Tool For Drug Development Research Articles

Novel Bioactive Compounds from Marine Sources as a Tool for Drug Development

The marine environment is a relatively unexplored source of functional ingredients that can be used in food processing, storage, and fortification in a variety of ways. Marine microorganisms are a possible source of novel bioactive chemicals with potential human utility. Some of these microbes can live in the harsh marine environments, resulting in complex compounds with unique biological properties that can be used in several industrial and biotechnological applications. So far, several marine microorganisms (fungi, myxomycetes, bacteria, and microalgae) have been isolated that produce antioxidant, antibacterial, apoptotic, antitumoral, and antiviral chemicals. Furthermore, it emphasizes the enormous potential for marine microbes to produce very important bioactive chemicals. They are used for new drug developments extensively across the world. Marine pharmacology offers the scope for research on these drugs of marine origin. Few institutes in India offer such opportunities which can help us in the quest for new drugs. This is an extensive review of the drugs developed and the potential new drug candidates from marine origin along with the opportunities for research on marine derived products. It also gives the information about the institutes in India which offer marine pharmacology related courses. Keywords: Anticancer, Bryostatin, Cytarabine, Keyhole limpet hemocyanin, Mariculture, Sponge, Ziconotide

GCMM: graph convolution network based on multimodal attention mechanism for drug repurposing

BackgroundThe main focus of in silico drug repurposing, which is a promising area for using artificial intelligence in drug discovery, is the prediction of drug–disease relationships. Although many computational models have been proposed recently, it is still difficult to reliably predict drug–disease associations from a variety of sources of data.ResultsIn order to identify potential drug–disease associations, this paper introduces a novel end-to-end model called Graph convolution network based on a multimodal attention mechanism (GCMM). In particular, GCMM incorporates known drug–disease relations, drug–drug chemical similarity, drug–drug therapeutic similarity, disease–disease semantic similarity, and disease–disease target-based similarity into a heterogeneous network. A Graph Convolution Network encoder is used to learn how diseases and drugs are embedded in various perspectives. Additionally, GCMM can enhance performance by applying a multimodal attention layer to assign various levels of value to various features and the inputting of multi-source information.Conclusion5 fold cross-validation evaluations show that the GCMM outperforms four recently proposed deep-learning models on the majority of the criteria. It shows that GCMM can predict drug–disease relationships reliably and suggests improvement in the desired metrics. Hyper-parameter analysis and exploratory ablation experiments are also provided to demonstrate the necessity of each module of the model and the highest possible level of prediction performance. Additionally, a case study on Alzheimer’s disease (AD). Four of the five medications indicated by GCMM to have the highest potential correlation coefficient with AD have been demonstrated through literature or experimental research, demonstrating the viability of GCMM. All of these results imply that GCMM can provide a strong and effective tool for drug development and repositioning.

Discovery of Potent Cholinesterase Inhibition-Based Multi-Target-Directed Lead Compounds for Synaptoprotection in Alzheimer's Disease.

Drug development efforts that focused on single targets failed to provide effective treatment for Alzheimer's disease (AD). Therefore, we designed cholinesterase inhibition (ChEI)-based multi-target-directed ligands (MTDLs) to simultaneously target AD-related receptors. We built a library of 70 compounds, sequentially screened for ChEI, and determined σ1R, σ2R, NMDAR-GluN2B binding affinities, and P2X7R antagonistic activities. Nine fulfilled in silico drug-likeness criteria and did not display toxicity in three cell lines. Seven displayed cytoprotective activity in two stress-induced cellular models. Compared to donepezil, six showed equal/better synaptic protection in a zebrafish model of acute amyloidosis-induced synaptic degeneration. Two P2X7R antagonists alleviated the activation state of microglia in vivo. Permeability studies were performed, and four did not inhibit CYP450 3A4, 2D6, and 2C9. Therefore, four ChEI-based lead MTDLs are promising drug candidates for synaptic integrity protection and could serve as disease-modifying AD treatment. Our study also proposes zebrafish as a useful preclinical tool for drug discovery and development.

Enhancing Techniques for Determining Inflammatory Edema Formation and Neutrophil Accumulation in Murine Skin

Inflammatory edema formation and polymorphonuclear leukocyte (neutrophil) accumulation are common components of cutaneous vascular inflammation, and their assessment is a powerful investigative and drug development tool but typically requires independent cohorts of animals to assess each. We have established the use of a mathematical formula to estimate the ellipsoidal-shaped volume of the edematous wheal or bleb after intradermal injections of substances in mice pretreated intravenously with Evans blue dye (which binds to plasma albumin) to act as an edema marker. Whereas previous extraction of Evans blue dye with formamide is suitable for all strains of mice, we report this quicker and more reliable assessment of edema volume in situ. This therefore allows neutrophil accumulation to be assessed from the same mouse using the myeloperoxidase assay. Importantly, we examined the influence of Evans blue dye on the spectrometry readout at the wavelength at which myeloperoxidase activity is measured. The results indicate that it is feasible to quantify edema formation and neutrophil accumulation in the same mouse skin site. Thus, we show techniques that can assess edema formation and neutrophil accumulation at the same site in the same mouse, allowing paired measurements and reducing the total use of mice by 50%.

Protective effect of fish oil targeting hadhaa (3-ketoacyl-CoA thiolase, alpha subunit a and hadhb (3-ketoacyl-CoA thiolase, beta subunit) against high cholesterol diet (HCD) induced atherosclerosis on Zebrafish

Currently a high mortality rate is observed due to heart diseases such as atherosclerosis and myocardial infarction, which are mainly caused due to high cholesterol. More novel drugs are needed to replace the currently available drugs to reduce the side effects. Zebrafish are an effective model for lipid metabolism studies in vertebrates. Because it shares 80% of diseases related genes similarity with humans. Zebrafish (Male) were fed with high cholesterol diet to induce atherosclerosis and the cholesterol levels of the Zebrafish are measured. Further, the m RNA expression of hadhaa and hadhb genes in the liver, intestine, and skeletal muscle of Zebrafish are studied. Finally, the atherosclerotic protective effects of fish oil are studied using fluorescence imaging of EGPF Zebrafish larvae and using nail red staining. In this study, we evaluated the effect of a fish oil-rich diet, dietary lipids reported having anti-obesity effects in animals, or cholesterol build-up in Zebrafish. Zebrafish were fed a high cholesterol diet containing 20% (w/w) fish oil. Zebrafish in the fish oil-fed group has 40% less cholesterol build-up than in the regular diet group. The genes encoding beta oxidases such as hadhaa and hadhb are expressed 2 fold higher in the gut of the fish oil treated group. Thiolase/enoyl coenzyme A-hydrates were 20% higher in the test (fish oil) diet group than in the normal diet (pellets) group (p < 0.05). The expression of the fatty acid synthesis gene (fasn) in the liver was considerably reduced in the fish oil group compared to the normal diet group (p < 0.05). These results show that fish oil may reduce cholesterol accumulation and might be used as an effective tool for anti-atherosclerotic drug development and on functional foods with further research. • In this research article we have discussed the possible effect of fish oil over HCD fed Zebrafish. • We have observed a positive effect on fish oil fed Zebrafish. • We suggest that the fish oil may have ability to reduce cholesterol accumulation and blood cholesterol level reduction. • All fishes subjected to the study are male Zebrafish.

Synthesis and evaluation of a novel analgesic conotoxin Lt7b that inhibits calcium currents and increases sodium currents

Conotoxins are promising neuropharmacological tools and drug candidates due to their high efficiency and specificity in targeting ion channels or neurotransmitter receptors. In this study, a novel O2‐superfamily conotoxin, Lt7b, was synthesized and its pharmacological functions were evaluated. Lt7b with three modified amino acids and three disulfide bonds was successfully synthesized. CD spectra showed that Lt7b had a typical α‐helix in the secondary structure. Patch clamp experiments on rat DRG neurons showed that Lt7b could significantly inhibit calcium currents with an IC50 value of 856 ± 95 nM. Meanwhile, 10 μM Lt7b could significantly increase the sodium currents by 77 ± 8%, but it had no obvious effects on the potassium currents in DRG neurons. In addition, patch clamp experiments on ion channel subtypes showed that 10 μM Lt7b could inhibit 7.0 ± 1.2%, 8.0 ± 1.5%, 4.6 ± 3.4%, and 9.5 ± 0.1% of the hCav1.2, hCav2.1, hCav2.2, and hCav3.2 currents, respectively, while it did not increase the rNav1.7, rNav1.8, hNav1.5, hNav1.7, and hNav1.8 currents. Lt7b had no obvious toxicity to HaCaT and ND7/23 cells up to 1 mM and significantly increased the pain threshold at the testing time of 0.5–4 h in a dose‐dependent manner in the mouse hotplate assay. This novel conotoxin Lt7b may be a useful tool for ion channel studies and analgesic drug development.

A merged molecular representation deep learning method for blood–brain barrier permeability prediction

The ability of a compound to permeate across the blood-brain barrier (BBB) is a significant factor for central nervous system drug development. Thus, for speeding up the drug discovery process, it is crucial to perform high-throughput screenings to predict the BBB permeability of the candidate compounds. Although experimental methods are capable of determining BBB permeability, they are still cost-ineffective and time-consuming. To complement the shortcomings of existing methods, we present a deep learning-based multi-model framework model, called Deep-B3, to predict the BBB permeability of candidate compounds. In Deep-B3, the samples are encoded in three kinds of features, namely molecular descriptors and fingerprints, molecular graph and simplified molecular input line entry system (SMILES) text notation. The pre-trained models were built to extract latent features from the molecular graph and SMILES. These features depicted the compounds in terms of tabular data, image and text, respectively. The validation results yielded from the independent dataset demonstrated that the performance of Deep-B3 is superior to that of the state-of-the-art models. Hence, Deep-B3 holds the potential to become a useful tool for drug development. A freely available online web-server for Deep-B3 was established at http://cbcb.cdutcm.edu.cn/deepb3/, and the source code and dataset of Deep-B3 are available at https://github.com/GreatChenLab/Deep-B3.

Structure of a Promiscuous Thioesterase Domain Responsible for Branching Acylation in Polyketide Biosynthesis.

Thioesterases (TEs) are fundamentally important enzymes present in all bacteria and eukaryotes, where they have conserved functions in fatty acid biosynthesis and secondary metabolism. This work provides the first structural insights into a functionally distinct group of TEs that perform diverse acylations in polyketide and peptide biosynthesis (TEB s). Structural analysis of the oocydin (OocS) TEB domain facilitated identification and engineering of the active site to modulate acyl-group acceptance. In this way, we achieved higher reactivity using a structure-based approach, building a foundation for biocatalytic development of TEB -mediated O-acylation, a modification known to improve the bioactivity of oocydin-type polyketides. Lastly, the promiscuity of the OocS TEB motivated us to investigate, and ultimately provide evidence for, the production of longer chain branched oocydins in the native host Serratia plymuthica 4Rx13. This work frames the OocS TEB and homologs as invaluable synthetic biology tools for polyketide drug development.

Structure of a Promiscuous Thioesterase Domain Responsible for Branching Acylation in Polyketide Biosynthesis

Thioesterases (TEs) are fundamentally important enzymes present in all bacteria and eukaryotes, where they have conserved functions in fatty acid biosynthesis and secondary metabolism. This work provides the first structural insights into a functionally distinct group of TEs that perform diverse acylations in polyketide and peptide biosynthesis (TEBs). Structural analysis of the oocydin (OocS) TEB domain facilitated identification and engineering of the active site to modulate acyl-group acceptance. In this way, we achieved higher reactivity using a structure-based approach, building a foundation for biocatalytic development of TEB-mediated O-acylation, a modification known to improve the bioactivity of oocydin-type polyketides. Lastly, the promiscuity of the OocS TEB motivated us to investigate, and ultimately provide evidence for, the production of longer chain branched oocydins in the native host Serratia plymuthica 4Rx13. This work frames the OocS TEB and homologs as invaluable synthetic biology tools for polyketide drug development.

Palmitoylation of Voltage-Gated Ion Channels.

Protein lipidation is one of the most common forms of posttranslational modification. This alteration couples different lipids, such as fatty acids, phospho- and glycolipids and sterols, to cellular proteins. Lipidation regulates different aspects of the protein’s physiology, including structure, stability and affinity for cellular membranes and protein–protein interactions. In this scenario, palmitoylation is the addition of long saturated fatty acid chains to amino acid residues of the proteins. The enzymes responsible for this modification are acyltransferases and thioesterases, which control the protein’s behavior by performing a series of acylation and deacylation cycles. These enzymes target a broad repertoire of substrates, including ion channels. Thus, protein palmitoylation exhibits a pleiotropic role by differential modulation of the trafficking, spatial organization and electrophysiological properties of ion channels. Considering voltage-gated ion channels (VGICs), dysregulation of lipidation of both the channels and the associated ancillary subunits correlates with the development of various diseases, such as cancer or mental disorders. Therefore, a major role for protein palmitoylation is currently emerging, affecting not only the dynamism and differential regulation of a moiety of cellular proteins but also linking to human health. Therefore, palmitoylation of VGIC, as well as related enzymes, constitutes a novel pharmacological tool for drug development to target related pathologies.

Quantitative electroencephalography parameters as neurophysiological biomarkers of schizophrenia-related deficits: A Phase II substudy of patients treated with iclepertin (BI 425809)

Patients with schizophrenia experience cognitive impairment related to neural network dysfunction and deficits in sensory processing. These deficits are thought to be caused by N-methyl-D-aspartate receptor hypofunction and can be assessed in patient populations using electroencephalography (EEG). This substudy from a Phase II, randomized, double-blind, placebo-controlled, parallel-group study investigating the safety and efficacy of the novel glycine transporter-1 inhibitor, iclepertin (BI 425809), assessed the potential of EEG parameters as clinically relevant biomarkers of schizophrenia and response to iclepertin treatment. Eligible patients were randomized to once-daily add-on iclepertin (2, 5, 10, or 25 mg), or placebo (1:1:1:1:2 ratio) for 12 weeks. EEG data were recorded from a subgroup of patients (n = 79) at baseline and end of treatment (EoT). EEG parameters of interest were mismatch negativity (MMN), auditory steady-state response (ASSR), and resting state gamma power, and their correlations with clinical assessments. At baseline, MMN and ASSR exhibited consistent correlations with clinical assessments, indicating their potential value as neurophysiological biomarkers of schizophrenia-related deficits. ASSR measures were positively correlated to the MATRICS Consensus Cognitive Battery overall and neurocognitive composite scores; MMN amplitude was positively correlated with Positive and Negative Syndrome Scale scores. However, correlations between change from baseline (CfB) at EoT in clinical assessments, and baseline or CfB at EoT for EEG parameters were modest and inconsistent between dose groups, which might indicate low potential of these EEG parameters as predictive and treatment response biomarkers. Further methodological refinement is needed to establish EEG parameters as useful drug development tools for schizophrenia.

Liposomes: preparation and characterization with a special focus on the application of capillary electrophoresis.

Liposomes are nowadays a matter of tremendous interest. Due to their amphiphilic character, various substances with different properties can be incorporated into them and they are especially suitable as a model system for controlled transport of bioactive substances and drugs to the final destination in the body; for example, COVID-19 vaccines use liposomes as a carrier of mRNA. Liposomes mimicking composition of various biological membranes can be prepared with a proper choice of the lipids used, which proved to be important tool in the early drug development. This review deals with commonly used methods for the preparation and characterization of liposomes which is essential for their later use. The alternative capillary electrophoresis methods for physico-chemical characterization such as determination of membrane permeability of liposome, its size and charge, and encapsulation efficiency are included. Two different layouts using liposomes to yield more efficient separation of various analytes are also presented, capillary electrochromatography, and liposomal electrokinetic chromatography.Graphical abstract

Development and validation of an LC-MS/MS method for the quantification of fascin proteins in human serum.

Background: Fascin is an actin-bundling protein that has been linked to tumor cell migration, invasion, metastasis, disease progression and mortality, thus serving as a novel cancer biomarker. Bioanalytical methods to measure fascin in biological matrices are sparsely reported, while accurate quantitation of fascin levels may lend support for fascin as a promising therapeutic target. Method: An LC-MS/MS-based method involving protein precipitation, enzymatic digestion and solid phase extraction was developed and validated for the quantitation of fascin in human serum. Linearity over a calibration range of 5-500ng/ml with aLLOQ of 5ng/ml, great accuracy and precision, excellent parallelismas well as high extraction recovery were achieved. Conclusion: This method provides a valuable tool for anticancer drug development and cancer treatment.

Stakeholders’ views on drug development: the congenital disorders of glycosylation community perspective

BackgroundCongenital disorders of glycosylation (CDG) are a large family of rare genetic diseases for which therapies are virtually nonexistent. However, CDG therapeutic research has been expanding, thanks to the continuous efforts of the CDG medical/scientific and patient communities. Hence, CDG drug development is a popular research topic. The main aim of this study was to understand current and steer future CDG drug development and approval by collecting and analysing the views and experiences of the CDG community, encompassing professionals and families. An electronic (e-)survey was developed and distributed to achieve this goal.ResultsA total of 128 respondents (46 CDG professionals and 82 family members), mainly from Europe and the USA, participated in this study. Most professionals (95.0%) were relatively familiar with drug development and approval processes, while CDG families revealed low familiarity levels, with 8.5% admitting to never having heard about drug development. However, both stakeholder groups agreed that patients and families make significant contributions to drug development and approval. Regarding their perceptions of and experiences with specific drug development and approval tools, namely biobanks, disease models, patient registries, natural history studies (NHS) and clinical trials (CT), the CDG community stakeholders described low use and participation, as well as variable familiarity. Additionally, CDG professionals and families shared conflicting views about CT patient engagement and related information sharing. Families reported lower levels of involvement in CT design (25.0% declared ever being involved) and information (60.0% stated having been informed) compared to professionals (60.0% and 85.7%, respectively). These contrasting perceptions were further extended to their insights and experiences with patient-centric research. Finally, the CDG community (67.4% of professionals and 54.0% of families) reported a positive vision of artificial intelligence (AI) as a drug development tool. Nevertheless, despite the high AI awareness among CDG families (76.8%), professionals described limited AI use in their research (23.9%).ConclusionsThis community-centric study sheds new light on CDG drug development and approval. It identifies educational, communication and research gaps and opportunities for CDG professionals and families that could improve and accelerate CDG therapy development.

Decoding kinase-adverse event associations for small molecule kinase inhibitors

Small molecule kinase inhibitors (SMKIs) are being approved at a fast pace under expedited programs for anticancer treatment. In this study, we construct a multi-domain dataset from a total of 4638 patients in the registrational trials of 16 FDA-approved SMKIs and employ a machine-learning model to examine the relationships between kinase targets and adverse events (AEs). Internal and external (datasets from two independent SMKIs) validations have been conducted to verify the usefulness of the established model. We systematically evaluate the potential associations between 442 kinases with 2145 AEs and made publicly accessible an interactive web application “Identification of Kinase-Specific Signal” (https://gongj.shinyapps.io/ml4ki). The developed model (1) provides a platform for experimentalists to identify and verify undiscovered KI-AE pairs, (2) serves as a precision-medicine tool to mitigate individual patient safety risks by forecasting clinical safety signals and (3) can function as a modern drug development tool to screen and compare SMKI target therapies from the safety perspective.

225 Identification of meaningful aspects of health connected to the symptom of nocturnal scratching in patients with atopic dermatitis

Substantial work is underway across both pharmaceutical companies and digital product manufacturers to apply digital technologies to better measure symptoms in acute dermatologic conditions. To date, among the more advanced and promising applications of digital clinical measures as a drug development tool is nocturnal scratch. Novel digital clinical measures could provide an additional tool in answering the need for improved, precise, long-term quantitative measures of nocturnal scratching. In this work, a consortium of industry, patient advocacy and non-profit organizations came together to develop a mixed methods study to explore patient experience with nocturnal scratch.

Biomarkers for Alzheimer's Disease: Context of Use, Qualification, and Roadmap for Clinical Implementation.

Background and Objectives: The US Food and Drug Administration (FDA) defines a biomarker as a characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or responses to an exposure or intervention. Biomarkers may be used in clinical care or as drug development tools (DDTs) in clinical trials. The goal of this review and perspective is to provide insight into the regulatory guidance for the use of biomarkers in clinical trials and clinical care. Materials and Methods: We reviewed FDA guidances relevant to biomarker use in clinical trials and their transition to use in clinical care. We identified instructive examples of these biomarkers in Alzheimer’s disease (AD) drug development and their application in clinical practice. Results: For use in clinical trials, biomarkers must have a defined context of use (COU) as a risk/susceptibility, diagnostic, monitoring, predictive, prognostic, pharmacodynamic, or safety biomarker. A four-stage process defines the pathway to establish the regulatory acceptance of the COU for a biomarker including submission of a letter of intent, description of the qualification plan, submission of a full qualification package, and acceptance through a qualification recommendation. Biomarkers used in clinical care may be companion biomarkers, in vitro diagnostic devices (IVDs), or laboratory developed tests (LDTs). A five-phase biomarker development process has been proposed to structure the biomarker development process. Conclusions: Biomarkers are increasingly important in drug development and clinical care. Adherence to regulatory guidance for biomarkers used in clinical trials and patient care is required to advance these important drug development and clinical tools.

A REVIEW ON CONTROLLED RELEASE BEADS OF ANTI-MICROBIAL DRUG

Alginate and chitosan polymers are widely used in the preparation of drug release. These two polymers can be used together or separately to form modified drug-loaded release beads. A method of ionotropic gelation and subtle modification in various ways is used to fix these beads of different characteristics. Bead characteristics such as morphology, buoyancy, inflammatory environment, drug efficacy, marketing, and liberal behavior are important and the therapeutic use of various bead modifications can be great for underwater soluble drugs, half-life biological Health, requires direct organ guidance, and has natural protein. The need for longer and better control over drug administration has increased the need for stitched polymers. Hydrocolloids such as alginate can play an important role in the production of a controlled by-product. At low pH the flow of, alginic acid leads to the formation of a high-viscosity ‘‘acid gel.’’ Alginate is also easily applied to the gel in the presence of a divalent cation like calcium ion. This review discusses the current use the future opportunities for alginate as a tool in drug development. Keywords: Alginate, chitosan, Controlled Release, Drug Delivery, ionotropic gelation, beads

A REVIEW ON TRANSDERMAL DRUG DEIVERY SYSTEM

Alginate and chitosan polymers are widely used in the preparation of drug release. These two polymers can be used together or separately to form modified drug-loaded release beads. A method of ionotropic gelation and subtle modification in various ways is used to fix these beads of different characteristics. Bead characteristics such as morphology, buoyancy, inflammatory environment, drug efficacy, marketing, and liberal behavior are important and the therapeutic use of various bead modifications can be great for underwater soluble drugs, half-life biological Health, requires direct organ guidance, and has natural protein. The need for longer and better control over drug administration has increased the need for stitched polymers. Hydrocolloids such as alginate can play an important role in the production of a controlled by-product. At low pH the flow of, alginic acid leads to the formation of a high-viscosity ‘‘acid gel.’’ Alginate is also easily applied to the gel in the presence of a divalent cation like calcium ion. This review discusses the current use the future opportunities for alginate as a tool in drug development. Keywords: Alginate, chitosan, Controlled Release, Drug Delivery, ionotropic gelation, beads.

Identifying and characterising sources of variability in digital outcome measures in Parkinson’s disease

Smartphones and wearables are widely recognised as the foundation for novel Digital Health Technologies (DHTs) for the clinical assessment of Parkinson’s disease. Yet, only limited progress has been made towards their regulatory acceptability as effective drug development tools. A key barrier in achieving this goal relates to the influence of a wide range of sources of variability (SoVs) introduced by measurement processes incorporating DHTs, on their ability to detect relevant changes to PD. This paper introduces a conceptual framework to assist clinical research teams investigating a specific Concept of Interest within a particular Context of Use, to identify, characterise, and when possible, mitigate the influence of SoVs. We illustrate how this conceptual framework can be applied in practice through specific examples, including two data-driven case studies.