A review of machine learning approaches for drug synergy prediction in cancer.

Combinational pharmacotherapy with the synergistic/additive effect is a powerful treatment strategy for complex diseases such as malignancies. Identifying synergistic combinations with various compounds and structures requires testing a large number of compound combinations. However, in practice, examining different compounds by in vivo and in vitro approaches is costly, infeasible and challenging. In the last decades, significant success has been achieved by expanding computational methods in different pharmacological and bioinformatics domains. As promising tools, computational approaches such as machine learning algorithms (MLAs) are used for prioritizing combinational pharmacotherapies. This review aims to provide the models developed to predict synergistic drug combinations in cancer by MLAs with various information, including gene expression, protein-protein interactions, metabolite interactions, pathways and pharmaceutical information such as chemical structure, molecular descriptor and drug-target interactions.

Astaxanthin-loaded alginate-chitosan gel beads activate Nrf2 and pro-apoptotic signalling pathways against oxidative stress.

Oxidative stress (OS) plays a crucial role in disease development. Astaxanthin (ATX), a valuable natural compound, may reduce OS and serve as a treatment for diseases like neurodegenerative disorders and cancer. Nuclear factor-erythroid 2-related factor 2 (Nrf2) regulates antioxidant enzymes and OS management. We evaluated ATX's antioxidant activity via Alg-CS/ATX gel beads in vitro. ATX-encapsulated alginate-chitosan (Alg-CS/ATX) gel beads were synthesized and structurally/morphologically characterized by SEM, FT-IR, and XRD. Their biological effects were examined in human umbilical vein endothelial cells (HUVECs) treated with H2O2 through MTT assay, Annexin V/PI, cell cycle studies, and western blotting. Alg-CS effectively carried ATX, with high capacity and reduced pore size. Alg-CS/ATX displayed an 84% encapsulation efficiency, maintaining stability for 30 days. In vitro studies showed a 1.4-fold faster release at pH 5.4 than at neutral pH, improving ATX's therapeutic potential. HUVECs treated with Alg-CS/ATX showed enhanced viability via increased Nrf2 expression. Alg-CS gel beads exhibit significant potential as a biocompatible vehicle for delivering ATX to combat OS with considerable opportunity for clinical applications.

A voting-based machine learning approach for classifying biological and clinical datasets.

BACKGROUND: Different machine learning techniques have been proposed to classify a wide range of biological/clinical data. Given the practicability of these approaches accordingly, various software packages have been also designed and developed. However, the existing methods suffer from several limitations such as overfitting on a specific dataset, ignoring the feature selection concept in the preprocessing step, and losing their performance on large-size datasets. To tackle the mentioned restrictions, in this study, we introduced a machine learning framework consisting of two main steps. First, our previously suggested optimization algorithm (Trader) was extended to select a near-optimal subset of features/genes. Second, a voting-based framework was proposed to classify the biological/clinical data with high accuracy. To evaluate the efficiency of the proposed method, it was applied to 13 biological/clinical datasets, and the outcomes were comprehensively compared with the prior methods. RESULTS: The results demonstrated that the Trader algorithm could select a near-optimal subset of features with a significant level of p-value < 0.01 relative to the compared algorithms. Additionally, on the large-sie datasets, the proposed machine learning framework improved prior studies by ~ 10% in terms of the mean values associated with fivefold cross-validation of accuracy, precision, recall, specificity, and F-measure. CONCLUSION: Based on the obtained results, it can be concluded that a proper configuration of efficient algorithms and methods can increase the prediction power of machine learning approaches and help researchers in designing practical diagnosis health care systems and offering effective treatment plans.

Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries.

To attain promising pharmacotherapies, researchers have applied drug repurposing (DR) techniques to discover the candidate medicines to combat the coronavirus disease 2019 (COVID-19) outbreak. Although many DR approaches have been introduced for treating different diseases, only structure-based DR (SBDR) methods can be employed as the first therapeutic option against the COVID-19 pandemic because they rely on the rudimentary information about the diseases such as the sequence of the severe acute respiratory syndrome coronavirus 2 genome. Hence, to try out new treatments for the disease, the first attempts have been made based on the SBDR methods which seem to be among the proper choices for discovering the potential medications against the emerging and re-emerging infectious diseases. Given the importance of SBDR approaches, in the present review, well-known SBDR methods are summarized, and their merits are investigated. Then, the databases and software applications, utilized for repurposing the drugs against COVID-19, are introduced. Besides, the identified drugs are categorized based on their targets. Finally, a comparison is made between the SBDR approaches and other DR methods, and some possible future directions are proposed.

Electrochemiluminescent immunosensor for detection of carcinoembryonic antigen using luminol-coated silver nanoparticles.

Recently, electrochemiluminescent (ECL) immunosensors have received much attention in the field of biomarker detection. Here, a highly enhanced ECL immunosensing platform was designed for ultrasensitive detection of carcinoembryonic antigen (CEA). The surface of the glassy carbon electrode was enhanced by applying functional nanostructures such as thiolated graphene oxide (S-GO) and streptavidin-coated gold nanoparticles (SA-AuNPs). The selectivity and sensitivity of the designed immunosensor were improved by entrapping CEA biomolecules using a sandwich approach. Luminol/silver nanoparticles (Lu-SNPs) were applied as the main core of the signaling probe, which were then coated with streptavidin to provide overloading of the secondary antibody. The highly ECL signal enhancement was obtained due to the presence of horseradish peroxidase (HRP) in the signaling probe, in which the presence of H2O2 further amplified the intensity of the signals. The engineered immunosensor presented excellent sensitivity for CEA detection, with limit of detection (LOD) and linear detection range (LDR) values of 58 fg mL-1 and 0.1 pg mL-1 to 5 pg mL-1 (R2 = 0.9944), respectively. Besides its sensitivity, the fabricated ECL immunosensor presented outstanding selectivity for the detection of CEA in the presence of various similar agents. Additionally, the developed immunosensor showed an appropriate repeatability (RSD 3.8%) and proper stability (2 weeks). Having indicated a robust performance in the real human serum with stated LOD and LDR, the engineered immunosensor can be considered for the detection and monitoring of CEA in the clinic.

Targeted Delivery of Sunitinib by MUC-1 Aptamer-Capped Magnetic Mesoporous Silica Nanoparticles.

Magnetic mesoporous silica nanoparticles (MMSNPs) are being widely investigated as multifunctional novel drug delivery systems (DDSs) and play an important role in targeted therapy. Here, magnetic cores were synthesized using the thermal decomposition method. Further, to improve the biocompatibility and pharmacokinetic behavior, mesoporous silica was synthesized using the sol-gel process to coat the magnetic cores. Subsequently, sunitinib (SUN) was loaded into the MMSNPs, and the particles were armed with amine-modified mucin 1 (MUC-1) aptamers. The MMSNPs were characterized using FT-IR, TEM, SEM, electrophoresis gel, DLS, and EDX. MTT assay, flow cytometry analysis, ROS assessment, and mitochondrial membrane potential analysis evaluated the nanoparticles' biological impacts. The physicochemical analysis revealed that the engineered MMSNPs have a smooth surface and spherical shape with an average size of 97.6 nm. The biological in vitro analysis confirmed the highest impacts of the targeted MMSNPs in MUC-1 overexpressing cells (OVCAR-3) compared to the MUC-1 negative MDA-MB-231 cells. In conclusion, the synthesized MMSNP-SUN-MUC-1 nanosystem serves as a unique multifunctional targeted delivery system to combat the MUC-1 overexpressing ovarian cancer cells.

Recombinant production and characterization of L-glutaminase (glsA) as a promiscuity therapeutic enzyme.

Because of the therapeutical impacts of hydrolytic enzymes in different diseases, in particular malignancies, we aimed to produce a recombinant putative L-glutaminase (GLS ASL-1) from a recently characterized halo-thermotolerant Bacillus sp. SL-1. For this purpose, the glsA gene was identified and efficiently overexpressed in the Origami™ B (DE3) strain. The yield of the purified GLS ASL-1 was ~ 20 mg/L, indicating a significant expression of recombinant enzyme in the Origami. The enzyme activity assay revealed a significant hydrolytic effect of the recombinant GLS ASL-1 on L-asparagine (Asn) (i.e., Km 39.8 µM, kcat 19.9 S-1) with a minimal affinity for L-glutamine (Gln). The GLS ASL-1 significantly suppressed the growth of leukemic Jurkat cells through apoptosis induction (47.5%) in the IC50 dosage of the enzyme. The GLS ASL-1 could also change the Bax/Bcl2 expression ratio, indicating its apoptotic effect on cancer cells. The in silico analysis was conducted to predict structural features related to the histidine-tag exposure in the N- or C-terminal of the recombinant GLS ASL-1. In addition, molecular docking simulation for substrate specificity revealed a greater binding affinity of Asn to the enzyme binding-site residues than Gln, which was confirmed in experimental procedures as well. In conclusion, the current study introduced a recombinant GLS ASL-1 with unique functional and structural features, highlighting its potential pharmaceutical and medical importance. GLS ASL-1 represents the first annotated enzyme from Bacillus with prominent asparaginase activity, which can be considered for developing alternative enzymes in therapeutic applications. KEY POINTS: • Hydrolytic enzymes have critical applications in different types of human malignancies. • A recombinant L-glutaminase (GLS ASL-1) was produced from halo-thermotolerant Bacillus sp. SL-1. • GLS ASL-1 displayed a marked hydrolytic activity on L-asparagine compared to the L-glutamine. • GLS ASL-1 with significant substrate promiscuity may be an alternative for developing novel pharmaceuticals.

Label-free electrochemical microfluidic biosensors: futuristic point-of-care analytical devices for monitoring diseases.

The integration of microfluidics with electrochemical analysis has resulted in the development of single miniaturized detection systems, which allows the precise control of sample volume with multianalyte detection capability in a cost- and time-effective manner. Microfluidic electrochemical sensing devices (MESDs) can potentially serve as precise sensing and monitoring systems for the detection of molecular markers in various detrimental diseases. MESDs offer several advantages, including (i) automated sample preparation and detection, (ii) low sample and reagent requirement, (iii) detection of multianalyte in a single run, (iv) multiplex analysis in a single integrated device, and (v) portability with simplicity in application and disposability. Label-free MESDs can serve an affordable real-time detection with a simple analysis in a short processing time, providing point-of-care diagnosis/detection possibilities in precision medicine, and environmental analysis. In the current review, we elaborate on label-free microfluidic biosensors, provide comprehensive insights into electrochemical detection techniques, and discuss the principles of label-free microfluidic-based sensing approaches.

Multifunctional magnetic nanoparticles for MRI-guided co-delivery of erlotinib and L-asparaginase to ovarian cancer.

The use of magnetic nanoparticles (MNPs) in biomedical applications has been wildly opted due to their unique properties. Here, we designed MNPs loaded with erlotinib (ERL/SPION-Val-PEG) and conjugated them with anti-mucin16 (MUC16) aptamer to introduce new image-guided nanoparticles (NPs) for targeted drug delivery as well as non-invasive magnetic resonance imaging (MRI) contrast agents. Also, the combination of our nanosystem (NS) along with L-Asparaginase (L-ASPN) led to synergistic effects in terms of reducing cell viability in ovarian cancer cells, which could suggest a novel combination therapy. The mean size of our NS was about 63.4 ± 3.4 nm evaluated by DLS analysis and its morphology was confirmed using TEM. Moreover, the functional groups, as well as magnetic properties of our NS, were examined by FT-IR and VSM tests, respectively. The loading efficacy of erlotinib on MNPs was about 80% and its release reached 70.85% over 7 days in the pH value of 5.4. The MR images and flow cytometry results revealed that the cellular uptake of ERL/SPION-Val-PEG-MUC16 NPs in cells with MUC16 overexpression was considerably higher than unarmed NPs. In addition, T2-weight MR images of ovarian cancer-bearing mice indicated significant signal intensity changes at the tumour site 4 h after intravenous injection compared to the non-target MNPs. Our data suggest ERL/SPION-Val-PEG NPs as an image-guided co-drug delivery system for ovarian cancer.

Multifunctional nanomedicines for targeting epidermal growth factor receptor in colorectal cancer.

Systemic administration of chemotherapeutics by nanocarriers (NCs) functionalized with targeting agents provides a localized accumulation of drugs in the target tissues and cells. Advanced nanoscaled medicaments can enter into the tumor microenvironment (TME) and overcome the uniquely dysregulated biological settings of TME, including highly pressurized tumor interstitial fluid in an acidic milieu. Such multimodal nanomedicines seem to be one of the most effective treatment modalities against solid tumors such as colorectal cancer (CRC). To progress and invade, cancer cells overexpress various oncogenes and molecular markers such as epidermal growth factor receptors (EGFRs), which can be exploited for targeted delivery of nanoscaled drug delivery systems (DDSs). In fact, to develop effective personalized multimodal nanomedicines, the type of solid tumor and status of the disease in each patient should be taken into consideration. While the development of such multimodal-targeted nanomedicines is largely dependent on the expression level of oncomarkers, the type of NCs and homing/imaging agents play key roles in terms of their efficient applications. In this review, we provide deep insights into the development of EGFR-targeting nanomedicines and discuss various types of nanoscale DDSs (e.g., organic and inorganic nanoparticles) for targeting of the EGFR-positive solid tumors such as CRC.

Drug databases and their contributions to drug repurposing.

Drug repurposing is an interesting field in the drug discovery scope because of reducing time and cost. It is also considered as an appropriate method for finding medications for orphan and rare diseases. Hence, many researchers have proposed novel methods based on databases which contain different information. Thus, a suitable organization of data which facilitates the repurposing applications and provides a tool or a web service can be beneficial. In this review, we categorize drug databases and discuss their advantages and disadvantages. Surprisingly, to the best of our knowledge, the importance and potential of databases in drug repurposing are yet to be emphasized. Indeed, the available databases can be divided into several groups based on data content, and different classes can be applied to find a new application of the existing drugs. Furthermore, we propose some suggestions for making databases more effective and popular in this field.

Targeted combined therapy in 2D and 3D cultured MCF-7 cells using metformin and erlotinib-loaded mesoporous silica magnetic nanoparticles.

AIM: This research aims to develop potential therapeutic nanostructures (NSs) encapsulating metformin (MET) and erlotinib (ER) for combinational therapy in breast cancer. METHODS: The ER and MET, both were loaded on mesoporous silica magnetic nanoparticles conjugated with polyethylene glycol and methotrexate to achieve targeted NSs. The developed NSs were characterised using SEM, DLS, and FTIR. Afterward, MTT, Trypan blue, and DNA extraction assays were operated for biological evaluations in the 2D and 3D MCF-7 cells. RESULTS: Physicochemical approaches indicated the mean diameter of 69.4 nm ± 9.5 (PDI = 0.64), and neutral charge (2 mv) for the developed NSs. MET and ER-loaded NSs exhibited 62.56% ± 4.41 and 67.73% ± 3.03 drug release amount in pH = 5.4, respectively. MTT assay revealed that ER- and MET-loaded NSs had less metabolic activity (≈ 20%) in comparison with non-targeted NSs. CONCLUSION: Overall, our combined ER and MET-loaded targeted NSs result in a synergistic inhibitory impact on MCF-7 cells.

Bioactive polymeric scaffolds for osteogenic repair and bone regenerative medicine.

The loss of bone tissue is a striking challenge in orthopedic surgery. Tissue engineering using various advanced biofunctional materials is considered a promising approach for the regeneration and substitution of impaired bone tissues. Recently, polymeric supportive scaffolds and biomaterials have been used to rationally promote the generation of new bone tissues. To restore the bone tissue in this context, biofunctional polymeric materials with significant mechanical robustness together with embedded materials can act as a supportive matrix for cellular proliferation, adhesion, and osteogenic differentiation. The osteogenic regeneration to replace defective tissues demands greater calcium deposits, high alkaline phosphatase activity, and profound upregulation of osteocalcin as a late osteogenic marker. Ideally, the bioactive polymeric scaffolds (BPSs) utilized for bone tissue engineering should impose no detrimental impacts and function as a carrier for the controlled delivery and release of the loaded molecules necessary for the bone tissue regeneration. In this review, we provide comprehensive insights into different synthetic and natural polymers used for the regeneration of bone tissue and discuss various technologies applied for the engineering of BPSs and their physicomechanical properties and biological effects.

Mitochondria-targeted antioxidant mito-TEMPO alleviate oxidative stress induced by antimycin A in human mesenchymal stem cells.

The cell therapy of damaged tissue, which is linked to hypoxia condition might fail, in large part due to the emergence of oxidative stress (OS) and/or mitochondrial dysfunctions. Thus, the invigoration of stem cells against oxidative stress could be a reliable strategy to improve the cell therapy outcome. Of various antioxidants, mito-Tempo (mito-T) is one of the potent antioxidants that could target and neutralize the mitochondrial oxidative stress. In this study, for the induction of hypoxia and oxidative stress in mitochondria of the mesenchymal stem cells (MSCs) isolated from human adipose tissue, antimycin A (AMA) was used and then several parameters were analyzed, including cell viability and cell cycle arrest of MSCs exposed to AMA, mito-T, antioxidant potential, redox homeostasis, and signaling pathways in MSCs under oxidative stress. Based on our findings, the treated MSCs were found to impose a high resistance to the OS-induced apoptosis, which correlated with the nuclear factor erythroid 2-related factor 2 (Nrf2) pathway required to manage OS. Upon exposure of the MSCs to high oxidative stress conditions using AMA, the cells failed to scavenge. The use of mito-T was found to alleviate the damage induced by oxidative stress through both direct functions of the free radical scavenging and the interplay in terms of cell signaling pathways including the upregulation of the Nrf2 pathway. These findings may pave the way in the stem cell therapy for the hypoxia-mediated tissue damage.

The role of Hippo signaling pathway and mechanotransduction in tuning embryoid body formation and differentiation.

Embryoid bodies (EBs) are the three-dimensional aggregates of pluripotent stem cells that are used as a model system for the in vitro differentiation. EBs mimic the early stages of embryogenesis and are considered as a potential biomimetic body in tuning the stem cell fate. Although EBs have a spheroid shape, they are not formed accidentally by the agglomeration of cells; they are formed by the deliberate and programmed aggregation of stem cells in a complex topological and biophysical microstructure instead. EBs could be programmed to promisingly differentiate into the desired germ layers with specific cell lineages, in response to intra- and extra-biochemical and biomechanical signals. Hippo signaling and mechanotransduction are the key pathways in controlling the formation and differentiation of EBs. The activity of the Hippo pathway strongly relies on cell-cell junctions, cell polarity, cellular architecture, cellular metabolism, and mechanical cues in the surrounding microenvironment. Although the Hippo pathway was initially thought to limit the size of the organ by inhibiting the proliferation and the promotion of apoptosis, the evidence suggests that this pathway even regulates stem cell self-renewal and differentiation. Considering the abovementioned explanations, the present study investigated the interplay of the Hippo signaling pathway, mechanotransduction, differentiation, and proliferation pathways to draw the molecular network involved in the control of EBs fate. In addition, this study highlighted several neglected critical parameters regarding EB formation, in the interplay with the Hippo core component involved in the promising differentiation.

The role of Piezo proteins and cellular mechanosensing in tuning the fate of transplanted stem cells.

Differentiation of stem cells can be modulated by a combination of internal and external signals, including mechanical cues from the surrounding microenvironment. Although numerous chemical and biological agents have been recognized in regulating stem cells' fate, little is known about their potential to directly sense the mechanical signals to choose differentiation into a specific lineage. The success of any stem cell transplantation effort, however, hinges on thorough understanding of the fate of these cells under different signals, including mechanical cues. Various proteins are involved in the mechanical sensing process. Of these, Piezo proteins, as the ion channels activated by membrane tension and mechanical signals, play an important role in translating the information of mechanical forces such as rigidity and topography of the extracellular matrix to the intracellular signaling pathways related to stem cell homing and differentiation. They also play a key role in terms of shear stresses and tensile loads in expansion systems. This review highlights key evidence for the potential of mechanically gated ion channels expressed by human stem cells, and the mechanotransduction and past mechanomemory in the fate of transplanted stem cells. With this knowledge in mind, by controlling the tissue-specific patterns of mechanical forces in the scaffolds, we may further improve the regulation of homing, the differentiation, and the fate of transplanted stem cells.

Nanobody-based therapeutics against colorectal cancer: Precision therapies based on the personal mutanome profile and tumor neoantigens.

Monoclonal antibodies and vaccines have widely been studied for the immunotherapy of cancer, while their large size appears to limit their functionality in solid tumors, in large part due to unique properties of tumor microenvironment such as high pressure of tumor interstitial fluid. To tackle such limitations, smaller formats of antibodies have been developed, including antigen-binding fragments, single-chain variable fragments, single variable domain of camelid antibody (so-called nanobody (Nb) or VHH). Of these, Nbs offer great immunotherapy potentials because of their advantageous physicochemical and pharmacological features, including small size, high stability, and excellent tissue penetration. Besides, the therapeutic impacts of Nbs can be improved by their modifications and functionalizations (e.g., PEGylation and conjugation to the Fc domain, peptide tags, drugs, toxins, aptamers, and radionuclides). This review aims to provide comprehensive insights into key signaling networks of colorectal cancer and discuss Nb-based precision immunotherapy of colorectal cancer.

Targeted enzyme delivery systems in lysosomal disorders: an innovative form of therapy for mucopolysaccharidosis.

Mucopolysaccharidoses (MPSs), which are inherited lysosomal storage disorders caused by the accumulation of undegraded glycosaminoglycans, can affect the central nervous system (CNS) and elicit cognitive and behavioral issues. Currently used enzyme replacement therapy methodologies often fail to adequately treat the manifestations of the disease in the CNS and other organs such as bone, cartilage, cornea, and heart. Targeted enzyme delivery systems (EDSs) can efficiently cross biological barriers such as blood-brain barrier and provide maximal therapeutic effects with minimal side effects, and hence, offer great clinical benefits over the currently used conventional enzyme replacement therapies. In this review, we provide comprehensive insights into MPSs and explore the clinical impacts of multimodal targeted EDSs.

Pathogenicity of Helicobacter pylori in cancer development and impacts of vaccination.

Helicobacter pylori affect around 50% of the population worldwide. More importantly, the gastric infection induced by this bacterium is deemed to be associated with the progression of distal gastric carcinoma and gastric mucosal lymphoma in the human. H. pylori infection and its prevalent genotype significantly differ across various geographical regions. Based on numerous virulence factors, H. pylori can target different cellular proteins to modulate the variety of inflammatory responses and initiate numerous "hits" on the gastric mucosa. Such reactions lead to serious complications, including gastritis and peptic ulceration, gastric cancer and gastric mucosa-associated lymphoid structure lymphoma. Therefore, H. pylori have been considered as the type I carcinogen by the Global Firm for Research on Cancer. During the two past decades, different reports revealed that H. pylori possess oncogenic potentials in the gastric mucosa through a complicated interplay between the bacterial factors, various facets, and the environmental factors. Accordingly, numerous signaling pathways could be triggered in the development of gastrointestinal diseases (e.g., gastric cancer). Therefore, the main strategy for the treatment of gastric cancer is controlling the disease far before its onset using preventive/curative vaccination. Increasing the efficiency of vaccines may be achieved by new trials of vaccine modalities, which is used to optimize the cellular immunity. Taken all, H. pylori infection may impose severe complications, for resolving of which extensive researches are essential in terms of immune responses to H. pylori. We envision that H. pylori-mediated diseases can be controlled by advanced vaccines and immunotherapies.

Selection of a fully human single domain antibody specific to Helicobacter pylori urease.

Helicobacter pylori bacteria are involved in gastroduodenal disorders, including gastric adenocarcinoma. Since the current therapies encounter with some significant shortcomings, much attention has been paid to the development of new alternative diagnostic and treatment modalities such as immunomedicines to target H. pylori. Having used phage display technology, we isolated fully humane small antibody (Ab) fragment (VL) against the Flap region of urease enzyme of H. pylori to suppress its enzymatic activity. Solution biopanning (SPB) and screening process against a customized biotinylated peptide corresponding to the enzyme Flap region resulted in the selection of VL single domain Abs confirmed by the enzyme-linked immunosorbent assay (ELISA), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and Western blotting. The selected Ab fragments showed a high affinity with a KD value of 97.8 × 10-9 and specificity to the enzyme with high inhibitory impact. For the first time, a VL single domain Ab was isolated by SPB process against a critical segment of H. pylori urease using a diverse semi-synthetic library. Based on our findings, the selected VL Ab fragments can be used for the diagnosis, imaging, targeting, and/or immunotherapy of H. pylori. Further, Flap region shows great potential for vaccine therapy.