Structure-based Drug Design Approach Research Articles

Pan-Transcriptional Enhanced Associated Domain Palmitoylation Pocket Covalent Inhibitor.

In the Hippo signaling pathway, the palmitoylated transcriptional enhanced associated domain (TEAD) protein interacts with the coactivator Yes-associated protein/PDZ-binding motif, leading to transcriptional upregulation of oncogenes such as Ctgf and Cyr61. Consequently, targeting the palmitoylation sites of TEAD has emerged as a promising strategy for treating TEAD-dependent cancers. Compound 1 was identified using a structure-based drug design approach, leveraging the molecular insights gained from the known TEAD palmitoylation site inhibitor, K-975. Optimization of the initial hit compound resulted in the development of compound 3, a covalent pan-TEAD inhibitor characterized by high potency and oral bioavailability.

Structural optimization and bioactivity evaluation of 2-(Methylcarbonylamino) thiazole derivatives as novel PDE4B inhibitors

Phosphodiesterase-4 (PDE4) is a protease belonging to the phosphodiesterase family, with a specific function of hydrolyzing intracellular cyclic adenosine monophosphate (cAMP). PDE4 is widely distributed across various human tissues and cells, where it plays a pivotal role in modulating intracellular cAMP levels, particularly in immune and inflammatory cells. Consequently, PDE4 inhibitors have been proven to effectively dampen inflammatory responses in these cells, leading to a reduction in the release of pro-inflammatory factors such as lipid mediators, reactive oxygen species (ROS) hydrolases, cytokines, and chemokines. Despite the considerable interest from both academia and pharmaceutical industries in exploiting this target for drug development, only a handful of PDE4 inhibitors are available in the market. The aim of this study was to identify novel PDE4B inhibitors through a combined approach of computer-aided drug design, synthesis, and activity evaluation. The study implemented three phases of structure optimization from the hit compound MR9, which was previously obtained by virtual screening, with reference to structure-based drug design (SBDD) and ligand-based drug design (LBDD) approaches. The optimized compound MR9-302 (PDE4B IC50=2.02±0.2888 μM) exhibited enhanced inhibitory activity compared to MR9.

How to drug a cloud? Targeting intrinsically disordered proteins.

Biologically active proteins/regions without stable structure (i.e., intrinsically disordered proteins and regions (IDPs and IDRs)) are commonly found in all proteomes. They have a unique functional repertoire that complements the functionalities of ordered proteins and domains. IDPs/IDRs are multifunctional promiscuous binders capable of folding at interaction with specific binding partners on a template- or context-dependent manner, many of which undergo liquid-liquid phase separation, leading to the formation of membrane-less organelles and biomolecular condensates. Many of them are frequently related to the pathogenesis of various human diseases. All this defines IDPs/IDRs as attractive targets for the development of novel drugs. However, their lack of unique structures, multifunctionality, binding promiscuity, and involvement in unusual modes of action preclude direct use of traditional structure-based drug design approaches for targeting IDPs/IDRs, and make disorder-based drug discovery for these "protein clouds" challenging. Despite all these complexities there is continuing progress in the design of small molecules affecting IDPs/IDRs. This article describes the major structural features of IDPs/IDRs and the peculiarities of the disorder-based functionality. It also discusses the roles of IDPs/IDRs in various pathologies, and shows why the approaches elaborated for finding drugs targeting ordered proteins cannot be directly used for the intrinsic disorder-based drug design, and introduces some novel methodologies suitable for these purposes. Finally, it emphasizes that regardless of their multifunctionality, binding promiscuity, lack of unique structures, and highly dynamic nature, "protein clouds" are principally druggable. Significance Statement Intrinsically disordered proteins and regions are highly abundant in nature, have multiple important biological functions, are commonly involved in the pathogenesis of a multitude of human diseases, and are therefore considered as very attractive drug targets. Although dealing with these unstructured multifunctional protein/regions is a challenging task, multiple innovative approaches have been designed to target them by small molecules.

In Silico Design of Novel RGS2-Galpha-q Interaction Inhibitors with Anticancer Activity.

Regulators of G-protein signaling (RGS) are a family of approximately 30 proteins that bind to and deactivate the alpha subunits of G-proteins (Gα) by accelerating their GTP hydrolysis rates, which terminates G-protein coupled receptor (GPCR) signaling. Thus, RGS proteins are essential in regulating GPCR signaling, and most members are implicated as critical nodes in human diseases such as hypertension, depression, and others. Regulator of G-protein signaling 2 (RGS2), a member of the R4 family of RGS proteins, is overexpressed in many solid breast cancers, and its levels in prostate cancer significantly correlate with the metastatic stage and poor prognosis. We sought to develop RGS2 inhibitors as potential chemotherapeutic agents utilizing structure-based drug design approaches. Available structures of the RGS2-Gα complex were used to extract a pharmacophore model for searching chemical databases. Docking of identified hits to RGS2 as well as other RGS structures was used to screen the hits for potent and selective RGS2 inhibitors. Whole cell assays showed the top 10 ranking compounds, AJ-1-AJ-10, to inhibit RGS2-Gαq interactions. Differential scanning fluorimetry showed AJ-3 to bind RGS2 but not Gαq. All 10 compounds inhibited the growth of several RGS2 expressing cancers in cell culture assays. In addition, AJ-3 inhibited the migration of LNCaP prostate cancer cells in wound healing assays. This is the first group of RGS2 inhibitors identified by structure-based approaches and that show anticancer activity. These results highlight the potential RGS2 inhibitors have to be a new class of chemotherapeutic agents.

Exploring Marine-Derived Compounds: In Silico Discovery of Selective Ketohexokinase (KHK) Inhibitors for Metabolic Disease Therapy.

The increasing prevalence of metabolic diseases, including nonalcoholic fatty liver disease (NAFLD), obesity, and type 2 diabetes, poses significant global health challenges. Ketohexokinase (KHK), an enzyme crucial in fructose metabolism, is a potential therapeutic target due to its role in these conditions. This study focused on the discovery of selective KHK inhibitors using in silico methods. We employed structure-based drug design (SBDD) and ligand-based drug design (LBDD) approaches, beginning with molecular docking to identify promising compounds, followed by induced-fit docking (IFD), molecular mechanics generalized Born and surface area continuum solvation (MM-GBSA), and molecular dynamics (MD) simulations to validate binding affinities. Additionally, shape-based screening was conducted to assess structural similarities. The findings highlight several potential inhibitors with favorable ADMET profiles, offering promising candidates for further development in the treatment of fructose-related metabolic disorders.

Drug-like screening, molecular docking, molecular dynamics simulations, and binding free energies on the interaction of pyrazole derivatives as inhibitors of lysosomal storage disorders and anticancer activity

Lysosomal membrane proteins (LAMPs) are a primary target for treating tumors because of their essential role in the cancer life cycle. In this study, some computational approaches, including drug-like screening, molecular docking, and molecular dynamics (MD) simulation studies coupled with the binding free energy, have been conducted to explore the putative binding modes of pyrazole derivatives as inhibitors of lysosomal storage disorders. Certain pyrazole derivatives outperformed typical medications in molecular docking experiments against the LAMPs receptor; among other substances, molecules CID 44555488 and 45,487,645 were deemed ideal. Additionally, these ligands (CID 44555488 and 45,487,645) were projected to be orally accessible in humans after successfully passing five separate drug-likeness criteria. In the end, it was anticipated that these ligands, CID 44555488 and 45,487,645, would have minimal human toxicity and good ADMET properties, particularly in terms of GI absorption and the lack of P-gp interaction. Compounds CID 44555488 and 45,487,645 with high predicted binding affinities were subjected to further molecular dynamics simulations based on the molecular docking data, and their potential binding mechanisms were investigated. The study's description of the structure-based drug design approach will be very helpful in the creation of novel inhibitors with excellent selectivity and potency.

De novo design of SARS-CoV-2 main protease inhibitors with characteristic binding modes

The coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which spreads rapidly all over the world. The main protease (Mpro) is significant to the replication and transcription of viruses, making it an attractive drug target against coronaviruses. Here, we introduce a series of novel inhibitors which are designed de novo through structure-based drug design approach that have great potential to inhibit SARS-CoV-2 Mproinvitro. High-resolution structures show that these inhibitors form covalent bonds with the catalytic cysteine through the novel dibromomethyl ketone (DBMK) as a reactive warhead. At the same time, the designed phenyl group beside the DBMK warhead inserts into the cleft between H41 and C145 through π-π stacking interaction, splitting the catalytic dyad and disrupting proton transfer. This unique binding model provides novel clues for the cysteine protease inhibitor development of SARS-CoV-2 as well as other pathogens.

Discovery of JNJ-74856665: A Novel Isoquinolinone DHODH Inhibitor for the Treatment of AML.

Acute myelogenous leukemia (AML), a heterogeneous disease of the blood and bone marrow, is characterized by the inability of myeloblasts to differentiate into mature cell types. Dihydroorotate dehydrogenase (DHODH) is an enzyme well-known in the pyrimidine biosynthesis pathway and preclinical findings demonstrated that DHODH is a metabolic vulnerability in AML as inhibitors can induce differentiation across multiple AML subtypes. As a result of virtual screening and structure-based drug design approaches, a novel series of isoquinolinone DHODH inhibitors was identified. Further lead optimization afforded JNJ-74856665 as an orally bioavailable, potent, and selective DHODH inhibitor with favorable physicochemical properties selected for clinical development in patients with AML and myelodysplastic syndromes (MDS).

Structure-based design of multitargeting ChEs-MAO B inhibitors based on phenyl ring bioisosteres: AChE/BChE selectivity switch and drug-like characterization

A structure-based drug design approach was focused on incorporating phenyl ring heterocyclic bioisosteres into coumarin derivative 1, previously reported as potent dual AChE-MAO B inhibitor, with the aim of improving drug-like features. Structure-activity relationships highlighted that bioisosteric rings were tolerated by hMAO B enzymatic cleft more than hAChE. Interestingly, linker homologation at the basic nitrogen enabled selectivity to switch from hAChE to hBChE. In the present work, we identified thiophene-based isosteres 7 and 15 as dual AChE-MAO B (IC50 = 261 and 15 nM, respectively) and BChE-MAO B (IC50 = 375 and 20 nM, respectively) inhibitors, respectively. Both 7 and 15 were moderately water-soluble and membrane-permeant agents by passive diffusion (PAMPA-HDM). Moreover, they were able to counteract oxidative damage induced by both H2O2 and 6-OHDA in SH-SY5Y cells and predicted to penetrate into CNS in a cell-based model mimicking blood-brain barrier. Molecular dynamics (MD) simulations shed light on key differences in AChE and BChE recognition processes promoted by the basic chain homologation from 7 to 15.

Discovery of meisoindigo derivatives as noncovalent and orally available Mpro inhibitors: their therapeutic implications in the treatment of COVID-19

The progressive emergence of SARS-CoV-2 variants has necessitated the urgent exploration of novel therapeutic strategies to combat the COVID-19 pandemic. The SARS-CoV-2 main protease (Mpro) represents an evolutionarily conserved therapeutic target for drug discovery. This study highlights the discovery of meisoindigo (Mei), derived from the traditional Chinese medicine (TCM) Indigo naturalis, as a novel non-covalent and nonpeptidic Mpro inhibitor. Substantial optimizations and structure-activity relationship (SAR) studies, guided by a structure-based drug design approach, led to the identification of several Mei derivatives, including S5-27 and S5-28, exhibiting low micromolar inhibition against SARS-CoV-2 Mpro with high binding affinity. Notably, S5-28 provided significant protection against wild-type SARS-CoV-2 in HeLa-hACE2 cells, with EC50 up to 2.66 μM. Furthermore, it displayed favorable physiochemical properties and remarkable gastrointestinal and metabolic stability, demonstrating its potential as an orally bioavailable drug for anti-COVID-19 therapy. This research presents a promising avenue for the development of new antiviral agents, offering hope in the ongoing battle against COVID-19.

Structure-based drug design of DNA minor groove binders and evaluation of their antibacterial and anticancer properties

Antimicrobial and chemotherapy resistance are escalating medical problem of paramount importance. Yet, research for novel antimicrobial and anticancer agents remains lagging behind. With their reported medical applications, DNA minor groove binders (MGBs) are worthy of exploration. In this study, the approach of structure-based drug design was implemented to generate 11 MGB compounds including a novel class of bioactive alkyne-linked MGBs. The NCI screening protocol was utilized to evaluate the antitumor activity of the target MGBs. Furthermore, a variety of bactericidal, cytopathogenicity, MIC90, and cytotoxicity assays were carried out using these MGBs against 6 medically relevant bacteria: Salmonella enterica, Escherichia coli, Serratia marcescens, Bacillus cereus, Streptococcus pneumoniae and Streptococcus pyogenes. Moreover, molecular docking, molecular dynamic simulations, DNA melting, and isothermal titration calorimetry (ITC) analyses were utilized to explore the binding mode and interactions between the most potent MGBs and the DNA duplex d(CGACTAGTCG)2. NCI results showed that alkyne-linked MGBs (26 & 28) displayed the most significant growth inhibition among the NCI-60 panel. In addition, compounds MGB3, MGB4, MGB28, and MGB32 showed significant bactericidal effects, inhibited B. cereus and S. enterica-mediated cytopathogenicity, and exhibited low cytotoxicity. MGB28 and MGB32 demonstrated significant inhibition of S. pyogenes, whereas MGB28 notably inhibited S. marcescens and all four minor groove binders significantly inhibited B. cereus. The ability of these compounds to bind with DNA and distort its groove dimensions provides the molecular basis for the allosteric perturbation of proteins-DNA interactions by MGBs. This study shed light on the mechanism of action of MGBs and revealed the important structural features for their antitumor and antibacterial activities, which are important to guide future development of MGB derivatives as novel antibacterial and anticancer agents.

Investigating the bioactive compounds from Capsicum annum as a probable alternative therapy for prostate cancer treatment: a structure-based drug design approach

Abstract Prostate cancer remains a significant global health challenge, necessitating the exploration of novel therapeutic approaches. Androgen receptor (AR) signaling plays a critical role in prostate cancer progression and is a primary target for therapy. This study investigates the potential of phytochemicals from Capsicum annuum (Bell pepper) along with two common standand drugs (Apalutamide and Enzalutamide) as inhibitors of the human androgen receptor (AR) and prostate-specific membrane antigen (PSMA). Utilizing computer-aided drug design techniques, molecular docking studies were conducted to evaluate the binding affinities of selected ligands against AR (PDB ID: 1XOW) and PSMA (PDB ID: 2XEI), their ADMET properties, drug-likeness, oral bioavailability, and bioactivity profiles were also examined. Coumaroylquinic acid and 5-O-caffeoylquinic acid methyl-ester emerged as top-performing ligands, demonstrating strong binding affinities of −9.4 kcal/mol and −9.2 kcal/mol, respectively, against PSMA. Additionally, molecular dynamics simulations provided insights into the stability of protein-ligand complexes, with Coumaroylquinic acid exhibiting a stable binding conformation throughout the simulation. These findings suggest the potential of C. annuum phytochemicals, particularly Coumaroylquinic acid and 5-O-caffeoylquinic acid methyl-ester, as promising inhibitors of PSMA. Moreover, other ligands (Caffeoylglucoside and 1-O-galloyl-beta-d-glucose) identified in the study demonstrate interactions with AR, highlighting a multifaceted approach to prostate cancer treatment. Overall, this study underscores the potential of C. annuum phytochemicals as a source of novel therapeutic agents for prostate cancer, laying the groundwork for further lead optimization efforts.

Discovery of a pocket network on the domain 5 of the TrkB receptor - A potential new target in the quest for the new ligands.

The important role that the neurotrophin tyrosine kinase receptor - TrkB has in the pathogenesis of several neurodegenerative conditions such are Alzheimer's disease, Parkinson's disease, Huntington's disease, has been well described. This shouldn't be a surprise, since in the physiological conditions, once activated by brain-derived neurotrophic factor (BDNF) and neurotrophin-4/5 (NT-4/5), the TrkB receptor promotes neuronal survival, differentiation and synaptic function. Considering that the natural ligands for TrkB receptor are large proteins, it is a challenge to discover small molecule capable to mimic their effects. Even though, the surface of receptor that is interacting with BDNF or NT-4/5 is known, there was always a question which pocket and interaction is responsible for activation of it. In order to answer this challenging question, we have used molecular dynamic (MD) simulations and Pocketron algorithm which enabled us to detect, for the first time, a pocket network existing in the interacting domain (d5) of the receptor; to describe them and to see how they are communicating with each other. This new discovery gave us potential new areas on receptor that can be targeted and used for structure-based drug design approach in the development of the new ligands.

Discovery and biological characterization of a novel mesoionic insecticide fenmezoditiaz.

Many piercing-sucking insects have developed resistance or cross-resistance to many insecticides targeting insect neural nicotinic acetylcholine receptor (nAChR). Here we are aiming to present the discovery of a novel mesoionic insecticide, fenmezoditiaz, by BASF through structure-based drug design (SBDD) approaches. It has recently been added to the Insecticide Resistance Action Committee mode of classification (IRAC 4E). It is being developed for plant protection against piercing-sucking pests, especially rice hopper complex. The soluble acetylcholine binding protein (AChBP) from the sea slug Aplysia californica was modified using site-directed mutagenesis and based on putative aphid nAChR subunit sequences to create soluble insect-like AChBPs. Among them, insect-like β1 AChBP and native aphid membrane preparation showed the highest correlated biochemical affinity toward structurally diverse ligands. This mutant AChBP was used to understand how insect nAChRs structurally interact with mesoionics, which was then utilized to design novel mesoionics including fenmezoditiaz. It is an excellent systemic insecticide with diverse application methods and has a broad insecticidal spectrum, especially against piercing/sucking insects. It lacks cross-resistance for neonicotinoid resistant plant hoppers. Field-collected brown plant hopper populations from Asian countries showed high susceptibility. Fenmezoditiaz is a systemic insecticide with a broad spectrum, lack of cross-resistance and it could be an additional tool for integrated pest management and insecticide resistance management, especially for the rice hopper complex. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Abstract 1183: A first-in-class and SHP1 allosteric inhibitor, SB8091, shows a good efficacy and safety profile in preclinical models

Abstract Introduction: Src homology 2 domain-containing phosphatase 1 (SHP1) is a cytoplasmic protein tyrosine phosphatase (PTP) that is primarily expressed in hematopoietic cells and is commonly recognized as a negative regulator of multiple signaling pathways1. Previously, we showed that inhibition of the phosphatase activity of SHP1 by a novel SHP1 allosteric inhibitor, SB6299, results in the activation of innate and adaptive immune cells and enhanced anti-tumor immune responses2. Here, we report SB8091, an advanced SHP1 allosteric inhibitor with a promising initial safety profile and improved pharmacokinetic properties. Methods: SHP1 inhibitors were developed through a structure-based drug design approach, and optimized for cellular activity on target, in vitro ADME, and in vivo pharmacokinetic properties. Pharmacokinetic (PK) and preliminary toxicity studies were performed with mice. The lead series was assessed in in-vitro studies with mouse or human primary immune cells. In-vivo efficacy and pharmacodynamic data were generated using mouse syngeneic tumor models. Results: Structurally, SB8091 seemed to stabilize the autoinhibitory form of SHP1 as an allosteric inhibitor, in a nanomolar range and which can explain the outstanding selectivity compared to other PTP enzymes, including SHP2. In several human primary immune cell types, SB8091 significantly increased cytokine responses and demonstrated significantly enhanced activity in NK cells and macrophages against various cancer target cells. As a single agent, this compound exhibited inhibitory effects on tumor growth when administered orally, and the efficacy was further enhanced when co-administered with anti-PD1 antibodies in various syngeneic tumor models. Notably, this effect was associated with a pharmacodynamic response marked by increased levels of phosphorylated substrates regulated by SHP1. SB8091 exhibited favorable pharmacokinetic properties for oral administration, and SafetyScreen data showed a very low potential for off-target activity and drug-drug interactions. Additionally, during a 2-week repeat pilot toxicity study in mice, SB8091 demonstrated excellent tolerability even at high doses, indicating a high therapeutic index (TI > 100). Conclusion: Our advanced compound, SB8091, is a potent, highly selective, and orally bioavailable allosteric inhibitor of SHP1. It has demonstrated excellent efficacy as a monotherapy or in combination with immune checkpoint blockers, with favorable drug properties and safety profiles. Research to advance to the clinical stage is being conducted.

Abstract 4507: Discovery of a smart molecular glue: A small-molecular compound selectively degrades Nrf2 in KEAP1-mutated tumor cells, by restoring the broken KEAP1 mutant/Nrf2 interaction

Abstract Overcoming therapeutic resistance without incurring prohibitive normal tissue toxicity is a great challenge in anticancer therapies. Transcription factor NRF2 is a master regulator of cellular protective response, which provides protective effects in normal tissues. KEAP1, the endogenous NRF2 inhibitor, binds NRF2 and redirect it towards proteasome-dependent degradation. KEAP1/NRF2 interaction is therefore critical for maintaining NRF2 at a basal level. Accumulated studies revealed cancer cells could hijack NRF2 pathway to confer drug resistance. A number of clinically-relevant KEAP1 mutations were shown to disrupt the KEAP1/NRF2 interaction, leading to elevated NRF2 level and confer drug resistance. Here, by structure-based drug design approach, we discovered a small-molecule NRF2 inhibitor, R16, which selectively binds KEAP1 mutants and restores their NRF2-inhibitory function in tumor cells. We performed in silico screening against the NCI-open database. Top-ranking candidates were initially evaluated by ARE-luc reporter assays, leading to discovery of R16. Effect of R16 in restoring interaction between KEAP1 mutants and NRF2 were evaluated by BRET2 assays. Among 14 KEAP1 mutations that result in disruption of KEAP1/NRF2 interaction, R16 is active against 11 of them. A variety of assays, including tryptophan quenching, cellular target engagement, BRET2 and GST-pull down assays, indicated that R16 selectively engage KEAP1 mutants and restore their interaction with NRF2, leading to NRF2 degradation. R16 at 0.5 uM substantially sensitizes KEAP1-mutated tumor cells to cisplatin and gefitinib, with no obvious effect in wild-type KEAP1 cells. Importantly, R16 showed significant in-vivo efficacy in sensitizing A549 xenograft bearing KEAP1 G333C mutation to cisplatin, while it has no effect on xenograft with wild-type KEAP1. KEAP1-mutated tumors are emerging as a sub-group with severe resistance to currently available therapies. Here, we have identified a KEAP1 mutant-selective NRF2 inhibitor, which potently sensitizes KEAP1-mutated cells/tumors to anticancer agents, with little effects on the WT-KEAP1. Our work demonstrated it is feasible to restore the NRF2-inhibitory function of KEAP1 mutants, by targeting the mutants with compounds to repair the disrupted KEAP1 mutant/NRF2 interactions. The KEAP1 mutant-selectivity is critical, as NRF2 is a master regulator of cellular defense response in WT-KEAP1 normal tissues. Citation Format: Xiaohong Tian, Tahar Aboulkassim, Qiang Liu, Mark Hancock, Jian Hui Wu, Gerald Batist. Discovery of a smart molecular glue: A small-molecular compound selectively degrades Nrf2 in KEAP1-mutated tumor cells, by restoring the broken KEAP1 mutant/Nrf2 interaction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4507.

1,3,5-triazine derivatives as potential anticancer agents against lung and breast cancer cell lines: Synthesis, biological evaluation, and structure-based drug design studies

Morpholine substituted 1,3,5-triazines have been recently recognized as potent inhibitors of PI3K-mTOR kinase signalling pathway. In this paper, we have performed synthesis and in vitro anti-cancer activity of trisubstituted 1,3,5-triazine derivatives against the A549 (Lung cancer) and MCF-7 (Breast cancer) cell lines. All synthesized analogs showed good inhibitory activity against both cell lines. Out of ten compounds, only two compounds, benzyl-4-(4-(4-(4-fluorophenyl)piperazin-1-yl)-6-morpholino-1,3,5-triazin-2-yl)piperazine-1-carboxylate (Compound 6b), shows 9.61 µM anticancer activity against A549 cell line and 22.68 µM activity against MCF-7 cell lines. Similarly, benzyl-4-(4-morpholino-6-thiomorpholino-1,3,5-triazin-2-yl)piperazine-1-carboxylate (Compound 6c) shows 39.70 µM anticancer activity against A549 cell line and 12.88 µM activity against MCF-7 cell lines. It shows that compound 6b is a potent inhibitor for A549 lung cancer cell line, and compound 6c shows excellent inhibitory activity for MCF-7 breast cancer cell line (9.16 µM and 12.88 µM, respectively). Both compounds (Compound 6b and Compound 6c) did not show toxicity to the non-cancerous HaCaT (Immortalized human keratinocytes) cells. Additionally, molecular descriptors of all synthesized compounds (6a-j) were calculated. After in vitro studies, the potent compounds 6b and 6c were validated using molecular docking and dynamics simulation studies and informed their binding affinities and conformational stability in the binding cavity. Structure-based drug design approach was followed for designing compounds based on potential ligand-receptor interaction. The result shows that triazine analogs serve as lead structures for generating new anti-cancer drugs.

Discovery and Optimization of Selective Brain-Penetrant EBP Inhibitors that Enhance Oligodendrocyte Formation.

The inhibition of emopamil binding protein (EBP), a sterol isomerase within the cholesterol biosynthesis pathway, promotes oligodendrocyte formation, which has been proposed as a potential therapeutic approach for treating multiple sclerosis. Herein, we describe the discovery and optimization of brain-penetrant, orally bioavailable inhibitors of EBP. A structure-based drug design approach from literature compound 1 led to the discovery of a hydantoin-based scaffold, which provided balanced physicochemical properties and potency and an improved in vitro safety profile. The long half-lives of early hydantoin-based EBP inhibitors in rodents prompted an unconventional optimization strategy, focused on increasing metabolic turnover while maintaining potency and a brain-penetrant profile. The resulting EBP inhibitor 11 demonstrated strong in vivo target engagement in the brain, as illustrated by the accumulation of EBP substrate zymostenol after repeated dosing. Furthermore, compound 11 enhanced the formation of oligodendrocytes in human cortical organoids, providing additional support for our therapeutic hypothesis.

Development of a Small Molecule Downmodulator for the Transcription Factor Brachyury.

Brachyury is an oncogenic transcription factor whose overexpression drives chordoma growth. The downmodulation of brachyury in chordoma cells has demonstrated therapeutic potential, however, as a transcription factor it is classically deemed "undruggable". Given that direct pharmacological intervention against brachyury has proven difficult, attempts at intervention have instead targeted upstream kinases. Recently, afatinib, an FDA-approved kinase inhibitor, has been shown to modulate brachyury levels in multiple chordoma cell lines. Herein, we use afatinib as a lead to undertake a structure-based drug design approach, aided by mass-spectrometry and X-ray crystallography, to develop DHC-156, a small molecule that more selectively binds brachyury and downmodulates it as potently as afatinib. We eliminated kinase-inhibition from this novel scaffold while demonstrating that DHC-156 induces the post-translational downmodulation of brachyury that results in an irreversible impairment of chordoma tumor cell growth. In doing so, we demonstrate the feasibility of direct brachyury modulation, which may further be developed into more potent tool compounds and therapies.

In silico Structure-based Screening of Potential Anticancer Bioactive Natural Constituents from African Natural Products

Introduction: Inhibitors of topoisomerases, essential regulators of cancer development, are promising as cancer treatments. These enzymes regulate DNA topology and eliminate topological constraints during various biological processes, including replication, transcription, and recombination. Nature has continually offered scientists pathways to explore the development of new drugs. Indeed, since ancient times, various plant extracts have been utilized in treating multiple pathologies. Objective: It’s intriguing to diversify the therapeutic classes of natural topoisomerase 1 inhibitors. We aimed to explore the relationship between the toxicity of certain medicinal plants in North Africa and their anti-topoisomerase 1 enzyme activity. This investigation aims to discover potentially valuable compounds for fighting cancer by inhibiting the Topo1 enzyme, enriching the anticancer therapeutic class. Methods: This study has conducted a virtual screening of the African Natural Products Database to identify new scaffolds as topoisomerase 1 inhibitors. Molecular docking as a structure-based drug design approach was selected as one of the best approaches, and the complex code ID: 1K4T was used for this purpose. Results and Discussion: The molecular docking of more than 5790 natural products extracted from this database was docked into the binding site of the above-cited complex using the Modlock optimizer and Moldock score as search and scoring function algorithms, respectively. The top-ranked compounds have been assessed, analyzed, and compared to Topotecan and Irinotecan as reference ligands and drugs. Conclusion: Consequently, the seven natural products have shown a strong affinity to topoisomerase 1 and DNA. They establish a clear link between topoisomerase 1 inhibition and the anticancer activity of their corresponding plant extracts. Therefore, these hits are promising and serve as a base for further development of new topoisomerase 1 inhibitors.