Genomic landscape of the emerging XDR Salmonella Typhi for mining druggable targets clpP, hisH, folP and gpmI and screening of novel TCM inhibitors, molecular docking and simulation analyses.

Typhoid fever is transmitted by ingestion of polluted water, contaminated food, and stool of typhoid-infected individuals, mostly in developing countries with poor hygienic environments. To find novel therapeutic targets and inhibitors, We employed a subtractive genomics strategy towards Salmonella Typhi and the complete genomes of eight strains were primarily subjected to the EDGAR tool to predict the core genome (n = 3207). Human non-homology (n = 2450) was followed by essential genes identification (n = 37). The STRING database predicted maximum protein-protein interactions, followed by cellular localization. The virulent/immunogenic ability of predicted genes were checked to differentiate drug and vaccine targets. Furthermore, the 3D models of the identified putative proteins encoded by the respective genes were constructed and subjected to druggability analyses where only "highly druggable" proteins were selected for molecular docking and simulation analyses. The putative targets ATP-dependent CLP protease proteolytic subunit, Imidazole glycerol phosphate synthase hisH, 7,8-dihydropteroate synthase folP and 2,3-bisphosphoglycerate-independent phosphoglycerate mutase gpmI were screened against a drug-like library (n = 12,000) and top hits were selected based on H-bonds, RMSD and energy scores. Finally, the ADMET properties for novel inhibitors ZINC19340748, ZINC09319798, ZINC00494142, ZINC32918650 were optimized followed by binding free energy (MM/PBSA) calculation for ligand-receptor complexes. The findings of this work are expected to aid in expediting the identification of novel protein targets and inhibitors in combating typhoid Salmonellosis, in addition to the already existing therapies.

Subtractive sequence analysis aided druggable targets mining in Burkholderia cepacia complex and finding inhibitors through bioinformatics approach.

Burkholderia cepacia complex (BCC) is a group of gram-negative bacteria composed of at least 20 different species that cause diseases in plants, animals as well as humans (cystic fibrosis and airway infection). Here, we analyzed the proteomic data of 47 BCC strains by classifying them in three groups. Phylogenetic analyses were performed followed by individual core region identification for each group. Comparative analysis of the three individual core protein fractions resulted in 1766 ortholog/proteins. Non-human homologous proteins from the core region gave 1680 proteins. Essential protein analyses reduced the target list to 37 proteins, which were further compared to a closely related out-group, Burkholderia gladioli ATCC 10,248 strain, resulting in 21 proteins. 3D structure modeling, validation, and druggability step gave six targets that were subjected to further target prioritization parameters which ultimately resulted in two BCC targets. A library of 12,000 ZINC drug-like compounds was screened, where only the top hits were selected for docking orientations. These included ZINC01405842 (against Chorismate synthase aroC) and ZINC06055530 (against Bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/Glucosamine-1-phosphate acetyltransferase glmU). Finally, dynamics simulation (200 ns) was performed for each ligand-receptor complex, followed by ADMET profiling. Of these targets, details of their applicability as drug targets have not yet been elucidated experimentally, hence making our predictions novel and it is suggested that further wet-lab experimentations should be conducted to test the identified BCC targets and ZINC scaffolds to inhibit them.

Targeting notch signaling pathway in breast cancer stem cells through drug repurposing approach.

Breast cancer is recognized globally as one of the leading causes of malignant morbidity. It is a heterogeneous disease that accounts for 30 percent of all women diagnosed with cancer. To bring an anti-cancer drug from the bench to the bedside is an expensive and time-consuming process. The drug repurposing approach targets new enemies (new diseases) with old weapons (known drugs). The present study identified an FDA-approved drug targeting the γ-secretase complex involved in the Notch signaling pathway in breast cancer stem cells (BCSCs). A literature survey and in-silico study identified Venetoclax as a γ-secretase inhibitor (GSI) from 1615 FDA-approved drug compounds. In-silico docking potential of Venetoclax was better than the standard γ-secretase inhibitor RO4929097. Also, the molecular dynamics simulations of 200 ns confirmed the stability of the Venetoclax-γ-secretase complex. These findings suggest that the use of Venetoclax represents a potential γ-secretase inhibitor in breast cancer stem cells. Eventually, the in vitro and clinical evaluation will be needed to confirm the potential chemopreventive and treatment effects of Venetoclax against breast cancer and breast cancer stem cells. Venetoclax appeared as the most promising drug of the 1615 FDA-approved drugs. Our in-silico findings suggest that Venetoclax may act as a γ-secretase inhibitor against the Notch signaling pathway in breast cancer stem cells.

Glycosylation is key for enhancing drug recognition into spike glycoprotein of SARS-CoV-2.

The emergence of COVID-19 caused by SARS-CoV-2 and its spread since 2019 represents the major public health problem worldwide nowadays, which has generated a high number of infections and deaths. The spike protein (S protein) is the most studied protein of SARS-CoV-2, and key to host-cell entry through ACE2 receptor. This protein presents a large pattern of glycosylations with important roles in immunity and infection mechanisms. Therefore, understanding key aspects of the molecular mechanisms of these structures, during drug recognition in SARS-CoV-2, may contribute to therapeutic alternatives. In this work, we explored the impact of glycosylations on the drug recognition on two domains of the S protein, the receptor-binding domain (RBD) and the N-terminal domain (NTD) through molecular dynamics simulations and computational biophysics analysis. Our results show that glycosylations in the S protein induce structural stability and changes in rigidity/flexibility related to the number of glycosylations in the structure. These structural changes are important for its biological activity as well as the correct interaction of ligands in the RBD and NTD regions. Additionally, we evidenced a roto-translation phenomenon in the interaction of the ligand with RBD in the absence of glycosylation, which disappears due to the influence of glycosylation and the convergence of metastable states in RBM. Similarly, glycosylations in NTD promote an induced fit phenomenon, which is not observed in the absence of glycosylations; this process is decisive for the activity of the ligand at the cryptic site. Altogether, these results provide an explanation of glycosylation relevance in biophysical properties and drug recognition to S protein of SARS-CoV-2, which must be considered in the rational drug development and virtual screening targeting S protein.

Repurposing potential of Ayurvedic medicinal plants derived active principles against SARS-CoV-2 associated target proteins revealed by molecular docking, molecular dynamics and MM-PBSA studies.

All the plants and their secondary metabolites used in the present study were obtained from Ayurveda, with historical roots in the Indian subcontinent. The selected secondary metabolites have been experimentally validated and reported as potent antiviral agents against genetically-close human viruses. The plants have also been used as a folk medicine to treat cold, cough, asthma, bronchitis, and severe acute respiratory syndrome in India and across the globe since time immemorial. The present study aimed to assess the repurposing possibility of potent antiviral compounds with SARS-CoV-2 target proteins and also with host-specific receptor and activator protease that facilitates the viral entry into the host body. Molecular docking (MDc) was performed to study molecular affinities of antiviral compounds with aforesaid target proteins. The top-scoring conformations identified through docking analysis were further validated by 100 ns molecular dynamic (MD) simulation run. The stability of the conformation was studied in detail by investigating the binding free energy using MM-PBSA method. Finally, the binding affinities of all the compounds were also compared with a reference ligand, remdesivir, against the target protein RdRp. Additionally, pharmacophore features, 3D structure alignment of potent compounds and Bayesian machine learning model were also used to support the MDc and MD simulation. Overall, the study emphasized that curcumin possesses a strong binding ability with host-specific receptors, furin and ACE2. In contrast, gingerol has shown strong interactions with spike protein, and RdRp and quercetin with main protease (Mpro) of SARS-CoV-2. In fact, all these target proteins play an essential role in mediating viral replication, and therefore, compounds targeting aforesaid target proteins are expected to block the viral replication and transcription. Overall, gingerol, curcumin and quercetin own multitarget binding ability that can be used alone or in combination to enhance therapeutic efficacy against COVID-19. The obtained results encourage further in vitro and in vivo investigations and also support the traditional use of antiviral plants preventively.

Camu-camu (Myrciaria dubia) seeds as a novel source of bioactive compounds with promising antimalarial and antischistosomicidal properties.

Parasitic diseases have attracted worldwide attention of their consequent impact on mortality and morbidity. Accordingly, several plants have been screened for antiparasitic activity aiming to create new alternatives for treatment. These diseases have been neglected and have not attracted worldwide attention (nowadays), the health concerns are focused in chronic diseases, but it is necessary to focus on parasitic diseases and look for prophylactic alternatives, such as plant extracts. Although camu-camu (Myrciaria dubia) seeds are a rich source of antioxidant antimutagenic, cytotoxic, anti-inflammatory, antimicrobial, antihypertensive and neuroprotective compounds, nothing is known about their antiparasitic effects. Thus, in the present study we aimed to evaluate five extracts of camu-camu seeds (100% water, 100% ethyl alcohol, 50% water + 50% ethyl alcohol, 25% water + 75% ethyl alcohol, and 75% water + 25% ethyl alcohol) in relation to their in vitro antimalarial, antischistosomicidal, leishmanicidal and anti-hemolytic effects. The extracts exhibited antischistosomicidal (ED50 values from 418.4 to >1000.0 µg/mL) and antimalarial activities (IC50 values from 24.2 to 240.8 µg/mL) for both W2 and 3D7 strains in all intra-erythrocytic stages. Correlation analysis showed that the toxic effects may mainly be attributed to methylvescalagin (r = -0.548 to -0.951, p < 0.05) and 2,4-dihydroxybenzoic acid (r = -0.612 to -0.917, p < 0.05) contents. Moreover, the anti-hemolytic effect was associated to methylvescalagin (r = -0.597, p < 0.05). No toxic effects were observed for leishmaniasis and IMR90 normal cells. Herein, methylvescalagin was the bioactive compound of greatest interest once it presented simultaneous relation with antiparasitic and anti-hemolytic activities.

Potential novel inhibitors against emerging zoonotic pathogen Nipah virus: a virtual screening and molecular dynamics approach.

Nipah virus is a pathogen considered highly infectious, and its lethality can cause between 40% and 70% of deaths in those infected. At present, no effective treatment is available which results in an imperative need to explore new approaches to the search for drugs. Through virtual screening techniques, docking and molecular dynamics, 183 ligands were evaluated against the Nipah virus glycoprotein (NiV-G), involved throughout the process of virus entry to the host cell, resulting in a good target for blocking the infection. Of the 183 drugs computationally screened, three of them (MMV020537, MMV688888 and MMV019838) were found to be potential inhibitors of NiV-G. Their calculated dissociation constants were 0.03 nM, 2.18 nM and 31.61 nM, respectively. Molecular dynamics studies confirm their stability binding modes in the active site of the protein. These potential inhibitors can be used later as leads for the development of new drugs that allow effective treatment of the disease.Communicated by Ramaswamy H. Sarma.

Novel multi-epitope protein containing conserved epitopes from different Leishmania species as potential vaccine candidate: Integrated immunoinformatics and molecular dynamics approach.

Leishmaniosis, caused by intracellular parasites of the genus Leishmania, has become a serious public health problem around the world, and for which there are currently extensive limitations. In this work, a theoretical model was proposed for the development of a multi-epitope vaccine. The protein GP63 of the parasite was selected for epitopes prediction, due to its important biological role for the infection process and abundance. IEDB tools were used to determine epitopes B and T in Leishmania braziliensis; besides, other conserved epitopes in three species were selected. To improve immunogenicity, 50S ribosomal protein L7 / L12 (ID: P9WHE3) was used as a domain of adjuvant in the assembly process. The folding arrangement of the vaccine was obtained through homologous modeling multi-template with MODELLER v9.21, and a Ramachandran plot analysis was done. Furthermore, physicochemical properties were described with the ProtParam tool and secondary structure prediction combining GOR-IV and SOPMA tools. Finally, a molecular dynamics simulation (50 ns) was performed to establish flexibility and conformational changes. The analysis of the results indicates high conservancy in the epitopes predicted among the four species. Moreover, Ramachandran plot, physicochemical parameters, and secondary structure prediction suggest a stable conformation of the vaccine, after a minimum conformational change that was evaluated with the free energy landscape. The conformational change does not drive any substantial change for epitope exposition on the surface. The vaccine proposed could be tested experimentally to guide new approaches in the development of pan-vaccines; vaccines with regions conserved in multiple species.

PQM130, a Novel Feruloyl-Donepezil Hybrid Compound, Effectively Ameliorates the Cognitive Impairments and Pathology in a Mouse Model of Alzheimer's Disease.

Alzheimer's disease (AD) is the most frequent type of dementia in older people. The complex nature of AD calls for the development of multitarget agents addressing key pathogenic processes. Donepezil, an acetylcholinesterase inhibitor, is a first-line acetylcholinesterase inhibitor used for the treatment of AD. Although several studies have demonstrated the symptomatic efficacy of donepezil treatment in AD patients, the possible effects of donepezil on the AD process are not yet known. In this study, a novel feruloyl-donepezil hybrid compound (PQM130) was synthesized and evaluated as a multitarget drug candidate against the neurotoxicity induced by Aß1-42 oligomer (AßO) injection in mice. Interestingly, PQM130 had already shown anti-inflammatory activity in different in vivo models and neuroprotective activity in human neuronal cells. The intracerebroventricular (i.c.v.) injection of AßO in mice caused the increase of memory impairment, oxidative stress, neurodegeneration, and neuroinflammation. Instead, PQM130 (0.5-1 mg/kg) treatment after the i.c.v. AßO injection reduced oxidative damage and neuroinflammation and induced cell survival and protein synthesis through the modulation of glycogen synthase kinase 3ß (GSK3ß) and extracellular signal-regulated kinases (ERK1/2). Moreover, PQM130 increased brain plasticity and protected mice against the decline in spatial cognition. Even more interesting is that PQM130 modulated different pathways compared to donepezil, and it is much more effective in counteracting AßO damage. Therefore, our findings highlighted that PQM130 is a potent multi-functional agent against AD and could act as a promising neuroprotective compound for anti-AD drug development.

Design, synthesis and pharmacological evaluation of N-benzyl-piperidinyl-aryl-acylhydrazone derivatives as donepezil hybrids: Discovery of novel multi-target anti-alzheimer prototype drug candidates.

A new series of sixteen multifunctional N-benzyl-piperidine-aryl-acylhydrazones hybrid derivatives was synthesized and evaluated for multi-target activities related to Alzheimer's disease (AD). The molecular hybridization approach was based on the combination, in a single molecule, of the pharmacophoric N-benzyl-piperidine subunit of donepezil, the substituted hydroxy-piperidine fragment of the AChE inhibitor LASSBio-767, and an acylhydrazone linker, a privileged structure present in a number of synthetic aryl- and aryl-acylhydrazone derivatives with significant AChE and anti-inflammatory activities. Among them, compounds 4c, 4d, 4g and 4j presented the best AChE inhibitory activities, but only compounds 4c and 4g exhibited concurrent anti-inflammatory activity in vitro and in vivo, against amyloid beta oligomer (AßO) induced neuroinflammation. Compound 4c also showed the best in vitro and in vivo neuroprotective effects against AßO-induced neurodegeneration. In addition, compound 4c showed a similar binding mode to donepezil in both acetylated and free forms of AChE enzyme in molecular docking studies and did not show relevant toxic effects on in vitro and in vivo assays, with good predicted ADME parameters in silico. Overall, all these results highlighted compound 4c as a promising and innovative multi-target drug prototype candidate for AD treatment.

The addition of inulin and Lactobacillus casei 01 in sheep milk ice cream.

The effect of the Lactobacillus casei 01 and inulin addition on sheep milk ice cream during storage (-18 °C, 150 days) was investigated. Control, probiotic and synbiotic ice cream (10% w/w sheep milk cream; 10% w/w sheep milk cream, L. casei 01, 6 log CFU/mL; 10% w/w inulin, L. casei 01, 6 log CFU/mL, respectively) were manufactured. Microbiological counts (probiotic count, survival after in vitro gastrointestinal resistance, Caco-2 cell adhesion), bioactivity and microstructure were analysed. Physical and textural characteristics, colour parameters, thermal analysis and organic acids/volatile compounds were also evaluated. All formulations supported L. casei 01 viability and maintained above the minimum therapeutic level (>6 log CFU/mL) during storage. Inulin did not affect L. casei 01 survival after the passage through simulated gastrointestinal tract and adhesion to Caco-2 cells while improved the ACE-inhibitory and antioxidant activity. L. casei 01 addition produced several volatile compounds, such as carboxylic acids, alcohols, aldehydes and ketones. Also, scanning electron microscopy showed an interaction between probiotic bacteria and inulin fibre on synbiotic ice cream and the adhesion of L. casei to Caco-2 cells was observed.

De Novo Design of New Inhibitor of Mutated Tyrosine-Kinase for the Myeloid Leukemia Treatment.

BACKGROUND: Chronic myelogenous leukemia is associated with hematopoietic stem cells that are manifested primarily with expansion myelopoiesis. It is the first cancer directly associated with a genetic abnormality. Specifically, it is associated to a particular cytogenetic abnormality, known as Philadelphia chromosome (Ph), which results from a fusion between part of the BCR ("breakpoint cluster region") gene from chromosome 22 and the Abelson (ABL) gene on chromosome 9 and leads to the formation a new gene leukemia-specific, the BCR-ABL. Since 2011, there are several tyrosine-kinase inhibitors in the market. Due to mutations in the tyrosine-kinase domain, these inhibitors are becoming less effective in the leukemia treatment, and then there is a need for new more effective inhibitors. METHODS: The aim of this work is to obtain new tyrosine-kinase inhibitors using in silico tools like de novo drug design, docking and absorption, distribution, metabolism and excretion studies. RESULTS: Using the proposed methodology, an initial library of more than 6000 molecules was obtained. This library was then filtered out using the Tanimoto metric to compute the similarity between the molecules using as parameter the 2D linear hashed fingerprint with a 64-bit address space. The resulting library was then used to run docking studies together with the reference market drugs and their ADME (absorption, distribution, metabolism and excretion) properties were determined. Three compounds with better inhibition capacity and better ADME properties that the commercially available not only for the wild form of enzymes under study but also to its mutated forms were obtained. CONCLUSION: The fragment based drug design method used in this work turns to be a good alternative to create new drugs that can control this neoplasm. Based on the calculated GScore, the de novo designed molecules have better inhibitor capacity than the tyrosine-kinase inhibitors most used in the market. These molecules shown strong potential to become drugs capable to inhibit all mutations, mainly the T315I mutation, now the leading cause of deaths due to the difficulty of inhibitors to control it.

First-principles calculations of nickel, cadmium, and lead adsorption on a single-walled (10,0) carbon nanotube.

The adsorption of Ni, Cd, and Pb on a zigzag (10, 0) carbon nanotube (CNT) surface was investigated using density functional theory. Binding energy calculations were performed, and the results indicated that the three metals are stably adsorbed on the nanotube surface. Moreover, the results showed that Cd is physisorbed whereas Ni and Pb are chemisorbed. Our studies show that the electronic properties of the CNT are modified by the chemisorption mechanism (Ni and Pb). After Ni and Pb adsorption, the nanotube changes from being a semiconductor to a metallic conductor. The nanotube remains semiconductive upon Cd physisorption, although a decrease in the band gap is observed. Also, Ni or Pb adsorption triggers a change in the magnetism of the nanotube through the induction of spin polarization. Not only can these results of our calculations be used to explain the adsorption mechanisms of these heavy metals on the CNT, but they are also useful for evaluating the potential of carbon nanotubes (CNTs) to act as filters and sensors of such metals.

Inhibition of cysteine proteases by a natural biflavone: behavioral evaluation of fukugetin as papain and cruzain inhibitor.

Cruzain is the major cysteine protease of Trypanosoma cruzi, the infectious agent responsible for Chagas disease, and cruzain inhibitors display considerable antitrypanosomal activity. In the present work we elucidated crystallographic data of fukugetin, a biflavone isolated from Garcinia brasiliensis, and investigated the role of this molecule as cysteine protease inhibitor. The kinetic analyses demonstrated that fukugetin inhibited cruzain and papain by a slow reversible type inhibition with K(I) of 1.1 and 13.4 µM, respectively. However, cruzain inhibition was about 12 times faster than papain inhibition. Lineweaver-Burk plots demonstrated partial competitive inhibition for cruzain and hyperbolic mixed-type inhibition for papain. Furthermore, the docking results showed that the biflavone binds to ring C' in the S2 pocket and to ring C in the S3 pocket through hydrophobic interactions and hydrogen bonds. Finally, fukugetin also presented inhibitory activity on proteases of the T. cruzi extract, with IC50 of 7 µM.

Semisynthesis and antimicrobial activity of novel guttiferone-A derivatives.

Six derivatives of guttiferone-A (LFQM-79, 80, 81, 82, 113 and 114) were synthesized and evaluated for their antimicrobial activity against the opportunistic or pathogenic fungi Candida albicans (ATCC 09548), Candida glabrata (ATCC 90030), Candida krusei (ATCC 6258), Candida parapsilosis (ATCC 69548), Candida tropicalis (ATCC 750), Cryptococcus neoformans (ATCC 90012), Trichophyton tonsurans, Microsporum gypseum and also against the opportunistic and pathogenic Gram-positive bacteria Staphylococcus aureus (ATCC 6538), Staphylococcus epidermidis (ATCC 12228), Bacillus cereus (ATCC 11778) and Gram-negative Escherichia coli (ATCC 25922), Pseudomonas aeruginosa (ATCC 9027), Salmonella typhimurium (ATCC 14028), Proteus mirabilis (ATCC 25933). The antimicrobial activities of derivatives were compared with guttiferone-A and they presented to be more potent than the original molecule and sometimes greater than standard drugs established in therapeutics. The current study showed that derivatives of guttiferone-A possess potent antimicrobial activity and are relatively non-cytotoxic, which reveal these new molecules as promising new drug prototype candidates, with innovative structural pattern.