossing, it allows only approximate energy conservation. In the current work, the range of applicability of conventional ARMD is explored, and a new multisurface ARMD (MS-ARMD) method is presented, implemented in CHARMM and applied to the vibrationally induced photodissociation of sulfuric acid (H2SO4) in the gas phase. For this, an accurate global potential energy surface (PES) involving 12 H2SO4 and 4 H2O + SO3 force fields fitted to MP2/6-311G++(2d,2p) reference energies is employed. The MS-ARMD simulations conserve total energy and feature both intramolecular H-transfer reactions and water elimination. An analytical treatment of the dynamics in the crossing region finds that conventional ARMD can approximately conserve total energy for limiting cases. In one of them, the reduced mass of the system is large, which often occurs for simulations of solvated biomolecular systems. On the other hand, MS-ARMD is a general approach for modeling chemical reactions including gas-phase, homogeneous, heterogeneous, and enzymatic catalytic reactions while conserving total energy in atomistic simulations.

Métodos semiempíricos para la evaluación rápida de orbitales frontera en la clasificación de agonistas y antagonistas de la subunidad NR1 de los receptores iGluR-NMDA / Semiempirical methods for the rapid evaluation of frontier orbitals in the classification of agonists and antagonists of the NR1 subunit of the iGluR-NMDA receptors / Métodos semi-empíricos de avaliação rápida de orbitais fronteira na classificação dos agonistas e antagonistas da subunidade NR1 dos receptores iGluRNMDA

Los receptores iGluR-NMDA poseen gran interés farmacológico debido a que están implicados en desórdenes neurodegenerativos y neurosiquiátricos incluso participan en procesos como plasticidad sináptica, esencial para la formación de la memoria. La subunidad NR1 de los iGluR-NMDA es fundamental para que este tipo de receptores se activen apropiadamente, de hecho muchos de los fármacos estudiados para los desórdenes anteriormente mencionados, están dirigidos específicamente a la subunidad NR1. Estudios previos han determinado que el orbital molecular de más baja energía (LUMO), puede ser usado como parámetro para estimar la actividad agonista o antagonista en la subunidad NR1. Objetivo. Evaluar el método semiempírico CNDO para el cálculo rápido de la energía LUMO, con la finalidad de crear un modelo sencillo para el diseño in silico de nuevos fármacos. Materiales y métodos. Fueron seleccionadas 168 moléculas entre agonistas y antagonistas de la subunidad NR1. La energía de cada estructura fue optimizada y posteriormente fueron calculadas las energías de los orbitales frontera, el LogP, la energía total, la capacidad de formar puentes de hidrógeno, la energía de unión y el momento dipolar. Resultados. Se demuestra que la energía LUMO es suficiente para discriminar entre moléculas agonistas y antagonistas de esta subunidad y que el método CNDO evalúa estas propiedades de manera rápida y eficiente. Conclusión. El método CNDO permite el cálculo rápido, generando a futuro procedimientos eficaces para la caracterización de fármacos potenciales que actúen sobre este sitio en particular.

The ionotropic glutamate receptors activated by N-Methyl-D-Aspartate (iGluR-NMDA) are of great importance in pharmacology since they are involved in neurodegenerative and neuropsychiatric disorders; they even participate in processes such as synaptic plasticity that are essential for memory formation. Subunit NR1 iGluRs-NMDA is of paramount importance for the appropriate activation of this type of receptors; in fact, many of the pharmaceutical products studied for the abovementioned disorders are targeted specifically to the NR1 subunit. Previous studies have shown that the lowest energy unoccupied molecular orbital (LUMO) can be used as a parameter to estimate the agonist and antagonist activity of the NR1subunit. Objective. Evaluate the semiemprical method CNDO for the rapid calculation of the LUMO energy with the aim of preparing a simple model for the in silico design of new pharmacological substances. Materials and methods. 168 molecules with agonist and antagonist activity in the NR1 subunit were selected. Energy of each structure was optimized and then we calculated the energy of the frontier orbital, the LogP, total energy, capacity of forming hydrogen bonds, binding energy, and dipolar moment. Results. We demonstrate that LUMO energy is enough for discriminating agonist and antagonist molecules of the NR1 subunit and that the CNDO method evaluates these properties in a rapid and efficient way. Conclusions. The CNDO method facilitates a rapid calculation, enabling a future development of effective procedures for the characterization of potential pharmacological substances acting on this particular site.

Os receptores IGluR-NMDA têm grande interesse farmacológico porque estão envolvidos em desordens neurodegenerativas e neuropsiquiátricas inclusive participam em processos de plasticidade sináptica, essenciais para a formação da memória. A subunidade NR1 dos iGluR-NMDA é fundamental para que este tipo de receptores se ativem de forma adequada, de fato, muitos dos fármacos estudados para os transtornos mencionados acima, são orientados especificamente pela subunidade NR1. Estudos prévios determinaram que o orbital molecular de mais baixa energia (LUMO), pode ser usado como um parâmetro para estimar a atividade agonista ou antagonista na subunidade NR1. Objetivo. Avaliar o método semi-empírico CNDO para o cálculo rápido da energia LUMO, a fim de criar um modelo simples para o desenho in silicio de novas drogas. Materiais e métodos. Foram selecionadas 168 moléculas entre agonistas e antagonistas da subunidade NR1. A energia de cada estrutura foi otimizada e, em seguida, foram calculadas as energias de orbitais fronteira, o LogP, a energia total, a capacidade de formar pontes de hidrogênio, a energia de ligação e o momento dipolar. Resultados. Foi demonstrado que a energia LUMO é suficiente para discriminar entre moléculas agonistas e antagonistas desta subunidade e que o método CNDO avalia essas propriedades de forma rápida e eficiente. Conclusão. O método CNDO permite o cálculo rápido, gerando a futuro procedimentos eficazes para a caracterização de potenciais medicamentos que agem neste sitio em particular.