Molecular dynamics simulations in pre-polymerization mixtures for peptide recognition.

CONTEXT: Molecularly imprinted polymers (MIPs) have promising applications as synthetic antibodies for protein and peptide recognition. A critical aspect of MIP design is the selection of functional monomers and their adequate proportions to achieve materials with high recognition capacity toward their targets. To contribute to this goal, we calibrated a molecular dynamics protocol to reproduce the experimental trends in peptide recognition of 13 pre-polymerization mixtures reported in the literature for the peptide toxin melittin. METHODS: Three simulation conditions were tested for each mixture by changing the box size and the number of monomers and cross-linkers surrounding the template in a solvent-explicit environment. Fully atomistic MD simulations of 350 ns were conducted with the AMBER20 software, with ff19SB parameters for the peptide, gaff2 parameters for the monomers and cross-linkers, and the OPC water model. Template-monomer interaction energies under the LIE approach showed significant differences between high-affinity and low-affinity mixtures. Simulation systems containing 100 monomers plus cross-linkers in a cubic box of 90 Å3 successfully ranked the mixtures according to their experimental performance. Systems with higher monomer densities resulted in non-specific intermolecular contacts that could not account for the experimental trends in melittin recognition. The mixture with the best recognition capacity showed preferential binding to the 13-26-α-helix, suggesting a relevant role for this segment in melittin imprinting and recognition. Our findings provide insightful information to assist the computational design of molecularly imprinted materials with a validated protocol that can be easily extended to other templates.

Computational method for designing vaccines applied to virus-like particles (VLPs) as epitope carriers.

Nonenveloped virus-like particles (VLPs) are self-assembled oligomeric structures composed of one or more proteins that originate from diverse viruses. Because these VLPs have similar antigenicity to the parental virus, they are successfully used as vaccines against cognate virus infection. Furthermore, after foreign antigenic sequences are inserted in their protein components (chimVLPs), some VLPs are also amenable to producing vaccines against pathogens other than the virus it originates from (these VLPs are named platform or epitope carrier). Designing chimVLP vaccines is challenging because the immunogenic response must be oriented against a given antigen without altering stimulant properties inherent to the VLP. An important step in this process is choosing the location of the sequence modifications because this must be performed without compromising the assembly and stability of the original VLP. Currently, many immunogenic data and computational tools can help guide the design of chimVLPs, thus reducing experimental costs and work. In this study, we analyze the structure of a novel VLP that originate from an insect virus and describe the putative regions of its three structural proteins amenable to insertion. For this purpose, we employed molecular dynamics (MD) simulations to assess chimVLP stability by comparing mutated and wild-type (WT) VLP protein trajectories. We applied this procedure to design a chimVLP that can serve as a prophylactic vaccine against the SARS-CoV-2 virus. The methodology described in this work is generally applicable for VLP-based vaccine development.

In silico structural features of the CgNR5A: CgDAX complex and its role in regulating gene expression of CYP target genes in Crassostrea gigas.

Contamination of aquatic environments has been steadily increasing due to human activities. The Pacific oyster Crassostrea gigas has been used as a key species in studies assessing the impacts of contaminants on human health and the aquatic biome. In this context, cytochrome P450 (CYPs) play a crucial role in xenobiotic metabolism. In vertebrates many of these CYPs are regulated by nuclear receptors (NRs) and little is known about the NRs role in C. gigas. Particularly, the CgNR5A represents a homologue of SF1 and LRH-1 found in vertebrates. Members of this group can regulate genes of CYPs involved in lipid/steroid metabolism, with their activity regulated by other NR, called as DAX-1, generating a NR complex on DNA response elements (REs). As C. gigas does not exhibit steroid biosynthesis pathways, CgNR5A may play other physiological roles. To clarify this issue, we conducted an in silico investigation of the interaction between CgNR5A and DNA to identify potential C. gigas CYP target genes. Using molecular docking and dynamics simulations of the CgNR5A on DNA molecules, we identified a monomeric interaction with extended REs. This RE was found in the promoter region of 30 CYP genes and also the NR CgDAX. When the upstream regulatory region was analyzed, CYP2C39, CYP3A11, CYP4C21, CYP7A1, CYP17A1, and CYP27C1 were mapped as the main genes regulated by CgNR5A. These identified CYPs belong to families known for their involvement in xenobiotic and lipid/steroid metabolism. Furthermore, we reconstructed a trimeric complex, previously proposed for vertebrates, with CgNR5A:CgDAX and subjected it to molecular dynamics simulations analysis. Heterotrimeric complex remained stable during the simulations, suggesting that CgDAX may modulate CgNR5A transcriptional activity. This study provides insights into the potential physiological processes involving these NRs in the regulation of CYPs associated with xenobiotic and steroid/lipid metabolism.

Effect of Organic Solvents on the Activity, Stability and Secondary Structure of asclepain cI, Using FTIR and Molecular Dynamics Simulations.

The present study aims at understanding the effect of organic solvents on the specific proteolytic activity and operational stability of asclepain cI in aqueous-organic media, using correlations between geometrical and structural parameters of asclepain cI. These correlations were determined by molecular dynamics (MD) simulations and the secondary structure of the enzyme validated by Fourier-transform Infrared (FTIR) spectroscopy. Asclepain cI exhibited significantly higher catalytic potential in 29 of the 42 aqueous-organic media tested, composed by 0.1 mM TRIS hydrochloride buffer pH 8 (TCB) and an organic solvent, than in buffer alone. Asclepain cI in water-organic miscible systems showed high FTIR spectral similarity with that obtained in TCB, while in immiscible systems the enzyme acquired different secondary structures than in buffer. Among the conditions studied, asclepain cI showed the highest catalytic potential in 50% v/v ethyl acetate in TCB. According to MD simulations, that medium elicited solvation and flexibility changes around the active center of asclepain cI and conducted to a new secondary structure with the active center preserved. These results provide valuable insights into the elucidation of the molecular mechanism of asclepain cI tolerance to organic solvents and pave the way for its future application for the synthesis of peptides in aqueous-organic media.

Integrated computational approaches assisted development of a novel multi-epitope vaccine against MDR Streptococcus pseudopneumoniae / Abordagens computacionais integradas que auxiliaram no desenvolvimento de uma nova vacina multiepítopo contra Streptococcus pseudopneumoniae multirresistente

The emergence of antibiotic resistance (AR) in bacteria is becoming an alarming health concern because it allows them to adapt themselves to changing environments. It is possible to prevent the spread of AR in many ways, such as reducing antibiotic misuse in human and veterinary medicine. Streptococcus pseudopneumoniae is one of these AR bacterial species that can cause pneumonia in humans and is responsible for high mortality and morbidity rates. It is oval shaped gram-positive bacterium that shows resistance to several antibiotics like penicillin, tetracycline, ciprofloxacin, erythromycin, and co-trimoxazale and no approved vaccine is available to overcome diseases of the pathogen. Thus, substantial efforts are necessary to select protective antigens from a whole genome of pathogens that are easily tested experimentally. The in silico designed vaccine was safe and potent in immunizing individuals against the aforementioned pathogens. Herein, we utilized a subtractive genomic approach to identify potential epitope-based vaccine candidates against S. pseudopneumoniae. In total, 50850 proteins were retrieved from the NCBI, representing the complete genome of S. pseudopneumoniae. Out of the total, CD-HIT analysis identified 1022 proteins as non-redundant and 49828 proteins as redundant and further subjected for subcellular localization in which bulk of proteins was located in the cytoplasm, with seven extracellular proteins (penicillin-binding protein, alpha-amylase, solute-binding protein, hypothetical protein, CHAP domain-containing protein, polysaccharide deacetylase family protein, hypothetical protein). Six immune cells epitopes (SNLQSENDRL, RNDSLQKQAR, NPTTTSEGF, KVKKKNNKK, AYSQGSQKEH, and SVVDQVSGDF) were predicted with the help of the IEDB server. To design a multi-epitopes vaccine these immune cell epitopes were together by GPGPG and adjuvant linker to enhance immune response efficacy. The 3D structure of the designed vaccine was modeled and conducted molecular docking and dynamic simulation studies were to check the binding efficacy with immune cells receptor and dynamic behavior of the docked complex. Finally, we concluded that the designed vaccine construct can provoke a proper and protective immune response against S. pseudopneumoniae.

O surgimento de resistência a antibióticos (AR) em bactérias tem se tornando uma preocupação sanitária alarmante, uma vez que permite que elas se adaptem a ambientes em constante alteração. É possível prevenir a disseminação da RA de várias maneiras, como reduzir o uso indevido de antibióticos na medicina humana e veterinária. O Streptococcus pseudopneumoniae é uma dessas espécies bacterianas de AR que podem causar pneumonia em humanos e são responsáveis por altas taxas de mortalidade e morbidade. É uma bactéria gram-positiva de forma oval que mostra resistência a diversos antibióticos como penicilina, tetraciclina, ciprofloxacina, eritromicina e cotrimoxazale, além disso, nenhuma vacina aprovada está disponível para superar as doenças do patógeno. Assim, esforços substanciais são necessários para selecionar antígenos protetores de todo um genoma de patógenos que são facilmente testados experimentalmente. A vacina projetada in silico foi considerada segura e potente na imunização de indivíduos contra os patógenos mencionados. Neste trabalho, utilizamos uma abordagem genômica subtrativa para identificar potenciais candidatos a vacinas baseadas em epítopos contra S. pseudopneumoniae. No total, 50.850 proteínas foram recuperadas do NCBI, representando o genoma completo de S. pseudopneumoniae. Do total, a análise de CD-HIT identificou 1.022 proteínas como não redundantes e 49.828 proteínas como redundantes e posteriormente submetidas à localização subcelular na qual a maior parte das proteínas estava localizada no citoplasma, com sete proteínas extracelulares (proteína de ligação à penicilina, alfa- amilase, proteína de ligação a soluto, proteína hipotética, proteína contendo domínio CHAP, proteína da família polissacarídeo desacetilase, proteína hipotética). Seis epítopos de células imunes (SNLQSENDRL, RNDSLQKQAR, NPTTTSEGF, KVKKKNNKK, AYSQGSQKEH e SVVDQVSGDF) foram previstos com a ajuda do servidor IEDB. Para projetar uma vacina de múltiplos epítopos, esses epítopos de células imunes foram reunidos por GPGPG e um ligante adjuvante para aumentar a eficácia da resposta imune. A estrutura 3D da vacina projetada foi modelada e conduzido estudos de docking molecular e simulação dinâmica para verificar a eficácia da ligação com o receptor de células imunes e o comportamento dinâmico do complexo docked. Finalmente, concluímos que a construção da vacina projetada pode provocar uma resposta imune adequada e protetora contra S. pseudopneumoniae.

Derivates of 1,6-dihyadroazaazulenes as inhibitors of tyrosine kinases BCR-ABL1 wild type and mutant T315I: a molecular dynamics approach.

The protein tyrosine kinase (PTK) produced by the BCR-ABL1 gene has generated significant interest in the development of inhibitors since the presence of punctual mutations causes resistance to currently approved drugs, mainly the T315I mutation has been the most difficult to address. In this work, derivatives of 1,6-dihydroazaazulenes are studied as possible inhibitors of this PTK in its wild form and the mutant T315I. The recognition of the ligands was explored through molecular docking, and the stability of the complexes and their evolution over time was studied using molecular dynamics (MD) simulations. Our results show that complexes are energetically stable and reside on the ATP binding site in all cases during the MD experiments. Interestingly, a few of our proposed ligands presented greater affinity for T315I, finding more favorable binding free energies (ΔG) than the reference drug axitinib. Furthermore, they may act as inhibitors for both isoforms. Our findings are promising because mutation of T315I does not prevent ligand recognition, as detailed in this work, which is very important to conduct further experimental research.Communicated by Ramaswamy H. Sarma.

Structural and Electromagnetic Signatures of Anatase and Rutile NTs and Sheets in Three Different Water Models under Different Temperature Conditions.

Experimental studies of TiO2 nanotubes have been conducted for nearly three decades and have revealed the remarkable advantages of this material. Research based on computer simulations is much rarer, with research using density functional theory (DFT) being the most significant in this field. It should be noted, however, that this approach has significant limitations when studying the macroscopic properties of nanostructures such as nanosheets and nanotubes. An alternative with great potential has emerged: classical molecular dynamics simulations (MD). MD Simulations offer the possibility to study macroscopic properties such as the density of phonon states (PDOS), power spectra, infrared spectrum, water absorption and others. From this point of view, the present study focuses on the distinction between the phases of anatase and rutile TiO2. The LAMMPS package is used to study both the structural properties by applying the radial distribution function (RDF) and the electromagnetic properties of these phases. Our efforts are focused on exploring the effect of temperature on the vibrational properties of TiO2 anatase nanotubes and an in-depth analysis of how the phononic softening phenomenon affects TiO2 nanostructures to improve the fundamental understanding in different dimensions and morphological configurations. A careful evaluation of the stability of TiO2 nanolamines and nanotubes at different temperatures is performed, as well as the adsorption of water on the nanosurface of TiO2, using three different water models.

Molecular Docking and Molecular Dynamics Simulations in Related to Leishmania donovani: An Update and Literature Review.

Leishmaniasis, a disease caused by Leishmania parasites and transmitted via sandflies, presents in two main forms: cutaneous and visceral, the latter being more severe. With 0.7 to 1 million new cases each year, primarily in Brazil, diagnosing remains challenging due to diverse disease manifestations. Traditionally, the identification of Leishmania species is inferred from clinical and epidemiological data. Advances in disease management depend on technological progress and the improvement of parasite identification programs. Current treatments, despite the high incidence, show limited efficacy due to factors like cost, toxicity, and lengthy regimens causing poor adherence and resistance development. Diagnostic techniques have improved but a significant gap remains between scientific progress and application in endemic areas. Complete genomic sequence knowledge of Leishmania allows for the identification of therapeutic targets. With the aid of computational tools, testing, searching, and detecting affinity in molecular docking are optimized, and strategies that assess advantages among different options are developed. The review focuses on the use of molecular docking and molecular dynamics (MD) simulation for drug development. It also discusses the limitations and advancements of current treatments, emphasizing the importance of new techniques in improving disease management.

Nuclear receptor superfamily structural diversity in pacific oyster: In silico identification of estradiol binding candidates.

The increasing presence of anthropogenic contaminants in aquatic environments poses challenges for species inhabiting contaminated sites. Due to their structural binding characteristics to ligands that inhibit or activate gene transcription, these xenobiotic compounds frequently target the nuclear receptor superfamily. The present work aims to understand the potential interaction between the hormone 17-ß-estradiol, an environmental contaminant, and the nuclear receptors of Crassostrea gigas, the Pacific oyster. This filter-feeding, sessile oyster species is subject to environmental changes and exposure to contaminants. In the Pacific oyster, the estrogen-binding nuclear receptor is not able to bind this hormone as it does in vertebrates. However, another receptor may exhibit responsiveness to estrogen-like molecules and derivatives. We employed high-performance in silico methodologies, including three-dimensional modeling, molecular docking and atomistic molecular dynamics to identify likely binding candidates with the target moecule. Our approach revealed that among the C. gigas nuclear receptor superfamily, candidates with the most favorable interaction with the molecule of interest belonged to the NR1D, NR1H, NR1P, NR2E, NHR42, and NR0B groups. Interestingly, NR1H and NR0B were associated with planktonic/larval life cycle stages, while NR1P, NR2E, and NR0B were associated with sessile/adult life stages. The application of this computational methodological strategy demonstrated high performance in the virtual screening of candidates for binding with the target xenobiotic molecule and can be employed in other studies in the field of ecotoxicology in non-model organisms.

Impact of the Role of the Clinical Pharmacist on the Underreporting of Adverse Drug Reactions at a Peruvian hospital.

Background: The clinical pharmacists play a key role in the Pharmacovigilance System. They are integrated to the health team performing pharmacotherapeutic follow-up (PF), drug information, at third level care hospital. The objective of this study was to assess the impact of the clinical pharmacists' role in increasing the reporting of suspected adverse drug reactions (SADRs) after including in-service training (IST) in their role, as well as to characterize the reported ADRs. Methods: A longitudinal study was performed, reports of SADRs received through medical interconsultations were evaluated, before and after applying IST, in 2 periods: January 2017 to June 2018 and July 2018 to December 2019. Results: Interconsultations after IST were increased by 168,4%; of these, 75 were ADRs reported to the Dirección General de Medicamentos, Insumos y Drogas (DIGEMID). Internal Medicine and Pneumology services reported more SADR in both periods. There was significant statistical difference in ADRs' causality (P = .001) and type (P = .009). Severe ADRs highlighted after IST (4 vs 12). The most affected organ and system in both periods was skin and appendages. Conclusion: The reporting of SADRs augmented, reflected in an increase in medical interconsultations as a modality of SADR notification, after including IST to the role of the clinical pharmacist, allowing the development of convenient FP, which led to the evaluation of SARs. A higher number of serious ADRs were reported.

A systematic mini-review of epigenetic mechanisms associated with electroconvulsive therapy in humans.

Introduction: Electroconvulsive therapy (ECT) is one of the most effective strategies for treating resistant major depression. Although the mechanism of action is not fully understood and studies are limited, epigenetics is a promising area for the development of biomarkers associated with ECT treatment response. Aim: We reviewed studies available in the literature that explored the epigenetics of ECT in peripheral samples from patients with major depressive disorder (MDD). Methods: A systematic review was performed following The PRISMA guidelines. The search was performed in seven electronic databases: Scopus, Web of Science, Medline, PsycINFO, Embase, Cochrane, and Cinahl. Results: Nine studies were included. Seven assessed DNA methylation and three investigated microRNAs (miR). Overall, most studies were exploratory, with small sample sizes, and we found high heterogeneity between the study's design, ECT protocols, molecular biology methods, and epigenetic findings. Investigated candidates with some evidence of association with ECT treatment response were BDNF, S100A10, RNF213M, TNKS, FKBP5, miR-126, miR-106a, and miR-24. Conclusion: The present findings seem to support previous preclinical research, suggesting that epigenetic mechanisms play an important role in the molecular mechanism underlying ECT effects.

Structural Basis of the Binding Mode of the Antineoplastic Compound Motixafortide (BL-8040) in the CXCR4 Chemokine Receptor.

Modulation of the CXCL12-CXCR4 signaling axis is of the utmost importance due to its central involvement in several pathological disorders, including inflammatory diseases and cancer. Among the different currently available drugs that inhibit CXCR4 activation, motixafortide-a best-in-class antagonist of this GPCR receptor-has exhibited promising results in preclinical studies of pancreatic, breast, and lung cancers. However, detailed information on the interaction mechanism of motixafortide is still lacking. Here, we characterize the motixafortide/CXCR4 and CXCL12/CXCR4 protein complexes by using computational techniques including unbiased all-atom molecular dynamics simulations. Our microsecond-long simulations of the protein systems indicate that the agonist triggers changes associated with active-like GPCR conformations, while the antagonist favors inactive conformations of CXCR4. Detailed ligand-protein analysis indicates the importance of motixafortide's six cationic residues, all of which established charge-charge interactions with acidic CXCR4 residues. Furthermore, two synthetic bulky chemical moieties of motixafortide work in tandem to restrict the conformations of important residues associated with CXCR4 activation. Our results not only elucidate the molecular mechanism by which motixafortide interacts with the CXCR4 receptor and stabilizes its inactive states, but also provide essential information to rationally design CXCR4 inhibitors that preserve the outstanding pharmacological features of motixafortide.

Therapeutic effects of hAMSCs secretome on proliferation of MDA-MB-231 breast cancer cells by the cell cycle arrest in G1/S phase.

BACKGROUND: Cancer refers to a disease resulting from the uncontrolled division and growth of abnormal cells. Among different cancer types, breast cancer is considered as one of the most commonly diagnosed cancers. Herein, we explored the therapeutic effects of human amniotic mesenchymal stromal cells (hAMSCs) secretome on breast cancer cells (MDA-MB-231) through analyzing cell cycle progression. METHODS: We employed a co-culture system using 6-well Transwell plates and after 72 h, the cell cycle progression was evaluated in the hAMSCs-treated MDA-MB-231 cells through analyzing the expressions of RB, CDK4/6, cyclin D, CDK2, cyclin E, p16/INK4a, p21/WAF1/CIP1, and p27/KIP1 using quantitative real-time PCR (qRT-PCR) and western blot method. Cell proliferation, apoptosis, and cell cycle progression were checked using an MTT assay, DAPI staining, and flow cytometry. RESULTS: Our results indicated that elevation of RB, p21/WAF1/CIP1, and p27/KIP1 and suppression of RB hyperphosphorylation, p16/INK4a, cyclin E, cyclin D1, CDK2, and CDK4/6 may contribute to inhibiting the proliferation of hAMSCs-treated MDA-MB-231 cells through cell cycle arrest in G1/S phase followed by apoptosis. CONCLUSION: hAMSCs secretome may be an effective approach on breast cancer therapy through the inhibition of cell cycle progression.

Computational assessment of phytochemicals of medicinal plants from Mexico as potential inhibitors of Salmonella enterica efflux pump AcrB protein.

The AcrAB-TolC efflux pump (EP) confers multidrug resistance to Salmonella enterica, a major etiological agent of foodborne infections. Phytochemicals that inhibit the functions of AcrAB-TolC EP present ideal candidates for reversal of antibiotic resistance. Progressive technological advancements, have facilitated the development of computational methods that offer a rapid low-cost approach to screen and identify phytochemicals with inhibitory potential against EP. In this study, 71 phytochemicals derived from plants used for medicinal purposes in Mexico were screened for their potential as inhibitors of Salmonella AcrB protein using in silico approaches including molecular docking and molecular dynamics (MD) simulation. Consequently, naringenin, 5-methoxypsoralen, and licarin A were identified as candidate inhibitors of AcrB protein. The three phytochemicals bound distal/deep pocket (DP) and hydrophobic trap (HPT) residues of AcrB protein critical for interactions with inhibitors, with estimated binding free energies of -95.5 kJ/mol, -97.4 kJ/mol, and -143.8 kJ/mol for naringenin, 5-methoxypsoralen, and licarin A, respectively. Data from the 50 ns MD simulation study revealed stability of the protein-ligand complex and alterations in the AcrB protein DP conformation upon binding of phytochemicals to the DP and HPT regions. Based on the estimated binding free energy and interactions with three out of five residues lining the hydrophobic trap, licarin A demonstrated the highest inhibitory potential, supporting its further application as a candidate for overcoming drug resistance in pathogens. Communicated by Ramaswamy H. Sarma.

Computational Analysis of Triazole-Based Kojic Acid Analogs as Tyrosinase Inhibitors by Molecular Dynamics and Free Energy Calculations.

Molecular docking, molecular dynamics (MD) simulations and the linear interaction energy (LIE) method were used here to predict binding modes and free energy for a set of 1,2,3-triazole-based KA analogs as potent inhibitors of Tyrosinase (TYR), a key metalloenzyme of the melanogenesis process. Initially, molecular docking calculations satisfactorily predicted the binding mode of evaluated KA analogs, where the KA part overlays the crystal conformation of the KA inhibitor into the catalytic site of TYR. The MD simulations were followed by the LIE method, which reproduced the experimental binding free energies for KA analogs with an r2 equal to 0.97, suggesting the robustness of our theoretical model. Moreover, the van der Waals contributions performed by some residues such as Phe197, Pro201, Arg209, Met215 and Val218 are responsible for the binding recognition of 1,2,3-triazole-based KA analogs in TYR catalytic site. Finally, our calculations provide suitable validation of the combination of molecular docking, MD, and LIE approaches as a powerful tool in the structure-based drug design of new and potent TYR inhibitors.

Calcium inhibits penetration of Alzheimer's Aß1 -42 monomers into the membrane.

Calcium ion regulation plays a crucial role in maintaining neuronal functions such as neurotransmitter release and synaptic plasticity. Copper (Cu2+ ) coordination to amyloid-ß (Aß) has accelerated Aß1-42 aggregation that can trigger calcium dysregulation by enhancing the influx of calcium ions by extensive perturbing integrity of the membranes. Aß1-42 aggregation, calcium dysregulation, and membrane damage are Alzheimer disease (AD) implications. To gain a detail of calcium ions' role in the full-length Aß1-42 and Aß1-42 -Cu2+ monomers contact, the cellular membrane before their aggregation to elucidate the neurotoxicity mechanism, we carried out 2.5 µs extensive molecular dynamics simulation (MD) to rigorous explorations of the intriguing feature of the Aß1-42 and Aß1-42 -Cu2+ interaction with the dimyristoylphosphatidylcholine (DMPC) bilayer in the presence of calcium ions. The outcome of the results compared to the same simulations without calcium ions. We surprisingly noted robust binding energies between the Aß1-42 and membrane observed in simulations containing without calcium ions and is two and a half fold lesser in the simulation with calcium ions. Therefore, in the case of the absence of calcium ions, N-terminal residues of Aß1-42 deeply penetrate from the surface to the center of the bilayer; in contrast to calcium ions presence, the N- and C-terminal residues are involved only in surface contacts through binding phosphate moieties. On the other hand, Aß1-42 -Cu2+ actively participated in surface bilayer contacts in the absence of calcium ions. These contacts are prevented by forming a calcium bridge between Aß1-42 -Cu2+ and the DMPC bilayer in the case of calcium ions presence. In a nutshell, Calcium ions do not allow Aß1-42 penetration into the membranes nor contact of Aß1-42 -Cu2+ with the membranes. These pieces of information imply that the calcium ions mediate the membrane perturbation via the monomer interactions but do not damage the membrane; they agree with the western blot experimental results of a higher concentration of calcium ions inhibit the membrane pore formation by Aß peptides.

Computational Analysis of SAM Analogs as Methyltransferase Inhibitors of nsp16/nsp10 Complex from SARS-CoV-2.

Methyltransferases (MTases) enzymes, responsible for RNA capping into severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are emerging important targets for the design of new anti-SARS-CoV-2 agents. Here, analogs of S-adenosylmethionine (SAM), obtained from the bioisosteric substitution of the sulfonium and amino acid groups, were evaluated by rigorous computational modeling techniques such as molecular dynamics (MD) simulations followed by relative binding free analysis against nsp16/nsp10 complex from SARS-CoV-2. The most potent inhibitor (2a) shows the lowest binding free energy (-58.75 Kcal/mol) and more potency than Sinefungin (SFG) (-39.8 Kcal/mol), a pan-MTase inhibitor, which agrees with experimental observations. Besides, our results suggest that the total binding free energy of each evaluated SAM analog is driven by van der Waals interactions which can explain their poor cell permeability, as observed in experimental essays. Overall, we provide a structural and energetic analysis for the inhibition of the nsp16/nsp10 complex involving the evaluated SAM analogs as potential inhibitors.

Synthesis and Chemopreventive Potential of 5-FU/Genistein Hybrids on Colorectal Cancer Cells.

A series of 5-FU-Genistein hybrids were synthesized and their structures were elucidated by spectroscopic analysis. The chemopreventive potential of these compounds was evaluated in human colon adenocarcinoma cells (SW480 and SW620) and non-malignant cell lines (HaCaT and CHO-K1). Hybrid 4a displayed cytotoxicity against SW480 and SW620 cells with IC50 values of 62.73 ± 7.26 µM and 50.58 ± 1.33 µM, respectively; compound 4g induced cytotoxicity in SW620 cells with an IC50 value of 36.84 ± 0.71 µM. These compounds were even more selective than genistein alone, the reference drug (5-FU) and the equimolar mixture of genistein plus 5-FU. In addition, hybrids 4a and 4g induced time- and concentration-dependent antiproliferative activity and cell cycle arrest at the S-phase and G2/M. It was also observed that hybrid 4a induced apoptosis in SW620 cells probably triggered by the extrinsic pathway in response to the activation of p53, as evidenced by the increase in the levels of caspases 3/8 and the tumor suppressor protein (Tp53). Molecular docking studies suggest that the most active compound 4a would bind efficiently to proapoptotic human caspases 3/8 and human Tp53, which in turn could provide valuable information on the biochemical mechanism for the in vitro cytotoxic response of this compound in SW620 colon carcinoma cell lines. On the other hand, molecular dynamics (MD) studies provided strong evidence of the conformational stability of the complex between caspase-3 and hybrid 4a obtained throughout 100 ns all-atom MD simulation. Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analyses of the complex with caspase-3 showed that the interaction between the ligand and the target protein is stable. Altogether, the results suggest that the active hybrids, mainly compound 4a, might act by modulating caspase-3 activity in a colorectal cancer model, making it a privileged scaffold that could be used in future investigations.

Concentration-dependent thermodynamic analysis of the partition process of small ligands into proteins.

In the category of functional low-affinity interactions, small ligands may interact with multiple protein sites in a highly degenerate manner. Better conceived as a partition phenomenon at the molecular interface of proteins, such low-affinity interactions appear to be hidden to our current experimental resolution making their structural and functional characterization difficult in the low concentration regime of physiological processes. Characterization of the partition phenomenon under higher chemical forces could be a relevant strategy to tackle the problem provided the results can be scaled back to the low concentration range. Far from being trivial, such scaling demands a concentration-dependent understanding of self-interactions of the ligands, structural perturbations of the protein, among other molecular effects. Accordingly, we elaborate a novel and detailed concentration-dependent thermodynamic analysis of the partition process of small ligands aiming at characterizing the stability and structure of the dilute phenomenon from high concentrations. In analogy to an "aggregate" binding constant of a small molecule over multiple sites of a protein receptor, the model defines the stability of the process as a macroscopic equilibrium constant for the partition number of ligands that can be used to analyze biochemical and functional data of two-component systems driven by low-affinity interactions. Acquisition of such modeling-based structural information is expected to be highly welcome by revealing more traceable protein-binding spots for non-specific ligands.