Molecular modeling studies on the interactions of aflatoxin B1 and its metabolites with the peripheral anionic site of human acetylcholinesterase

Computational Studies of Aflatoxin B1 (AFB1): A Review

Aflatoxin B₁ (AFB₁) exhibits the most potent mutagenic and carcinogenic activity among aflatoxins. For this reason, AFB₁ is recognized as a human group 1 carcinogen by the International Agency of Research on Cancer. Consequently, it is essential to determine its properties and behavior in different chemical systems. The chemical properties of AFB₁ can be explored using computational chemistry, which has been employed complementarily to experimental investigations. The present review includes in silico studies (semiempirical, Hartree-Fock, DFT, molecular docking, and molecular dynamics) conducted from the first computational study in 1974 to the present (2022). This work was performed, considering the following groups: (a) molecular properties of AFB₁ (structural, energy, solvent effects, ground and the excited state, atomic charges, among others); (b) theoretical investigations of AFB₁ (degradation, quantification, reactivity, among others); (c) molecular interactions with inorganic compounds (Ag⁺, Zn²⁺, and Mg²⁺); (d) molecular interactions with environmentally compounds (clays); and (e) molecular interactions with biological compounds (DNA, enzymes, cyclodextrins, glucans, among others). Accordingly, in this work, we provide to the stakeholder the knowledge of toxicity of types of AFB₁-derivatives, the structure-activity relationships manifested by the bonds between AFB₁ and DNA or proteins, and the types of strategies that have been employed to quantify, detect, and eliminate the AFB₁ molecule.

Identification and evaluation of boronic compounds ameliorating cognitive deficit in orchiectomized rats

BACKGROUND

Boron is a trace element with increasing importance in drug design. In this sense, boronic acids are emerging as therapeutic agents for several diseases.

METHODS

Herein, 3- and 4- acetamidophenylboronic acids and 4-acetamidophenylboronic acid pinacol ester were identified as potential inhibitors of acetylcholinesterase through docking assays on eel, rat, and human acetylcholinesterases indicating binding on the gorge region of the target enzymes. Then, these compounds were evaluated in vitro and in vivo.

RESULTS

It was found these compounds showed ability to inhibit acetylcholinesterase as competitive and non-competitive inhibitors. But also, these compounds were non-toxic to PC12 cells at micromolar concentration, and they have the ability to protect those cells against damage by amyloid-beta.

CONCLUSIONS

Noticeably, intraperitoneal administration of these boronic compounds to rats with the cognitive deficit induced by orchiectomy provided ameliorative effects on disrupted behavior and neuronal damage induced by hormonal deprivation. Additional approaches are required to evaluate the possibility of multiple mechanisms of action for the observed effects in the central nervous system.

Key criteria for engineering mycotoxin binding aptamers via computational simulations: Aflatoxin B1 as a case study

Due to the difficulties in monoclonal antibody production specific to mycotoxins, aptameric probes have been considered as suitable alternatives. The low efficiency of the SELEX procedure in screening high affinity aptamers for binding mycotoxins as small molecules can be significantly improved through computational techniques. Previously, we designed five new aptamers to aflatoxin B₁ (AFB1) based on a known aptamer sequence (Patent: PCT/CA2010/001 292, Apt1) through a genetic algorithm-based in silico maturation strategy and experimentally measured their affinity to the target toxin. Here, integrated molecular dynamic simulation (MDs) studies with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis to clarify the binding modes, critical interacting nucleic bases and energy component contributions in the six AFB1-binding aptamers. The aptamer F20, which was selected in the first work, showed the best free binding energy and complex stability compared to other aptamers. The trajectory analysis revealed that AFB1 recognized F20 through the groove binding mode along with precise shape complementarity. The MD simulation results revealed that dynamic water intermediate interactions also play a key role in promoting complex stability. According to the MM-PBSA calculations, van der Waals contacts were identified as dominant energy components in all complexes. Interestingly, a high consistency is observed between the experimentally obtained binding affinities of the six aptamers with their free energy solvation. The computational findings, confirmed via previous experiments, highlighted the binding modes, the dynamic hydration of complex components and the total free interacting energy as the crucial criteria in discovering high functional aptameric probes.

Global trend of clinical biomarkers of health and disease during the period (1913–2021): systematic review and bibliometric analysis

Background

The literature review provides a concise and detailed description of the available and published data on the investigated research problem. The study summarizes findings over the last 100 years regarding clinical biomarkers during health and disease. Research expanded to present the range of enzyme acetylcholinesterase in human blood utilizing diverse methodology during the 1949–2021 year.

Main body

Data analysis includes program SPSS v23.0, frequency, percentage, numbers and graphical presentation of results. Information from the papers gathers in Microsoft Excel 2007 and contains information: study type, journal, publisher, year of publication, continent, the health status of respondents, biomarkers, number and age of participants, types of samples, methodology, goals and conclusions. Data collection includes electronic databases, the National Center for Biotechnology Information and Google Scholar, with several inclusion criteria: (1) anthropometry (2) urine (3) blood in the healthy and diseased population parameters during different physiological states of the organism. The initial number of collected and analyzed papers is 1900. The final analysis included 982 studies out of 1454 selected papers. After the selection process, 67.53% remains useful. The range of enzyme acetylcholinesterase included 107 publications.

Conclusion

The number of published scientific papers has been increasing over the years. Little practical information in scientific and clinical practice exists. There is an urgent need for concise highlighting of literature key arguments and ideas. Results apply to a specialized area of research.

Searching for potential drugs against SARS-CoV-2 through virtual screening on several molecular targets

The acute respiratory syndrome caused by the SARS-CoV-2, known as COVID-19, has been ruthlessly tormenting the world population for more than six months. However, so far no effective drug or vaccine against this plague have emerged yet, despite the huge effort in course by researchers and pharmaceutical companies worldwide. Willing to contribute with this fight to defeat COVID-19, we performed a virtual screening study on a library containing Food and Drug Administration (FDA) approved drugs, in a search for molecules capable of hitting three main molecular targets of SARS-CoV-2 currently available in the Protein Data Bank (PDB). Our results were refined with further molecular dynamics (MD) simulations and MM-PBSA calculations and pointed to 7 multi-target hits which we propose here for experimental evaluation and repurposing as potential drugs against COVID-19. Additional rounds of docking, MD simulations and MM-PBSA calculations with remdesivir suggested that this compound can also work as a multi-target drug against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

Identification of novel potential ricin inhibitors by virtual screening, molecular docking, molecular dynamics and MM-PBSA calculations: a drug repurposing approach

Ricin is a potent cytotoxin with no available antidote. Its catalytic subunit, RTA, damages the ribosomal RNA (rRNA) of eukaryotic cells, preventing protein synthesis and eventually leading to cell death. The combination between easiness of obtention and high toxicity turns ricin into a potential weapon for terrorist attacks, urging the need of discovering effective antidotes. On this context, we used computational techniques, in order to identify potential ricin inhibitors among approved drugs. Two libraries were screened by two different docking algorithms, followed by molecular dynamics simulations and MM-PBSA calculations in order to corroborate the docking results. Three drugs were identified as potential ricin inhibitors: deferoxamine, leucovorin and plazomicin. Our calculations showed that these compounds were able to, simultaneously, form hydrogen bonds with residues of the catalytic site and the secondary binding site of RTA, qualifying as potential antidotes against intoxication by ricin.Communicated by Ramaswamy H. Sarma.

Synthesis, biological activity, molecular docking studies of a novel series of 3-Aryl-7H-thiazolo[3,2-b]-1,2,4-triazin-7-one derivatives as the acetylcholinesterase inhibitors

The acetylcholinesterase inhibitors play a critical role in the drug therapy for Alzheimer's disease. In this study, twenty-nine novel 3-aryl-7H-thiazolo[3,2-b]-1,2,4-triazin-7-one derivatives were synthesized and assayed for their human acetylcholinesterase (hAChE) inhibitory activities. Inhibitory ratio values of seventeen compounds were above 55% with 4c having the highest value as 77.19%. The compounds with the halogen atoms in the aromatic ring, and N,N-diethylamino or N,N-dimethylamino groups in the side chains at C-3 positions exhibited good inhibitory activity. SAR study was carried out by means of molecular docking technique. According to molecular docking results, the common interacting site for all compounds were found to be peripheral anionic site whereas highly active compounds were interacting with the catalytic active site too. HIGHLIGHTSA novel series of 3-aryl-7H-thiazolo[3,2-b]-1,2,4-triazin-7-one derivatives were synthesized and assayed for their human acetylcholinesterase (hAChE) inhibitory activities.The SAR study of the target 3-aryl-7H-thiazolo[3,2-b]-1,2,4-triazin-7-one derivatives was summarized.The active sites in the acetylcholinesterase were analyzed by molecular docking technique.Communicated by Ramaswamy H. Sarma.

Functionalized nanoflower-like hydroxyl magnesium silicate for effective adsorption of aflatoxin B1

Aflatoxin B1 (AFB1), which is widely found in food and feed, poses a serious threat to the health of human and livestock. In this work, functionalized nanoflower-like hydroxyl magnesium silicate (FNHMS) was synthesized for adsorption of AFB1. First, bulk magnesium silicate (MS) was converted into nanoflower-like hydroxyl magnesium silicate (NHMS) by hydroxylation. Cetyltrimethylammonium bromide (CTMAB) modification then enhanced the hydrophobicity and the affinity to AFB1 of NHMS. The adsorption performance for AFB1 followed the order of MS < NHMS < FNHMS, and the adsorption performance increased with the increase of the dose of CTMAB. Isothermal adsorption analysis indicated that the surface of FNHMS was heterogeneous. The adsorption capacity of FNHMS-0.4 to AFB1 was estimated to be 27.34 mg g^-1 and 28.61 mg g^-1 by Freundlich and Dubinin-Radushkevich isotherm adsorption model, respectively. By analyzing the adsorption kinetics and adsorption thermodynamics, both physical adsorption and chemisorption existed in the process of AFB1 being adsorbed on FNHMS-0.4. Adsorption mechanisms analysis indicated that the adsorption followed the adsorption site priority of H > O > Mg. This work demonstrates that FNHMS could be a promising adsorbent for removal of AFB1.

Cholinesterase as a Target for Drug Development in Alzheimer's Disease

Alzheimer's disease (AD) is an enormous healthcare challenge, and 50 million people are currently suffering from it. There are several pathophysiological mechanisms involved, but cholinesterase inhibitors remained the major target from the last 2-3 decades. Among four available therapeutics (donepezil, rivastigmine, galantamine, and memantine), three of them are cholinesterase inhibitors. Herein, we describe the role of acetylcholine sterase (AChE) and related hypothesis in AD along with the pharmacological and chemical aspects of the available cholinesterase inhibitors. This chapter discusses the development of several congeners and hybrids of available cholinesterase inhibitors along with their binding patterns in enzyme active sites.

Sitagliptin protects liver against aflatoxin B1-induced hepatotoxicity through upregulating Nrf2/ARE/HO-1 pathway

Dipeptidyl peptidase-4 inhibitor (DPP-4 inhibitor) such as sitagliptin has been presented as antidiabetic drugs and has numerous restorative advantages over different diseases; however, its defensive role against aflatoxin b1 (AFB1) liver toxicity has not been previously examined. Wistar rats (65 weeks, male) were utilized in the investigation. Animals were divided into five different groups (n = 10): control; AFB1; AFB1 + Sita (50); AFB1 + Sita (100); and Sita (100). Sitagliptin significantly (*p ≤ .05, **p ≤ .01, and ***p ≤ .001) altered the levels of various serum liver enzymes (lactate dehydrogenase, alkaline phosphate, aspartate aminotransferase, and alanine aminotransferase). It decreased the concentration of an oxidative stress marker, that is, malondialdehyde and increased the level of antioxidant enzymes such as reduced glutathione, catalase, superoxide dismutase, and glutathione peroxidase in AFB1-administered rats. It also improved the Nrf2 expression and HO-1 level in AFB1-intoxicated rats. This investigation discusses innovative evidence on the protective role of sitagliptin against AFB1-induced hepatotoxicity in rats.

Design of inhibitors of thymidylate kinase from Variola virus as new selective drugs against smallpox: part II

Acknowledging the importance of studies toward the development of measures against terrorism and bioterrorism, this study aims to contribute to the design of new prototypes of potential drugs against smallpox. Based on a former study, nine synthetic feasible prototypes of selective inhibitors for thymidylate kinase from Variola virus (VarTMPK) were designed and submitted to molecular docking, molecular dynamics simulations and binding energy calculations. The compounds are simplifications of two more complex scaffolds, with a guanine connected to an amide or alcohol through a spacer containing ether and/or amide groups, formerly suggested as promising for the design of selective inhibitors of VarTMPK. Our study showed that, despite the structural simplifications, the compounds presented effective energy values in interactions with VarTMPK and HssTMPK and that the guanine could be replaced by a simpler imidazole ring linked to a -NH2 group, without compromising the affinity for VarTMPK. It was also observed that a positive charge in the imidazole ring is important for the selectivity toward VarTMPK and that an amide group in the spacer does not contribute to selectivity. Finally, prototype 3 was pointed as the most promising to be synthesized and experimentally evaluated. Communicated by Ramaswamy H. Sarma.

Surface screening, molecular modeling and in vitro studies on the interactions of aflatoxin M1 and human enzymes acetyl- and butyrylcholinesterase

Aflatoxin M1 (AFM1) is a mycotoxin produced by Aspergillus fungi and found in contaminated milk, breastfeed and dairy products, being highly toxic and carcinogenic to humans and other mammalian species. It is also produced in the human body as a metabolite of aflatoxin B1 (AFB1), one of the most toxic natural products known. Previous studies have shown that AFM1 is a potential inhibitor of the enzyme acetylcholinesterase (AChE), and therefore, a potential neurotoxic agent. In this work, surface screening (SS) and molecular dynamics (MD) simulation on human acetylcholinesterase AChE (HssAChE) were performed to corroborate literature data regarding preferential binding sites and type of inhibition. Also, an inedited theoretical study on the interactions of AFM1 with human butyrylcholinesterase (HssBChE) was performed. In vitro inhibition tests on both enzymes were done to support theoretical results. MD simulations suggested the catalytic anionic site of HssAChE as the preferential binding site for AFM1 and also that this metabolite is not a good inhibitor of HssBChE, corroborating previous studies. In vitro assays also corroborated molecular modeling studies by showing that AFM1 did not inhibit BChE and was able to inhibit AChE, although not as much as AFB1.

Comprehensive review of mechanisms of pathogenesis involved in Alzheimer's disease and potential therapeutic strategies

AD is a progressive neurodegenerative disorder and a leading cause of dementia in an aging population worldwide. The enormous challenge which AD possesses to global healthcare makes it as urgent as ever for the researchers to develop innovative treatment strategies to fight this disease. An in-depth analysis of the extensive available data associated with the AD is needed for a more comprehensive understanding of underlying molecular mechanisms and pathophysiological pathways associated with the onset and progression of the AD. The currently understood pathological and biochemical manifestations include cholinergic, Aβ, tau, excitotoxicity, oxidative stress, ApoE, CREB signaling pathways, insulin resistance, etc. However, these hypotheses have been criticized with several conflicting reports for their involvement in the disease progression. Several issues need to be addressed such as benefits to cost ratio with cholinesterase therapy, the dilemma of AChE selectivity over BChE, BBB permeability of peptidic BACE-1 inhibitors, hurdles related to the implementation of vaccination and immunization therapy, and clinical failure of candidates related to newly available targets. The present review provides an insight to the different molecular mechanisms involved in the development and progression of the AD and potential therapeutic strategies, enlightening perceptions into structural information of conventional and novel targets along with the successful applications of computational approaches for the design of target-specific inhibitors.

Molecular Modeling Studies on the Interactions of Aflatoxin B1 and Its Metabolites with Human Acetylcholinesterase. Part II: Interactions with the Catalytic Anionic Site (CAS)

The most common type of aflatoxin (AFT) found in nature is aflatoxin B1 (AFB1). This micotoxin is extremely hepatotoxic and carcinogenic to mammals, with acute and chronic effects. It is believed that this could be related to the capacity of AFB1 and its metabolites in inhibiting the enzyme acetylcholinesterase (AChE). In a previous work, we performed an inedited theoretical investigation on the binding modes of these molecules on the peripheral anionic site (PAS) of human AChE (HssAChE), revealing that the metabolites can also bind in the PAS in the same way as AFB1. Here, we investigated the binding modes of these compounds on the catalytic anionic site (CAS) of HssAChE to compare the affinity of the metabolites for both binding sites as well as verify which is the preferential one. Our results corroborated with experimental studies pointing to AFB1 and its metabolites as mixed-type inhibitors, and pointed to the residues relevant for the stabilization of these compounds on the CAS of HssAChE.