Target-based Drug Research Articles

Reductionism and proxy failure: From neuroscience to target-based drug discovery.

Reductionist methodologies reduce phenomena to some of their lower-level components. Researchers gradually shift their focus away from observing the actual object of study toward investigating and optimizing such lower-level proxies. Following reductionism, these proxies progressively diverge further from the original object of study. We vividly illustrate this in the evolution of target-based drug discovery from rational and phenotypic drug discovery.

Target-Based Design, Synthesis, and Biological Evaluation of Novel 1,2,4-Triazolone Derivatives as Potential nAChR Modulators.

Novel agrochemicals have been successfully developed using target-based drug design (TBDD). To discover a novel, efficient, and highly selective nicotinic insecticide candidate, we developed a unified pharmacological model using TBDD by studying the binding modes of 11 nicotinic acetylcholine receptor (nAChR) modulators with acetylcholine binding protein (AChBP) targets for the first time. This model was used to design and develop a series of 1,2,4-triazolone derivatives. Bioassays demonstrated excellent insecticidal activities against Aphis glycines of compounds 4k (LC50 = 4.95 mg/L) and 4q (LC50 = 3.17 mg/L), and low toxicities to Apis mellifera. Additionally, compound 4q was stably bound to Aplysia californica AChBP, which was consistent with the pharmacological model obtained via molecular docking and molecular dynamics simulations. Therefore, compound 4q could be a potential lead candidate targeting nAChR. The explicit pharmacological model of nAChR modulators with Ac-AChBP in this study may facilitate the future rational design of eco-friendly nicotinic insecticides.

Identification of potent inhibitors for Leishmania donovani homoserine kinase: an integrated in silico and kinetic study

Leishmaniasis is caused by ∼20 species of Leishmania that affects millions in endemic areas. Available therapies are not sufficient to effectively control the disease, cause severe side effects and eventually lead to drug resistance, making the discovery of novel therapeutic molecules an immediate need. Molecular target-based drug discovery, where the target is a defined molecular gene, protein or a mechanism, is a rationale driven approach for novel therapeutics. Humans obtain the essential amino acid such as threonine from dietary sources, while Leishmania synthesize it de-novo. Enzymes of the threonine biosynthesis pathway, including the rate limiting Homoserine kinase (HSK) which converts L-homoserine into ortho-phospho homoserine are thus attractive targets for rationale driven therapy. The absence of HSK in humans and its presence in Leishmania donovani enhances the opportunity to exploit HSK as a molecular target for anti-leishmanials therapeutic development. In this study, we utilize structure-based high throughput drug discovery (SBDD), followed by biochemical validation and identified two potential inhibitors (RH00038 and S02587) from Maybridge chemical library that targets L. donovani HSK. These two inhibitors effectively induced the mortality of Leishmania donovani in both amastigote and promastigote stages, with one of them being specific to parasite and twice as effective as the standard therapeutic molecule.

Unrealized targets in the discovery of antibiotics for Gram-negative bacterial infections.

Advances in areas that include genomics, systems biology, protein structure determination and artificial intelligence provide new opportunities for target-based antibacterial drug discovery. The selection of a 'good' new target for direct-acting antibacterial compounds is the first decision, for which multiple criteria must be explored, integrated and re-evaluated as drug discovery programmes progress. Criteria include essentiality of the target for bacterial survival, its conservation across different strains of the same species, bacterial species and growth conditions (which determines the spectrum of activity of a potential antibiotic) and the level of homology with human genes (which influences the potential for selective inhibition). Additionally, a bacterial target should have the potential to bind to drug-like molecules, and its subcellular location will govern the need for inhibitors to penetrate one or two bacterial membranes, which is a key challenge in targeting Gram-negative bacteria. The risk of the emergence of target-based drug resistance for drugs with single targets also requires consideration. This Review describes promising but as-yet-unrealized targets for antibacterial drugs against Gram-negative bacteria and examples of cognate inhibitors, and highlights lessons learned from past drug discovery programmes.

Is Target-Based Drug Discovery Efficient? Discovery and "Off-Target" Mechanisms of All Drugs.

Target-based drug discovery is the dominant paradigm of drug discovery; however, a comprehensive evaluation of its real-world efficiency is lacking. Here, a manual systematic review of about 32000 articles and patents dating back to 150 years ago demonstrates its apparent inefficiency. Analyzing the origins of all approved drugs reveals that, despite several decades of dominance, only 9.4% of small-molecule drugs have been discovered through "target-based" assays. Moreover, the therapeutic effects of even this minimal share cannot be solely attributed and reduced to their purported targets, as they depend on numerous off-target mechanisms unconsciously incorporated by phenotypic observations. The data suggest that reductionist target-based drug discovery may be a cause of the productivity crisis in drug discovery. An evidence-based approach to enhance efficiency seems to be prioritizing, in selecting and optimizing molecules, higher-level phenotypic observations that are closer to the sought-after therapeutic effects using tools like artificial intelligence and machine learning.

Internal stimuli-responsive nanocarriers for controlled anti-cancer drug release: a review.

Cancer disease is one of the most frequent life-threatening, with a high fatality rate worldwide. However, recent immunotherapy studies in various tumours have yielded unsatisfactory outcomes, with just a few individuals experiencing long-term responses. To overcome these issues, nowadays internal stimuli-responsive nanocarriers have been widely exploited to transport a wide range of active substances, including peptides, genesand medicines. These nanosystems could be chemically adjusted to produce target-based drug release at the target location, minimizing pathological and physiological difficulties while increasing therapeutic efficiency. This review highlights the various types of internal stimuli-responsive nanocarriers and applications in cancer diagnosis. This study can provide inspiration and impetus for exploiting more promising internal stimuli-responsive nanosystems for drug delivery.

A Discursive Review of Recent Development and Patents on Glycerosomes.

To achieve a target-based drug delivery with minimal side effects, novel drug delivery systems are being continuously explored. Vesicular systems are one such system that can ameliorate the bioavailability of the encapsulated drug by delivering the drug at the targeted site and can minimize the side effect. The objective of this patent review is to provide a vivid description of glycerosomes and their applications. Glycerosomes are sphere-shaped versatile vesicles consisting of one or more phospholipid bilayers similar to liposomes but contain a high concentration of glycerol, which modifies the liposome bilayer fluidity. Glycerosomes can encapsulate both hydrophobic and hydrophilic drugs, which makes them the promising vehicle in the field of drug delivery. Most of the glycerosome formulations prepared were targeted for topical delivery and in particular, a cutaneous route where they have shown promising results. These vesicles are biocompatible and due to the high glycerol concentration, they have improved spreadability and penetrability. It is therefore imperative to explore the other topical routes such as ocular, vaginal, nasal, and rectal for delivery of drugs.

Discovery of first novel sigma/HDACi dual-ligands with a potent in vitro antiproliferative activity

Designing and discovering compounds for dual-target inhibitors is challenging to synthesize new, safer, and more efficient drugs than single-target drugs, especially to treat multifactorial diseases such as cancer. The simultaneous regulation of multiple targets might represent an alternative synthetic approach to optimize patient compliance and tolerance, minimizing the risk of target-based drug resistance due to the modulation of a few targets. To this end, we conceived for the first time the design and synthesis of dual-ligands σR/HDACi to evaluate possible employment as innovative candidates to address this complex disease. Among all synthesized compounds screened for several tumoral cell lines, compound 6 (Kiσ1R = 38 ± 3.7; Kiσ2R = 2917 ± 769 and HDACs IC50 = 0.59 µM) is the most promising candidate as an antiproliferative agent with an IC50 of 0.9 µM on the HCT116 cell line and no significant toxicity to normal cells. Studies of molecular docking, which confirmed the affinity over σ1R and a pan-HDACs inhibitory behavior, support a possible balanced affinity and activity between both targets.

Identification of novel carbonic anhydrase II receptor-targeting drugs for treating myocardial infarction through the mechanism of Xue-Fu-Zhu-Yu decoction

Myocardial infarction (MI) is a significant threat to human health and life. Xue-Fu-Zhu-Yu Decoction (XFZYD), a renowned traditional Chinese medicine prescription for treating myocardial infarction, is known to play a significant role in the management of MI. However, its mechanism of action remains unclear. Through network pharmacology analysis of compound-target interactions, we have identified Carbonic Anhydrase II (CA2) as a critical target for XFZYD in the treatment of MI. Subsequently, we will embark on a target-based drug design approach with a focus on CA2 as the key target: Pharmacophore modeling: Two pharmacophore models were developed and validated to screen for small molecules with CA2 inhibitory features. Virtual screening: Based on two pharmacophore models, small molecules with the property of binding to the CA2 target were screened from a virtual screening library. Molecular docking: Molecular docking was employed to identify small molecules with stable binding affinity to CA2. ADMET prediction: ADMET models were utilized to screen for small molecules with favorable pharmacological properties. Molecular dynamics: Molecular dynamics simulations were further conducted to analyze the binding modes of the selected small molecules with CA2, ultimately resulting in the identification of Ligand 3 and Ligand 5 as small molecule inhibitors targeting CA2. Finally, the mechanisms underlying the anti-MI effects were discussed. The primary objective of this article is to uncover the mechanism by which XFZYD acts on MI and utilize it for drug development. These findings provide novel avenues for the development of anti-MI drugs. Communicated by Ramaswamy H. Sarma

Unraveling the Potential of EphA4: A Breakthrough Target and Beacon of Hope for Neurological Diseases.

Erythropoietin-producing hepatocellular carcinoma A4 (EphA4) is a transmembrane receptor protein which is a part of the most prominent family of receptor tyrosine kinases (RTKs). It serves a crucial role in both physiological, biological, and functional states binding with their ligand like Ephrins. Its abundance in the majority of the body's systems has been reported. Moreover, it draws much attention in the CNS since it influences axonal and vascular guidance. Also, it has a widespread role at the pathological state of various CNS disorders. Reports suggest it obstructs axonal regeneration in various neurodegenerative diseases and neurological disorders. Although, neuro-regeneration is still an open challenge to the modern drug discovery community. Hence, in this review, we will provide information about the role of EphA4 in neurological diseases by which it may emerge as a therapeutic target for CNS disease. We will also provide a glance at numerous signaling pathways that activate or inhibit the EphA4-associated biological processes contributing to the course of neurodegenerative diseases. Thus, this work might serve as a basis for futuristic studies that are related to the target-based drug discovery in the field of neuro-regeneration. Pathological and physiological events associated with EphA4 and Ephrin upregulation and interaction.

Biological activities of 4H-thiochromen-4-one 1,1-dioxide derivatives against tropical disease parasites: A target-based drug design approach

A promising strategy for developing novel therapies against tropical diseases, including malaria, leishmaniasis, and trypanosomiasis, is to detect biological targets such as trypanothione reductase, a vital parasite enzyme that regulates oxidative stress. This enzyme is highly selective and conserved in the Trypanosotidae family and has an ortholog in the Plasmodium genus. Previous studies have established that an isosteric replacement of naphthoquinone's carbonyl group with a sulfone group leads to compounds with high bioactivity and selectivity (half-maximal inhibitory concentration = 3 μM against intracellular amastigotes of L. panamensis, selectivity index = 153 over monocytes U-937). In this study, we analyzed the reactive oxygen species (ROS) levels of parasites through indirect measurements of the tryparedoxin system after treatment with these isosteric compounds. This strategy proved that a significant increase in the ROS levels and strong mitochondrial perturbation led to the death of parasites due to cell homeostatic imbalance, confirming the compounds' effectiveness in disrupting this important metabolic pathway. To improve understanding of the parasite-molecule interaction, 27 new compounds were synthesized and assessed against parasites of the three principal tropical diseases (malaria, leishmaniasis, and trypanosomiasis), displaying an EC50 below 10 μM and good correlation with in-silico studies, indicating that the 4H-thiochromen-4-one 1,1-dioxide core is a special allosteric modulator. It can interact in the binding pocket through key amino acids like Ser-14, Leu-17, Trp-21, Ser-109, Tyr-110, and Met-113, leading to interhelical disruption.

DAIKON: A Data Acquisition, Integration, and Knowledge Capture Web Application for Target-Based Drug Discovery.

Primitive data organization practices struggle to deliver at the scale and consistency required to meet multidisciplinary collaborations in drug discovery. For effective data sharing and coordination, a unified platform that can collect and analyze scientific information is essential. We present DAIKON, an open-source framework that integrates targets, screens, hits, and manages projects within a target-based drug discovery portfolio. Its knowledge capture components enable teams to record subsequent molecules as their properties improve, facilitate team collaboration through discussion threads, and include modules that visually illustrate the progress of each target as it advances through the pipeline. It serves as a repository for scientists sourcing data from Mycobrowser, UniProt, PDB. The goal is to globalize several variations of the drug-discovery program without compromising local aspects of specific workflows. DAIKON is modularized by abstracting the database and creating separate layers for entities, business logic, infrastructure, APIs, and frontend, with each tier allowing for extensions. Using Docker, the framework is packaged into two solutions: daikon-server-core and daikon-client. Organizations may deploy the project to on-premises servers or VPC. Active-Directory/SSO is supported for user administration. End users can access the application with a web browser. Currently, DAIKON is implemented in the TB Drug Accelerator program (TBDA).

Investigation of Zika virus methyl transferase inhibitors using steered molecular dynamics

Zika virus (ZIKV) spread is considered a major public health threat by the World Health Organization (WHO). There are no vaccines or drugs available to control the infection of the Zika virus, therefore a highly effective medicinal molecule is urgently required. In this study, a computationally intensive investigation was performed to identify a potent natural compound that could inhibit the ZIKV NS5 methyltransferase. This research approach is based on target-based drug identification principles where the native inhibitor SAH (S-adenosylhomocysteine) of ZIKV NS5 methyltransferase was selected as a reference. High-throughput virtual screening and tanimoto similarity coefficient were applied to the natural compound library for ranking the potential candidates. The top five compounds were selected for interaction analysis, MD simulation, total binding free energy through MM/GBSA, and steered MD simulation. Among these compounds, Adenosine 5'-monophosphate monohydrate, Tubercidin, and 5-Iodotubercidin showed stable binding to the protein compared to the native compound, SAH. These three compounds also showed less fluctuations in RMSF in contrast to native compound. Additionally, the same interacting residues observed in SAH also made strong interactions with these three compounds. Adenosine 5'-monophosphate monohydrate and 5-Iodotubercidin had greater total binding free energies than the reference ligand. Moreover, the dissociation resistance of all three compounds was equivalent to that of the reference ligand. This study suggested binding properties of three-hit compounds that could be used to develop drugs against Zika virus infections. Communicated by Ramaswamy H. Sarma

Drug–Target Interaction Deep Learning-Based Model Identifies the Flavonoid Troxerutin as a Candidate TRPV1 Antagonist

Based on the advances made by artificial intelligence (AI) technologies in drug discovery, including target identification, hit molecule identification, and lead optimization, this study investigated natural compounds that could act as transient receptor potential vanilloid 1 (TRPV1) channel protein antagonists. Using a molecular transformer drug–target interaction (MT-DTI) model, troxerutin was predicted to be a TRPV1 antagonist at IC50 582.73 nM. In a TRPV1-overexpressing HEK293T cell line, we found that troxerutin antagonized the calcium influx induced by the TRPV1 agonist capsaicin in vitro. A structural modeling and docking experiment of troxerutin and human TRPV1 confirmed that troxerutin could be a TRPV1 antagonist. A small-scale clinical trial consisting of 29 participants was performed to examine the efficacy of troxerutin in humans. Compared to a vehicle lotion, both 1% and 10% w/v troxerutin lotions reduced skin irritation, as measured by skin redness induced by capsaicin, suggesting that troxerutin could ameliorate skin sensitivity in clinical practice. We concluded that troxerutin is a potential TRPV1 antagonist based on the deep learning MT-DTI model prediction. The present study provides a useful reference for target-based drug discovery using AI technology and may provide useful information for the integrated research field of AI technology and biology.

Abstract 5319: EU-OPENSCREEN - An open-access initiative in chemical biology to support anti-cancer drug discovery

Abstract Over the past two decades, an increasing number of small molecule drugs that target unique molecular changes underlying a specific cancer have been approved, and small molecule drugs represent a major therapeutic class for cancer treatment. Chemical ‘probes’ are also indispensable tools to advance our understanding of pathologies at the molecular and cellular level and to validate novel drug targets. A major bottleneck in identifying and developing these chemical compounds in academia is often access to robust disease-relevant assays, high-throughput screening platforms, comprehensive screening libraries, medicinal expertise for the hit-to-lead optimization. In order to democratize access to these resources for a broader scientific community, the publicly funded EU-OPENSCREEN (www.eu-openscreen.eu) initiative has been established with the aim to accelerate drug discovery efforts in an open-access setting in collaboration with researchers from academia and industry. EU-OPENSCREEN’s 30 expert centers offer access to their cancer target-based and phenotypic drug screening expertise, capabilities in developing disease-relevant assays and hit-to-lead optimization capabilities. The identified bioactive ‘hit’ compounds will be progressed into high-quality chemical starting points to be further developed into drug leads or chemical probes for the elucidation of mechanisms of cancer onset, progression, resistance and effects of drug therapy. All generated tool compounds and associated bioactivity data are made available to the global scientific community. Here we will present an overview of anti-cancer drug discovery projects of EU-OPENSCREEN and explain the opportunities and benefits for other international scientists to collaboratively develop novel anti-cancer drug leads and chemical probes. EU-OPENSCREEN receives funding from the European Union's Horizon 2020 and Horizon Europe research and innovation programs under grant agreements No 654248 and 101058620. Citation Format: Bahne Stechmann, Charlotte Wit. EU-OPENSCREEN - An open-access initiative in chemical biology to support anti-cancer drug discovery. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5319.

Synthesis of Novel 2,9-Disubstituted-6-morpholino Purine Derivatives Assisted by Virtual Screening and Modelling of Class I PI3K Isoforms.

The phosphatidylinositol-3 kinase (PI3K) pathway is one of the most frequently activated pathogenic signalling cascades in a wide variety of cancers. In the last 15 years, there has been an increase in the search for selective inhibitors of the four class I isoforms of PI3K, as they demonstrate better specificity and reduced toxicity in comparison to existing inhibitors. A ligand-based and target-based rational drug design strategy was employed to build a virtual library of 105 new compounds. Through this strategy, the four isoforms were compared regarding their activity pocket availability, amino acid sequences, and prone interactions. Additionally, a known active scaffold was used as a molecular base to design new derivatives. The virtual screening of the resultant library toward the four isoforms points to the obtention of 19 selective inhibitors for the PI3Kα and PI3Kγ targets. Three selective ligands, one for α-isoform and two for γ-isoform, present a ∆ (∆Gbinding) equal or greater than 1.5 Kcal/mol and were identified as the most promising candidates. A principal component analysis was used to establish correlations between the affinity data and some of the physicochemical and structural properties of the ligands. The binding modes and interactions established by the selective ligands in the active centre of the α and γ isoforms of PI3K were also investigated. After modelling studies, a synthetic approach to generate selective ligands was developed and applied in synthesising a set of derivatives that were obtained in good to excellent yield.

In Silico Binding of 2-Aminocyclobutanones to SARS-CoV-2 Nsp13 Helicase and Demonstration of Antiviral Activity

The landscape of viral strains and lineages of SARS-CoV-2 keeps changing and is currently dominated by Delta and Omicron variants. Members of the latest Omicron variants, including BA.1, are showing a high level of immune evasion, and Omicron has become a prominent variant circulating globally. In our search for versatile medicinal chemistry scaffolds, we prepared a library of substituted ɑ-aminocyclobutanones from an ɑ-aminocyclobutanone synthon (11). We performed an in silico screen of this actual chemical library as well as other virtual 2-aminocyclobutanone analogs against seven SARS-CoV-2 nonstructural proteins to identify potential drug leads against SARS-CoV-2, and more broadly against coronavirus antiviral targets. Several of these analogs were initially identified as in silico hits against SARS-CoV-2 nonstructural protein 13 (Nsp13) helicase through molecular docking and dynamics simulations. Antiviral activity of the original hits as well as ɑ-aminocyclobutanone analogs that were predicted to bind more tightly to SARS-CoV-2 Nsp13 helicase are reported. We now report cyclobutanone derivatives that exhibit anti-SARS-CoV-2 activity. Furthermore, the Nsp13 helicase enzyme has been the target of relatively few target-based drug discovery efforts, in part due to a very late release of a high-resolution structure accompanied by a limited understanding of its protein biochemistry. In general, antiviral agents initially efficacious against wild-type SARS-CoV-2 strains have lower activities against variants due to heavy viral loads and greater turnover rates, but the inhibitors we are reporting have higher activities against the later variants than the wild-type (10-20X). We speculate this could be due to Nsp13 helicase being a critical bottleneck in faster replication rates of the new variants, so targeting this enzyme affects these variants to an even greater extent. This work calls attention to cyclobutanones as a useful medicinal chemistry scaffold, and the need for additional focus on the discovery of Nsp13 helicase inhibitors to combat the aggressive and immune-evading variants of concern (VOCs).

Multifaceted Target Specificity Analysis as a Tool in Antimicrobial Drug Development: Type III Pantothenate Kinases as a Case Study.

The research and development of a new antimicrobial drug using a target-based approach raises the question of whether any resulting hits will also show activity against the homologous target in other closely related organisms. While an assessment of the similarities of the predicted interactions between the identified inhibitor and the various targets is an obvious first step in answering this question, no clear and consistent framework has been proposed for how this should be done. Here we developed Multifaceted Target Specificity Analysis (MTSA) and applied it to type III pantothenate kinase (PanKIII ) - an essential enzyme required for coenzyme A biosynthesis in a wide range of pathogenic bacteria - as a case study to establish if targeting a specific organism's PanKIII would lead to a narrow- or broad-spectrum agent. We propose that MTSA is a useful tool and aid for directing new target-based antimicrobial drug development initiatives.

Discovery of a Potential Molluscicide Based on Protein PcRoo in Gill Cilia of Pomacea canaliculata.

In modern pesticide discovery, target-based drug design is an attractive and cost-effective approach. Previous studies found that protein rootletin (PcRoo) is a target protein of arecoline, when interacted with Pomacea canaliculata. In this study, we modeled the target protein through threading, and the binding energy between arecoline and protein PcRoo was calculated as -5.02 kcal/mol by molecular docking. Furthermore, two target compounds, baclofen and acedoben, with molluscicidal activity in theory were obtained by virtual screening in database DrugBank. The in vivo bioassay showed that baclofen could induce typical poisoning symptoms on P. canaliculata, which were characterized by weakness of foot muscles and loss of gill cilia, and the LC50 value was 16.2437 mg/L (72 h). Additionally, after 15 mg/L baclofen treatment, the oxygen consumption rate, ammonia excretion rate, and oxygen nitrogen ratio of P. canaliculata declined. Furthermore, the treatment of baclofen also decreased the gene expression level of PcRoo. These trends were the same as the changes after 5 mg/L arecoline treatment. The pharmacophore characteristics were further analyzed, and the results showed that the chemical structures of baclofen and arecoline were correlated in molluscicidal activity. These findings indicate that baclofen has the potential to be used as a molluscicide in agricultural production, and other new molluscicides may be obtained by virtual screening based on protein PcRoo.

Design, synthesis and biological evaluation of novel phenylfuran-bisamide derivatives as P-glycoprotein inhibitors against multidrug resistance in MCF-7/ADR cell

The co-administration of anticancer drugs and P-glycoprotein (P-gp) inhibitors was a treatment strategy to surmount multidrug resistance (MDR) in anticancer chemotherapy. In this study, novel phenylfuran-bisamide derivatives were designed as P-gp inhibitors based on target-based drug design, and 31 novel compounds were synthesized and screened on MCF-7/ADR cells. The result of bioassay revealed that compound y12d exhibited low cytotoxicity and promising MDR reversal activity (IC50 = 0.0320 μM, reversal fold = 1163.0), 3.64-fold better than third-generation P-gp inhibitor tariquidar (IC50 = 0.1165 μM, reversal fold = 319.3). The results of Western blot and rhodamine 123 accumulation verified that compound y12d exhibited excellent MDR reversal activity by inhibiting the efflux function of P-gp but not expression. Furthermore, molecular docking showed that compound y12d bound to target P-gp by forming the double H-bond interactions with residue Gln 725. These results suggest that compound y12d might be a potential MDR reveal agent acting as a P-gp inhibitor in clinical therapeutics, and provide insight into design strategy and skeleton optimization for the development of P-gp inhibitors.