Identification Of New Compounds Research Articles

Identification of New Compounds from the Roots of Rubia tibetica Hook. f.

Rubia tibetica Hook. f is a traditional Tibetan medicinal plant, with its roots serving as the primary medicinal part. Two new compounds, Rubiaxylm C and E (1 and 3), and one new natural compound, Rubiaxylm D (2) were isolated from R. tibetica, along with five known compounds (4-8). The structures of the previously undescribed compounds were elucidated by HR-ESIMS, 1D/2D NMR spectroscopic data and electronic circular dichroism calculations. Compound 1 is a rare anthrone substituted with a carbonyl group at position 1. Furthermore, all isolated compounds were tested for their cytotoxicity against HepG2 cell lines.

Ruta graveolens, but Not Rutin, Inhibits Survival, Migration, Invasion, and Vasculogenic Mimicry of Glioblastoma Cells.

Glioblastoma (GBM) is the most aggressive type of brain tumor, characterized by poor outcome and limited therapeutic options. During tumor progression, GBM may undergo the process of vasculogenic mimicry (VM), consisting of the formation of vascular-like structures which further promote tumor aggressiveness and malignancy. The resulting resistance to anti-angiogenetic therapies urges the identification of new compounds targeting VM. Extracts of natural plants may represent potential therapeutic tools. Among these, components of Ruta graveolens water extract (RGWE) display a wide range of biological activities. To test the effect of RGWE on human GBM and rat glioma cell line VM, tube formation on a gelled matrix was monitored. Quantitative assessment of VM formation shows the clear-cut inhibitory activity of RGWE. Unlike rutin, one of the most abundant extract components, the whole RGWE strongly reduced the migration and invasion of GBM tumor cells. Moreover, RGWE induced cell death of GBM patient-derived cancer stem cells and impaired VM at sub-lethal doses. Overall, our data reveal a marked RGWE-dependent inhibition of GBM cell survival, migration, invasion, and VM formation. Thus, the clear-cut ability of RGWE to counteract GBM malignancy deserves attention, holding the promise to bring natural products to clinical use, thus uncovering new therapeutic opportunities.

Virtual design and screening of new (+)-catechin derivates N- and/or S-heterocyclic fragment for anti-malarial and anti-SARS-CoV-2 activities by In silico simulation

Hemisynthesis makes it possible to improve the activity or reduce the toxicity of a biocompound by modifying or adding peripheral groups. Catechin present in different plant species was known for its moderate anti-malarial and anti-SARS-CoV-2 activities. The aim of this work was focused on the identification of new compounds with potential anti-SARS-CoV-2 and/or anti-malarial activities, evaluated through In silico simulation. A polyphenol pharmacophore model, based on (+)-catechin (1) was virtually constructed using previously reported inhibitors. N- and/or S-heterocyclic fragments were inserted on the backbone of (+)-catechin and 12 pharmacophore hypotheses were studied. This study targeted 3 proteins biologically responsible for SARS-CoV-2 (PDB ID: 7JYC, 6M0J, and 6HZD) and one protein responsible for malaria (PDB ID: 3SRJ). Molecular docking had shown that the new catechin-aldehyde candidates have good Ligand-Protein affinity in terms of free energy compared to the study reference Narlaprevir and Artesunate for SARS-CoV-2 and malaria respectively. Theoretically, most compounds didn’t show toxicity except compounds 2a, 2i, and 2k, exhibiting hepatotoxic activity. Molecular dynamics was used to prove and assess their binding stability to the target protein for each activity. The 3SRJ-2f and 6HZD-2l structures were selected for anti-malarial and anti-SARS-CoV-2 activity respectively. The 3SRJ-2f and 6HZD-2l complexes showed stable interactions to 100 ns between the inhibitor fragments and the residual amino acids of the protein. To conclude, these novel compounds are probably to become promising lead molecules for the development of effective anti-SARS-CoV-2 and/or anti-malarial of all drugs. Keywords: Catechin, Anti-malarial, Anti-SARS-CoV-2, Docking and Dynamic Molecular, ADMET Analysis.

Phosphodiesterase-4 Inhibitors Increase Pigment Cell Proliferation and Melanization in Cultured Melanocytes and within a 3-Dimensional Skin Equivalent Model

Vitiligo is a common chronic autoimmune disease characterized by white macules and patches of the skin, having a negative impact on patients' life, and without any definitive cure at present. Identification of new compounds to reverse depigmentation is therefore a pressing need for this disease. The pharmacologic compounds phosphodiesterase-4 inhibitors (PDE4i) are small molecules with immunomodulatory properties, used for treatment of inflammatory dermatoses. PDE4i have shown repigmentation effects in vitiligo patients, in some case reports. We characterized the proliferative and melanogenic potential of two known PDE4i, crisaborole and roflumilast, and of a more recently designed compound, PF-07038124. We used two in vitro model systems, the primary human melanocyte culture and a 3D co-cultured skin model (MelanoDermTM), with an exploratory testing platform composed of complementary assays (spectrophotometry, melanin and proliferation assays, immunostaining, Fontana-Masson staining, qRT-PCR, western blot and whole transcriptome RNA-Sequencing). We identified that the treatment with PDE4i was associated with increased melanocyte proliferation and melanization in both in vitro models, and with increase in the melanogenic genes and proteins expression in cultured melanocytes. These effects were found to be enhanced by addition of α-MSH. Our findings support the further evaluation of PDE4i with or without α-MSH agonists in vitiligo trials.

Applying Molecular Modeling to the Design of Innovative, Non-Symmetrical CXCR4 Inhibitors with Potent Anticancer Activity.

The identification of new compounds with potential activity against CXC chemokine receptor type 4 (CXCR4) has been broadly studied, implying several chemical families, particularly AMD3100 derivatives. Molecular modeling has played a pivotal role in the identification of new active compounds. But, has its golden age ended? A virtual library of 450,000 tetraamines of general structure 8 was constructed by using five spacers and 300 diamines, which were obtained from the corresponding commercially available cyclic amines. Diversity selection was performed to guide the virtual screening of the former database and to select the most representative set of compounds. Molecular docking on the CXCR4 crystal structure allowed us to rank the selection and identify those candidate molecules with potential antitumor activity against diffuse large B-cell lymphoma (DLBCL). Among them, compound A{17,18} stood out for being a non-symmetrical structure, synthetically feasible, and with promising activity against DLBCL in in vitro experiments. The focused study of symmetrical-related compounds allowed us to identify potential pre-hits (IC50~20 µM), evidencing that molecular design is still relevant in the development of new CXCR4 inhibitor candidates.

An algorithm-driven intelligent mining and identification strategy for natural product mass spectrometry

Efficiently mining and identification of new compounds from the extensive MS/MS datasets of plant extracts poses a significant challenge due to the structural diversity and compositional complexity inherent in natural products (NPs). Various data post-processing techniques have been developed to simplify the interpretation of MS/MS data; however, they often suffer from limited specificity and precision. Meanwhile, structure annotation following data post-processing is particularly time-consuming. In this study, we introduced an innovative strategy named MS-SMART, which integrates three intelligent algorithms: automatic mining of diagnostic ions, rapid filtration of alkaloids from untargeted MS/MS data, and structural recommendations for filtered components. The feasibility of this approach for rapidly discovering novel compounds was demonstrated using berberine-type alkaloids as an example. Firstly, diagnostic ions were automatically extracted and validated using available reference data. Subsequently, berberine-type compounds were filtered from raw MS/MS data. Finally, the structures of the target components were recommended using building blocks derived from berberines reported in various plants. A total of 103, 198, 60, 80 and 51 berberines were efficiently identified in diverse families and genera, including Stephaniae Epigaeae Radix, Coptidis Rhizoma, Phellodendri Chinensis Cortex, Phellodendri Amurensis Cortex and Corydalis Decumbentis Rhizoma, with 99, 169, 50, 64 and 40 new compounds identified, respectively. Among these, 8, 14, 8, 7 and 12 berberines were confirmed by reference compounds. This strategy provides a new research paradigm for the rapid discovery and identification of different types of new compounds in complex samples.

Transition metal atoms (TM = Sc, Ti, V, Cr, and Mn) decorated PBCF-graphene as a possible reversible hydrogen storage material: A DFT-D2 investigation

One of the most pressing concerns for hydrogen energy development is the identification of new compounds with high capacity and effective reversibility for hydrogen storage. This study employs a unique all-sp2 hybridized two-dimensional (2D) carbon allotrope inspired by graphene synthesis using benzene as a precursor. This 2D carbon allotrope is a polybutadiene cyclooctatetraene framework known as PBCF-graphene. This work investigated the electrical and structural properties of transition metal-decorated PBCF-G (TM-PBCF-G) for H2 adsorption using the DFT-D2 technique. Next, the most stable structures' H2 uptake and storage were examined. According to the results, the hollow site in the hexagonal ring's center is the most stable location for all TM decorations. Additionally, PBCF-G which has been adorned with Sc and Ti has the highest energy stability, with Eb values of −7.599 and −8.380 eV, respectively. The analysis of H2's adsorption behavior on TM-PBCF-G indicates that Cr-PBCF-G has the greatest adsorption energies (−0.701 eV), and that H2's horizontal direction has a greater stability energy. Upon gradually adding more H2 molecules to pristine and Cr-PBCF-G, it is shown that these materials can store 4 and 17H2 molecules, respectively, with average adsorption energies of −0.102 and −0.167 eV/H2, and corresponding H2 storage capacities of 5.26 and 9.10 wt%. These results demonstrate the potential of Cr-PBCF-G as a viable H2 storage material in the future.

Exploring the Potential of Myrcia Genus Essential Oils: A Review of Biological Activities and Recent Advances.

The present study provides a comprehensive analysis of the chemical composition of essential oils from species of the Myrcia genus and their applications. The compiled results highlight the chemical diversity and biological activities of these oils, emphasizing their potential importance for various therapeutic and industrial applications. The findings reveal that Myrcia essential oils present a variety of bioactive compounds, such as monoterpenes and sesquiterpenes, which demonstrate antimicrobial activities against a range of microorganisms, including Gram-positive and Gram-negative bacteria, as well as yeasts. Furthermore, this study highlights the phytotoxic activity of these oils, indicating their potential for weed control. The results also point to the insecticidal potential of Myrcia essential oils against a range of pests, showing their viability as an alternative to synthetic pesticides. Additionally, species of the genus Myrcia have demonstrated promising hypoglycemic effects, suggesting their potential in diabetes treatment. This comprehensive synthesis represents a significant advancement in understanding Myrcia essential oils, highlighting their chemical diversity and wide range of biological activities. However, the need for further research is emphasized to fully explore the therapeutic and industrial potential of these oils, including the identification of new compounds, understanding of their mechanisms of action, and evaluation of safety and efficacy in different contexts.

Antimicrobial activity of some vinyl-triazole derivatives

Mycoses and bacterioses in agricultural crops are very devastating, bringing enormous economic damage through direct crop losses and compromising it due to pathogen toxin pollution, which makes them toxic to humans and animals. Chemical plant protection procedures often become ineffective due to the easy adaptation of causative agents to pesticides, the reduction of the protective effect under the influence of unfavorable conditions, toxicity, ecological consequences. Starting from this, the aim of the research consisted in the identification of new compounds with antifungal (Fusarium avenaceum) and antibacterial (Erwinia amilovora, E. carotovora, Xanthomonas campestris) activity in in vitro conditions for further utilization in plant protection measures. Based on the growth of fungal colonies and minimum bactericidal concentration, it was found that vinyl-triazole derivatives EPS-869, EPS-877, EPS-880, EPS-892, EPS-165 (0,00125; 0,0025; 0,005; 0, 01%) shows high antimicrobial activity, the phenomenon being due in particular to the compound factor.

Discovery of a series of portimine-A fatty acid esters in mussels

Vulcanodinium rugosum is a benthic dinoflagellate known for producing pinnatoxins, pteriatoxins, portimines and kabirimine. In this study, we aimed to identify unknown analogs of these emerging toxins in mussels collected in the Ingril lagoon, France. First, untargeted data acquisitions were conducted by means of liquid chromatography coupled to hybrid quadrupole-orbitrap mass spectrometry. Data processing involved a molecular networking approach, and a workflow dedicated to the identification of biotransformed metabolites. Additionally, targeted analyses by liquid chromatography coupled to triple quadrupole mass spectrometry were also implemented to further investigate and confirm the identification of new compounds. For the first time, a series of 13-O-acyl esters of portimine-A (n = 13) were identified, with fatty acid chains ranging between C12:0 and C22:6. The profile was dominated by the palmitic acid conjugation. This discovery was supported by fractionation experiments combined with the implementation of a hydrolysis reaction, providing further evidence of the metabolite identities. Furthermore, several analogs were semi-synthesized, definitively confirming the discovery of these metabolization products. A new analog of pinnatoxin, with a molecular formula of C42H65NO9, was also identified across the year 2018, with the highest concentration observed in August (4.5 μg/kg). The MS/MS data collected for this compound exhibited strong structural similarities with PnTX-A and PnTX-G, likely indicating a substituent C2H5O2 in the side chain at C33. The discovery of these new analogs will contribute to deeper knowledge of the chemodiversity of toxins produced by V. rugosum or resulting from shellfish metabolism, thereby improving our ability to characterize the risks associated with these emerging toxins.

Synthetic Identification of New Compounds with Anti-fungal Properties of “1-[3-(2-Hydroxyphenyl)-3-Oxop ropanoyl]- 5,5-Diphenylimidazolidine -2,4-Dione and its Derivatives”

Synthetic Identification of New Compounds with Anti-fungal Properties of “1-[3-(2-Hydroxyphenyl)-3-Oxop ropanoyl]- 5,5-Diphenylimidazolidine -2,4-Dione and its Derivatives”

New cycloartane triterpenoids from Dysoxylum malabaricum and their cytotoxic evaluation

The cytotoxic dichloromethane-methanol bark extract of Dysoxylum malabaricum was subjected to bioassay-guided fractionation, followed by systematic dereplication to focus on the identification of new compounds. From the bark of Dysoxylum malabaricum, two new cycloartane-type triterpenoids were isolated in addition to two previously known triterpenoids. The structures and absolute configurations of the isolated compounds were elucidated unambiguously via NMR, HRESIMS data, and electronic circular dichroism calculations. The isolated compounds were tested for their cytotoxic potential against the panel of breast, lung, and hypopharynx cancer cell lines and displayed notable cytotoxicity against breast cancer cell lines. Compound 3 exhibited the most potent cytotoxic effect with an IC50 14 µM against MCF-7 cell lines and induced cell cycle arrest. Through western blot and cell cycle analysis, it was revealed that compound 3 halts the G0/G1 phase of the cell cycle by inhibiting CDC20 and CDC25 enzymes.

Suberoylanilide Hydroxamic Acid (SAHA) Is a Driver Molecule of Neuroplasticity: Implication for Neurological Diseases.

Neuroplasticity is a crucial property of the central nervous system to change its activity in response to intrinsic or extrinsic stimuli. This is mainly achieved through the promotion of changes in the epigenome. One of the epi-drivers priming this process is suberoylanilide hydroxamic acid (SAHA or Vorinostat), a pan-histone deacetylase inhibitor that modulates and promotes neuroplasticity in healthy and disease conditions. Knowledge of the specific molecular changes induced by this epidrug is an important area of neuro-epigenetics for the identification of new compounds to treat cognition impairment and/or epilepsy. In this review, we summarize the findings obtained in cellular and animal models of various brain disorders, highlighting the multiple mechanisms activated by SAHA, such as improvement of memory, learning and behavior, and correction of faulty neuronal functioning. Supporting this evidence, in vitro and in vivo data underline how SAHA positively regulates the expression of neuronal genes and microtubule dynamics, induces neurite outgrowth and spine density, and enhances synaptic transmission and potentiation. In particular, we outline studies regarding neurodevelopmental disorders with pharmaco-resistant seizures and/or severe cognitive impairment that to date lack effective drug treatments in which SAHA could ameliorate defective neuroplasticity.

Exploring New Therapeutic Avenues for Ophthalmic Disorders: Glaucoma-Related Molecular Docking Evaluation and Bibliometric Analysis for Improved Management of Ocular Diseases.

Ophthalmic disorders consist of a broad spectrum of ailments that impact the structures and functions of the eye. Due to the crucial function of the retina in the vision process, the management of eye ailments is of the utmost importance, but several unmet needs have been identified in terms of the outcome measures in clinical trials, more proven minimally invasive glaucoma surgery, and a lack of comprehensive bibliometric assessments, among others. The current evaluation seeks to fulfill several of these unmet needs via a dual approach consisting of a molecular docking analysis based on the potential of ripasudil and fasudil to inhibit Rho-associated protein kinases (ROCKs), virtual screening of ligands, and pharmacokinetic predictions, emphasizing the identification of new compounds potentially active in the management of glaucoma, and a comprehensive bibliometric analysis of the most recent publications indexed in the Web of Science evaluating the management of several of the most common eye conditions. This method resulted in the finding of ligands (i.e., ZINC000000022706 with the most elevated binding potential for ROCK1 and ZINC000034800307 in the case of ROCK2) that are not presently utilized in any therapeutic regimen but may represent a future option to be successfully applied in the therapeutic scheme of glaucoma following further comprehensive testing validations. In addition, this research also analyzed multiple papers listed in the Web of Science collection of databases via the VOSviewer application to deliver, through descriptive analysis of the results, an in-depth overview of publications contributing to the present level of comprehension in therapeutic approaches to ocular diseases in terms of scientific impact, citation analyses, most productive authors, journals, and countries, as well as collaborative networks. Based on the molecular docking study's preliminary findings, the most promising candidates must be thoroughly studied to determine their efficacy and risk profiles. Bibliometric analysis may also help researchers set targets to improve ocular disease outcomes.

Different Extraction Procedures Revealed the Anti-Proliferation Activity from Vegetable Semi-Purified Sources on Breast Cancer Cell Lines.

Breast cancer (BC) remains the leading cause of mortality in women, despite significant advancements in diagnosis. Thus, the identification of new compounds for its treatment is critical. Phytochemicals are known to exhibit anti-cancer properties. Here, we investigated the anti-proliferation potential of extracts from carrot, Calendula officinalis flower, and Aloe vera on breast cancer vs. epithelial cell lines. Various extraction methods were used, and the proliferative effect of the resulting extracts was assessed by proliferation assay on breast cancer and epithelial cell lines. Carrot, Aloe leaf, and Calendula flower extracts were extracted by hexane and methanol methods, and their semi-purified extracts were able to specifically inhibit the proliferation of breast cancer cell lines. The extract composition was investigated by colorimetric assays, UHPLC-HRMS, and MS/MS analysis. All the extracts contained monogalactosyl-monoacylglycerol (MGMG), while digalactosyl-monoacylglycerol (DGMG) and aloe-emodin were found in Aloe, and glycerophosphocholine (GPC) derivatives were identified in Calendula, except for the isomer 2 detected in carrot, suggesting that their observed different anti-proliferative properties may be associated with the different lipid compounds. Interestingly, Calendula extract was able to strongly inhibit the triple negative breast cancer MDA-MB-231 cell line proliferation (about 20% cell survival), supporting MGMG and GPC derivatives as potential drugs for this BC subtype treatment.

Identification of New Compounds against PRRSV Infection by Directly Targeting CD163.

The porcine reproductive and respiratory syndrome viruses (PRRSV) led to a global panzootic and huge economical losses to the pork industry. PRRSV targets the scavenger receptor CD163 for productive infection. However, currently no effective treatment is available to control the spread of this disease. Using bimolecular fluorescence complementation (BiFC) assays, we screened a set of small molecules potentially targeting the scavenger receptor cysteine-rich domain 5 (SRCR5) of CD163. We found that the assay examining protein-protein interactions (PPI) between PRRSV glycoprotein 4 (GP4) and the CD163-SRCR5 domain mainly identifies compounds that potently inhibit PRRSV infection, while examining the PPI between PRRSV-GP2a and the SRCR5 domain maximized the identification of positive compounds, including additional ones with various antiviral capabilities. These positive compounds significantly inhibited both types 1 and 2 PRRSV infection of porcine alveolar macrophages. We confirmed that the highly active compounds physically bind to the CD163-SRCR5 protein, with dissociation constant (KD) values ranging from 28 to 39 μM. Structure-activity-relationship (SAR) analysis revealed that although both the 3-(morpholinosulfonyl)anilino and benzenesulfonamide moieties in these compounds are critical for the potency to inhibit PRRSV infection, the morpholinosulfonyl group can be replaced by chlorine substituents without significant loss of antiviral potency. Our study established a system for throughput screening of natural or synthetic compounds highly effective on blocking of PRRSV infection and shed light on further SAR modification of these compounds. IMPORTANCE Porcine reproductive and respiratory syndrome virus (PRRSV) causes significant economic losses to the swine industry worldwide. Current vaccines cannot provide cross protection against different strains, and there are no effective treatments available to hamper the spread of this disease. In this study, we identified a group of new small molecules that can inhibit the PRRSV interaction with its specific receptor CD163 and dramatically block the infection of both types 1 and type 2 PRRSVs to host cells. We also demonstrated the physical association of these compounds with the SRCR5 domain of CD163. In addition, molecular docking and structure-activity relationship analyses provided new insights for the CD163/PRRSV glycoprotein interaction and further improvement of these compounds against PRRSV infection.

Novel and holistic approaches are required to realize allelopathic potential for weed management.

Allelopathy, that is, plant-plant inhibition via the release of secondary metabolites into the environment, has potential for the management of weeds by circumventing herbicide resistance. However, mechanisms underpinning allelopathy are notoriously difficult to elucidate, hindering real-world application either in the form of commercial bioherbicides or allelopathic crops. Such limited application is exemplified by evidence of limited knowledge of the potential benefits of allelopathy among end users. Here, we examine potential applications of this phenomenon, paying attention to novel approaches and influential factors requiring greater consideration, with the intention of improving the reputation and uptake of allelopathy. Avenues to facilitate more effective allelochemical discovery are also considered, with a view to stimulating the identification of new compounds and allelopathic species. Synthesis and Applications: We conclude that tackling increasing weed pressure on agricultural productivity would benefit from greater integration of the phenomenon of allelopathy, which in turn would be greatly served by a multi-disciplinary and exhaustive approach, not just through more effective isolation of the interactions involved, but also through greater consideration of factors which may influence them in the field, facilitating optimization of their benefits for weed management.

An analytical platform for near real-time drug landscape monitoring using paraphernalia residues

Deaths attributed to drug overdoses are constantly on the rise, but drug trends are frequently changing and often differ across geographical regions. Current analytical techniques are limited in their abilities to rapidly identify drugs that would inform both public health and law enforcement officials about the evolving drug landscape. The work presented here outlines an analytical platform that utilizes ambient ionization mass spectrometry and additional techniques (e.g., tandem mass spectrometry) to qualitatively analyze trace residues from drug paraphernalia to quickly detect both drugs and cutting agents. To demonstrate proof-of-concept, samples collected from syringe service programs throughout the state of Maryland were analyzed by direct analysis in real time – mass spectrometry (DART-MS) to provide rapid, near complete chemical profiles (drugs, cutting agents, and other compounds of interest). To obtain a more complete chemical profile, it was found that a small subset of samples (7.5 %) benefited from additional analysis by either direct analysis in real time – tandem mass spectrometry (DART-MS/MS) or liquid chromatography – tandem mass spectrometry (LC-MS/MS). This additional analysis enabled confirmation of the presence or absence of questioned compounds, assisted in identification of new compounds, and provided isomer differentiation without hindering the rapid reporting of results. This analytical platform utilizing DART-MS and, where necessary, tandem mass spectrometry techniques, was found to detect a wide range of drugs and cutting agents in a manner that can better inform public health and public safety personnel about the drug landscape in “near real-time”.

High-Throughput Quantitative Screening of Glucose-Stimulated Insulin Secretion and Insulin Content Using Automated MALDI-TOF Mass Spectrometry

Type 2 diabetes (T2D) is a metabolic disorder characterized by loss of pancreatic β-cell function, decreased insulin secretion and increased insulin resistance, that affects more than 537 million people worldwide. Although several treatments are proposed to patients suffering from T2D, long-term control of glycemia remains a challenge. Therefore, identifying new potential drugs and targets that positively affect β-cell function and insulin secretion remains crucial. Here, we developed an automated approach to allow the identification of new compounds or genes potentially involved in β-cell function in a 384-well plate format, using the murine β-cell model Min6. By using MALDI-TOF mass spectrometry, we implemented a high-throughput screening (HTS) strategy based on the automation of a cellular assay allowing the detection of insulin secretion in response to glucose, i.e., the quantitative detection of insulin, in a miniaturized system. As a proof of concept, we screened siRNA targeting well-know β-cell genes and 1600 chemical compounds and identified several molecules as potential regulators of insulin secretion and/or synthesis, demonstrating that our approach allows HTS of insulin secretion in vitro.

Identification of Selective BRD9 Inhibitor via Integrated Computational Approach.

Bromodomain-containing protein 9 (BRD9), a member of the bromodomain and extra terminal domain (BET) protein family, works as an epigenetic reader. BRD9 has been considered an essential drug target for cancer, inflammatory diseases, and metabolic disorders. Due to its high similarity among other isoforms, no effective treatment of BRD9-associated disorders is available. For the first time, we performed a detailed comparative analysis among BRD9, BRD7, and BRD4. The results indicate that residues His42, Gly43, Ala46, Ala54, Val105, and Leu109 can confer the BRD9 isoform selectivity. The predicted crucial residues were further studied. The pharmacophore model's features were precisely mapped with some key residues including, Gly43, Phe44, Phe45, Asn100, and Tyr106, all of which play a crucial role in BRD9 inhibition. Docking-based virtual screening was utilized with the consideration of the conserved water network in the binding cavity to identify the potential inhibitors of BRD9. In this workflow, 714 compounds were shortlisted. To attain selectivity, 109 compounds were re-docked to BRD7 for negative selection. Finally, four compounds were selected for molecular dynamics studies. Our studies pave the way for the identification of new compounds and their role in causing noticeable, functional differences in isoforms and between orthologues.