Structure-based screening of FDA-approved drugs identifies potential histone deacetylase 3 repurposed inhibitor: molecular docking and molecular dynamic simulation approaches.

Histone deacetylase 3 (HDAC3) is a member of the histone deacetylase family that has emerged as a crucial target in the quest for novel therapeutic interventions against various complex diseases, including cancer. The repositioning of FDA-approved drugs presents a promising avenue for the rapid discovery of potential HDAC3 inhibitors. In this study, we performed a structure-based virtual screening of FDA-approved drugs obtained from DrugBank. Candidate hits were selected based on their binding affinities and interactions with HDAC3. These promising hits were then subjected to a comprehensive assessment of their biological properties and drug profiles. Our investigation identified two FDA-approved drugs, Imatinib and Carpipramine, characterized by their exceptional affinity and specificity for the binding pocket of HDAC3. These molecules demonstrated a strong preference for HDAC3 binding site and formed interactions with functionally significant residues within the active site pocket. To gain deeper insights into the binding dynamics, structural stability, and interaction mechanisms, we performed molecular dynamics (MD) simulations spanning 300 nanoseconds (ns). The results of MD simulations indicated that Imatinib and Carpipramine stabilized the structure of HDAC3 and induced fewer conformational changes. Taken together, the findings from this study suggest that Imatinib and Carpipramine may offer significant therapeutic potential for treating complex diseases, especially cancer.

Systematic computational strategies for identifying protein targets and lead discovery.

Computational algorithms and tools have retrenched the drug discovery and development timeline. The applicability of computational approaches has gained immense relevance owing to the dramatic surge in the structural information of biomacromolecules and their heteromolecular complexes. Computational methods are now extensively used in identifying new protein targets, druggability assessment, pharmacophore mapping, molecular docking, the virtual screening of lead molecules, bioactivity prediction, molecular dynamics of protein-ligand complexes, affinity prediction, and for designing better ligands. Herein, we provide an overview of salient components of recently reported computational drug-discovery workflows that includes algorithms, tools, and databases for protein target identification and optimized ligand selection.

Computational and spectroscopic insight into the binding of citral with human transferrin: Targeting neurodegenerative diseases.

The involvement of neuroinflammation in the pathogenesis of neurodegenerative disorders (NDs) is very significant. Currently, only symptomatic treatments exist, and there are no drugs that modify the progression of Alzheimer's disease (AD) or other NDs. Consequently, there is increasing attention on addressing AD-related neuroinflammation using anti-inflammatory compounds and antioxidants. Currently, there is a growing exploration of dietary phytochemicals as potential therapeutic agents for treating inflammation. Citral, a monoterpene, is under increasing investigation due to its neuroprotective effects. The dysregulation of iron homeostasis is a crucial factor in supporting neuroinflammation, underscoring the significance of proper iron balance. Human transferrin (htf) is a major player involved in iron homeostasis. In this study, we examined binding and dynamics of htf-citral complex through diverse experimental methods. Molecular docking studies revealed that citral binds to crucial residues of htf, forming a stable complex. UV-visible spectroscopy demonstrated binding of citral with htf with good affinity, evident from binding constant of 1.48 × 105 M-1. Further, fluorescence spectroscopy entrenched a stable htf-citral complex formation; citral demonstrates an excellent binding affinity to htf with a binding constant of 106 M-1. Moreover, fluorescence binding assay at various temperatures deciphered htf-citral complex to be driven by both static and dynamic quenching. The analysis of enthalpy change (ΔH) and entropy change (ΔS) demonstrated that htf-citral complex formation was driven mainly by hydrophobic interactions.The current work gives a platform to develop innovative therapeutic strategies targeting neuroinflammation through citral, particularly iron homeostasis.

Computational Screening of Repurposed Drugs for HMG-CoA Synthase 2 in Alzheimer's Disease.

Background: HMGCS2 (mitochondrial 3-hydroxy-3-methylglutaryl-COA synthase 2) plays a pivotal role as a control enzyme in ketogenesis, and its association with the amyloid-ß protein precursor (AßPP) in mitochondria implicates a potential involvement in Alzheimer's disease (AD) pathophysiology. Objective: Our study aimed at identifying repurposed drugs using the DrugBank database capable of inhibiting HMGCS2 activity. Methods: Exploiting the power of drug repurposing in conjunction with virtual screening and molecular dynamic (MD) simulations against 'HMGCS2', we present new in-silico insight into structure-based drug repurposing. Results: The initial molecules were screened for their binding affinity to HMGCS2. Subsequent interaction analyses and extensive 300 ns MD simulations were conducted to explore the conformational dynamics and stability of HMGCS2 in complex with the screened molecules, particularly Penfluridol and Lurasidone. Conclusions: The study revealed that HMGCS2 forms stable protein-ligand complexes with Penfluridol and Lurasidone. Our findings indicate that Penfluridol and Lurasidone competitively bind to HMGCS2 and warrant their further exploration as potential repurposed molecules for anti-Alzheimer's drug development.

Understanding the interactions between repurposed drugs sertindole and temoporfin with receptor for advanced glycation endproducts: Therapeutic implications in cancer and metabolic diseases.

CONTEXT: In the pursuit of novel therapeutic possibilities, repurposing existing drugs has gained prominence as an efficient strategy. The findings from our study highlight the potential of repurposed drugs as promising candidates against receptor for advanced glycation endproducts (RAGE) that offer therapeutic implications in cancer, neurodegenerative conditions and metabolic syndromes. Through careful analyses of binding affinities and interaction patterns, we identified a few promising candidates, ultimately focusing on sertindole and temoporfin. These candidates exhibited exceptional binding affinities, efficacy, and specificity within the RAGE binding pocket. Notably, they displayed a pronounced propensity to interact with the active site of RAGE. Our investigation further revealed that sertindole and temoporfin possess desirable pharmacological properties that highlighted them as attractive candidates for targeted drug development. Overall, our integrated computational approach provides a comprehensive understanding of the interactions between repurposed drugs, sertindole and temoporfin and RAGE that pave the way for future experimental validation and drug development endeavors. METHODS: We present an integrated approach utilizing molecular docking and extensive molecular dynamics (MD) simulations to evaluate the potential of FDA-approved drugs, sourced from DrugBank, against RAGE. To gain deeper insights into the binding mechanisms of the elucidated candidate repurposed drugs, sertindole and temoporfin with RAGE, we conducted extensive all-atom MD simulations, spanning 500 nanoseconds (ns). These simulations elucidated the conformational dynamics and stability of the RAGE-sertindole and RAGE-temoporfin complexes.

Exploring the promising potential of noscapine for cancer and neurodegenerative disease therapy through inhibition of integrin-linked kinase-1.

Integrin-linked kinase (ILK), a ß1-integrin cytoplasmic domain interacting protein, supports multi-protein complex formation. ILK-1 is involved in neurodegenerative diseases by promoting neuro-inflammation. On the other hand, its overexpression induces epithelial-mesenchymal transition (EMT), which is a major hallmark of cancer and activates various factors associated with a tumorigenic phenotype. Thus, ILK-1 is considered as an attractive therapeutic target. We investigated the binding affinity and ILK-1 inhibitory potential of noscapine (NP) using spectroscopic and docking approaches followed by enzyme inhibition activity. A strong binding affinity of NP was measured for the ILK-1 with estimated Ksv (M-1) values of 1.9 × 105, 3.6 × 105, and 4.0 × 105 and ∆G0 values (kcal/mol) -6.19554, -7.8557 and -8.51976 at 298 K, 303 K, and 305 K, respectively. NP binds to ILK-1 with a docking score of -6.6 kcal/mol and forms strong interactions with active-site pocket residues (Lys220, Arg323, and Asp339). The binding constant for the interaction of NP to ILK-1 was 1.04 × 105 M-1, suggesting strong affinity and excellent ILK-1 inhibitory potential (IC50 of ∼5.23µM). Conformational dynamics of ILK-1 were also studied in the presence of NP. We propose that NP presumably inhibits ILK-1-mediated phosphorylation of various downstream signalling pathways that are involved in cancer cell survival and neuroinflammation.

In vitro and Ex vivo study targeting the development of a Lavandula stoechas L. (Ustukhuddus) loaded Unani Transdermal patch: Implication of Unani Medicine in the treatment of Nisyan (Dementia).

Ustukhuddus (Lavandula stoechas L.) has been extensively used orally and topically in treating various neurological disorders, including dementia. The optimum potential of traditional dosage forms of Ustukhuddus is limited for various reasons. Transdermal drug delivery system (TDDS) is a novel means of drug delivery and is known to overcome the drawbacks associated with traditional dosage forms. The current study aimed at fabricating and evaluating Ustukhuddus hydro-alcoholic extract (UHAE) and essential oil (UEO) loaded matrix-type transdermal patches having a combination of hydrophilic - hydroxyl propyl methyl cellulose (HPMC) and hydrophobic - ethyl cellulose (EC) polymers. ATR-FTIR, DSC, XRD, and SEM analysis were carried out to study drug-polymer interactions, confirming the formation of developed patches and drug compatibility with excipients. We assessed the fabricated patches to evaluate their physicochemical properties, in vitro drug release, and permeation characteristics via ex vivo experiments. The physicochemical characteristics of patches showcased the development of good and stable films with clarity, smoothness, homogeneity, optimum flexibility and free from causing skin irritancy or sensitization. In vitro drug release and ex vivo permeation profile of developed patches were evaluated employing Franz diffusion cells. UHAE and UEO patches exhibited a cumulative drug release of 81.61 and 85.24 %, respectively, in a sustained-release manner and followed non-Fickian release mechanisms. The ex vivo permeation data revealed 66.82 % and 76.41 % of drug permeated from UHAE and UEO patches, respectively. The current research suggests that the formulated patches are more suitable for TDDS and hold potential significance in the treatment of dementia, contributing to enhanced patient compliance, thereby highlighting the implication of Unani Medicine in Nisyan (Dementia) treatment.

Identification of High-Affinity Inhibitors of TANK-Binding Kinase 1 (TBK1): A Promising Frontier for Controlling Inflammatory Signaling in Cancer.

BACKGROUND: TANK-binding kinase 1 (TBK1) is an important serine/threonine kinase involved in inflammatory signaling pathways, influencing cellular processes such as proliferation, programmed cell death, autophagy, and immune response regulation. Dysregulation of TBK1 has been linked to cancer progression and neurodegenerative disorders, making it an attractive target for therapeutic development. This study aimed to identify potential TBK1 inhibitors using a structure-based virtual screening approach. METHODS: We conducted a comprehensive screening of the ZINC database to identify compounds with high binding affinity for TBK1, employing molecular docking as the primary selection criterion. The top candidates were then subjected to extensive 200 ns molecular dynamics (MD) simulations to assess the conformational dynamics of TBK1 and the stability of the protein-ligand complexes, with a focus on ZINC02095133 and ZINC02130647. RESULTS: The findings revealed that TBK1 forms stable complexes with ZINC02095133 and ZINC02130647, demonstrating consistent interactions throughout the MD simulations. This suggests that these compounds hold promise as potential lead molecules for future therapies targeting TBK1. CONCLUSIONS: This study identifies ZINC02095133 and ZINC02130647 as promising TBK1 inhibitors with therapeutic potential. However, further experimental validation and optimization are required to develop novel inhibitors for diseased conditions associated with TBK1 signaling. These findings pave the way for future investigations into the clinical utility of these compounds in combating TBK1-related pathologies.

Targeting PDE4A for therapeutic potential: exploiting drug repurposing approach through virtual screening and molecular dynamics.

cAMP-specific 3',5'-cyclic phosphodiesterase 4 A (PDE4A) holds a pivotal role in modulating intracellular levels of cyclic adenosine monophosphate (cAMP). Targeting PDE4A with novel therapeutic agents shows promise in addressing neurological disorders (e.g. Alzheimer's and Parkinson's diseases), mood disorders (depression, anxiety), inflammatory conditions (asthma, chronic obstructive pulmonary disease), and even cancer. In this study, we present a comprehensive approach that integrates virtual screening and molecular dynamics (MD) simulations to identify potential inhibitors of PDE4A from the existing pool of FDA-approved drugs. The initial compound selection was conducted focusing on binding affinity scores, which led to the identification of several high-affinity compounds with potential PDE4A binding properties. From the refined selection process, two promising compounds, Fluspirilene and Dihydroergocristine, emerged as strong candidates, displaying substantial affinity and specificity for the PDE4A binding site. Interaction analysis provided robust evidence of their binding capabilities. To gain deeper insights into the dynamic behavior of Fluspirilene and Dihydroergocristine in complex with PDE4A, we conducted 300 ns MD simulations, principal components analysis (PCA), and free energy landscape (FEL) analysis. These analyses revealed that Fluspirilene and Dihydroergocristine binding stabilized the PDE4A structure and induced minimal conformational changes, highlighting their potential as potent binders. In conclusion, our study systematically explores repurposing existing FDA-approved drugs as PDE4A inhibitors through a comprehensive virtual screening pipeline. The identified compounds, Fluspirilene and Dihydroergocristine, exhibit a strong affinity for PDE4A, displaying characteristics that support their suitability for further development as potential therapeutic agents for conditions associated with PDE4A dysfunction.Communicated by Ramaswamy H. Sarma.

Identifying repurposed drugs as potential inhibitors of Apolipoprotein E: A bioinformatics approach to target complex diseases associated with lipid metabolism and neurodegeneration.

Apolipoprotein E (ApoE), a pivotal contributor to lipid metabolism and neurodegenerative disorders, emerges as an attractive target for therapeutic intervention. Within this study, we deployed an integrated in-silico strategy, harnessing structure-based virtual screening, to identify potential compounds from DrugBank database. Employing molecular docking, we unveil initial hits by evaluating their binding efficiency with ApoE. This first tier of screening narrows our focus to compounds that exhibit a strong propensity to bind with ApoE. Further, a detailed interaction analysis was carried out to explore the binding patterns of the selected hits towards the ApoE binding site. The selected compounds were then evaluated for the biological properties in PASS analysis, which showed anti-neurodegenerative properties. Building upon this foundation, we delve deeper, employing all-atom molecular dynamics (MD) simulations extending over an extensive 500 ns. In particular, Ergotamine and Dihydroergocristine emerge as noteworthy candidates, binding to ApoE in a competitive mode. This intriguing binding behavior positions these compounds as potential candidates warranting further analysis in the pursuit of novel therapeutics targeting complex diseases associated with lipid metabolism and neurodegeneration. This approach holds the promise of catalyzing advancements in therapeutic intervention for complex disorders, thereby reporting a meaningful pace towards improved healthcare outcomes.

Identification of mitogen-activated protein kinase 7 inhibitors from natural products: Combined virtual screening and dynamic simulation studies.

Mitogen-activated protein kinase 7 (MAPK7) is a serine/threonine protein kinase that belongs to the MAPK family and plays a vital role in various cellular processes such as cell proliferation, differentiation, gene transcription, apoptosis, metabolism, and cell survival. The elevated expression of MAPK7 has been associated with the onset and progression of multiple aggressive tumors in humans, underscoring the potential of targeting MAPK7 pathways in therapeutic research. This pursuit holds promise for the advancement of anticancer drug development by developing potential MAPK7 inhibitors. To look for potential MAPK7 inhibitors, we exploited structure-based virtual screening of natural products from the ZINC database. First, the Lipinski rule of five criteria was used to filter a large library of ~90,000 natural compounds, followed by ADMET and pan-assay interference compounds (PAINS) filters. Then, top hits were chosen based on their strong binding affinity as determined by molecular docking. Further, interaction analysis was performed to find effective and specific compounds that can precisely bind to the binding pocket of MAPK7. Consequently, two compounds, ZINC12296700 and ZINC02123081, exhibited significant binding affinity and demonstrated excellent drug-like properties. All-atom molecular dynamics simulations for 200 ns confirmed the stability of MAPK7-ZINC12296700 and MAPK7-ZINC02123081 docked complexes. According to the molecular mechanics Poisson-Boltzmann surface area investigation, the binding affinities of both complexes were considerable. Overall, the result suggests that ZINC12296700 and ZINC02123081 might be used as promising leads to develop novel MAPK7 inhibitors. Since these compounds would interfere with the kinase activity of MAPK7, therefore, may be implemented to control cell growth and proliferation in cancer after required validations.

An integrated docking and molecular dynamics simulation approach to discover potential inhibitors of activin receptor-like kinase 1.

Activin receptor-like kinase 1 (ALK1) is a transmembrane receptor involved in crucial signaling pathways associated with angiogenesis and vascular development. Inhibition of ALK1 signaling has emerged as a promising therapeutic strategy for various angiogenesis-related diseases, including cancer and hereditary hemorrhagic telangiectasia. This study aimed to investigate the potential of phytoconstituents as inhibitors of ALK1 using a combined approach of virtual screening and molecular dynamics (MDs) simulations. Phytoconstituents from the IMPPAT 2.0 database underwent virtual screening to identify potential inhibitors of ALK1. The compounds were initially filtered based on physicochemical parameters, following Lipinski's rules and the PAINS filter. Subsequently, compounds demonstrating high binding affinities in docking analysis were further analyzed. Additional assessments, including ADMET, PAINS, and PASS evaluations, were conducted to identify more potent hits. Through interaction analysis, a phytoconstituent, Candidine, exhibited appreciable affinity and specific interactions with the ALK1 active site. To validate the results, MD simulations and principal components analysis were performed. The MD simulations demonstrated that Candidine stabilized the ALK1 structure and reduced conformational fluctuations. In conclusion, Candidine shows promising potential as binding partners of ALK1. These findings provide a foundation for further exploration and development of Candidine as a lead molecule for therapeutic interventions targeting ALK1-associated diseases.

Identifying Phosphodiesterase-5 Inhibitors with Drug Repurposing Approach: Implications in Vasodysfunctional Disorders.

Phosphodiesterase type 5 (PDE5) is a multidomain protein that plays a crucial role in regulating cellular cyclic guanosine monophosphate (cGMP), a key signaling molecule involved in various physiological processes. Dysregulation of PDE5 and cGMP signaling is associated with a range of vasodysfunctional disorders, necessitating the development of effective therapeutic interventions. This study adopts comprehensive approach, combining virtual screening and molecular dynamics (MD) simulations, to repurpose FDA-approved drugs as potential PDE5 inhibitors. The initial focus involves selecting compounds based on their binding affinity. Shortlisted compounds undergo a meticulous analysis for their drug profiling and biological significance, followed by the activity evaluation and interaction analysis. Notably, based on binding potential and drug profiling, two molecules, Dutasteride and Spironolactone, demonstrate strong potential as PDE5 inhibitors. Furthermore, all atom MD simulations were employed (500 ns) to explore dynamic behavior of Dutasteride and Spironolactone in complexes with PDE5. Principal components analysis (PCA) and free energy landscape (FEL) analyses are further leveraged to decipher that the binding of Dutasteride and Spironolactone stabilizes the structure of PDE5 with minimal conformational changes. In summary, Dutasteride and Spironolactone exhibit remarkable affinity for PDE5 and possess characteristics that suggest their potential as therapeutic agents for conditions associated with PDE5 dysfunction.

Experimental and Computational Insights into the Molecular Interactions between Human Transferrin and Apigenin: Implications of Natural Compounds in Targeting Neuroinflammation.

Neuroinflammation plays a vital role in Alzheimer's disease (AD) pathogenesis and other neurodegenerative disorders (NDs). Presently, only symptomatic treatments are available and no disease-modifying drugs are available for AD and other NDs. Thus, targeting AD-associated neuroinflammation with anti-inflammatory compounds and antioxidants has recently been given much focus. Now, flavonoids are being increasingly investigated as therapeutic agents to treat inflammation; apigenin has a neuroprotective effect. Iron dyshomeostasis plays a key role in sustaining the neuroinflammatory phenotype, highlighting the importance of maintaining iron balance, in which human transferrin (HTF) plays a vital role in this aspect. Herein, we explored the binding and dynamics of the HTF-apigenin complex using multifaceted computational and experimental approaches. Molecular docking revealed that apigenin occupies the iron-binding pocket of HTF, forming hydrogen bonds with critical residues Arg475 and Thr686. Molecular dynamics simulations deciphered a dynamic view of the HTF-apigenin complex's behavior (300 ns) and suggested that the complex maintained a relatively stable conformation. The results of spectroscopic observations delineated significant binding of apigenin with HTF and stable HTF-apigenin complex formation. The observed binding mechanism and conformational stability could pave the way for developing novel therapeutic strategies to target neuroinflammation by apigenin in the context of iron homeostasis.

Temperature dependent charge carrier dynamics in 2D ternary Cu2MoS4 nanoflakes: An effect of electron-phonon coupling.

Two-dimensional transition metal chalcogenides (2D TMCs) like MoS2, WS2 etc., have established significant dominance in the field of nanoscience and nanotechnology, owing to their unique properties like strong light-matter interaction, high carrier mobility, large photo-responsivity etc. Despite the widespread utilization of these binary TMCs, their potential in the advancement of the optoelectronic research is limited due to the constraints in band tuning and charge carrier lifetime. To overcome these limitations, ternary transition metal chalcogenides have emerged as promising alternatives. Although, the optical properties of these materials have never been explored properly. Herein, we have investigated one such promising member of this group, Cu2MoS4 (CMS) using both steady state and time-resolved spectroscopic techniques. The material exhibits a broad range of visible light absorption, peaking at 576 nm. Photoluminescence spectroscopy confirmed the presence of both band gap emission and trap state-mediated emissions. Transient absorption spectroscopy unraveled the excited state charge carrier dynamics of CMS in sub-ps timescale, upon irradiation of visible light. We found significant influence of the trap mediated recombination, while Auger process being dominant at high charge density. We extended our study in a wide temperature range (5-300 K), which reveals the impact of electron-phonon coupling strength on the band gap and charge carrier dynamics of this material. This detailed study would draw more attention toward the unexplored optical properties of ternary 2D chalcogenides and will open new avenues for the construction of 2D material-based optical devices.

Investigating molecular interactions between human transferrin and resveratrol through a unified experimental and computational approach: Role of natural compounds in Alzheimer's disease therapeutics.

Disruptions to iron metabolism and iron homeostasis have emerged as significant contributors to the development and progression of Alzheimer's disease (AD). Human transferrin plays a key part in maintaining iron equilibrium throughout the body, highlighting its importance in AD. Many plant-derived compounds and dietary constituents show promise for preventing AD. Polyphenols that are abundant in fruits, vegetables, teas, coffee, and herbs possess neuroprotective attributes. Resveratrol is a natural polyphenol present in various plant sources like grapes, berries, peanuts, and red wine that has garnered research interest due to its wide range of biological activities. Notably, resveratrol exhibits neuroprotective effects that may help prevent or treat AD through multiple mechanisms. In the present study, we employed a combination of molecular docking and all-atom molecular dynamic simulations (MD) along with experimental approaches to unravel the intricate interactions between transferrin and resveratrol deciphering the binding mechanism. Through molecular docking analysis, it was determined that resveratrol occupies the iron binding pocket of transferrin. Furthermore, MD simulations provided a more profound insight into the stability and conformational dynamics of the complex suggesting that the binding of resveratrol introduced localized flexibility, while maintaining overall stability. The spectroscopic observations yielded clear evidence of substantial binding between resveratrol and transferrin, confirming the computational findings. The identified binding mechanism and conformational stability hold potential for advancing the development of innovative therapeutic approaches targeting AD through resveratrol, particularly concerning iron homeostasis. These insights serve as a platform for considering the natural compounds in the realm of AD therapeutics.

Comprehensive insight into the molecular interaction of rutin with human transferrin: Implication of natural compounds in neurodegenerative diseases.

Neurodegeneration, a process of irreversible neuronal damage, is characterized by a damaged neuronal structure and function. The interplay between various proteins maintains homeostasis of essential metals in the brain, shielding neurons from degeneration; human transferrin (Htf) is essential in maintaining iron homeostasis. Any disruption in iron homeostasis results in the development of neurodegenerative diseases (NDs) and their pathology, mainly Alzheimer's disease (AD). Rutin is a known compound for its neuroprotective effects. In this work, we deciphered the binding of rutin with Htf in a bid to understand the interaction mechanism. The results of fluorescence and UV-vis spectroscopy demonstrated strong interaction between rutin and Htf. The enthalpy change (∆H°) and entropy change (∆S°) analysis demonstrated hydrophobic interactions as the prevalent forces. The binding mechanism of rutin was further assessed atomistically by molecular docking and extensive 200 ns molecular dynamic simulation (MD) studies; molecular docking showed binding of rutin within Htf's binding pocket. MD results suggested that binding of rutin to Htf does not cause significant structural switching or disruption of the protein's native packing. Overall, the study deciphers the binding of rutin with hTf, delineating the binding mechanism and providing a platform to use rutin in NDs therapeutics.

Clinical Significance of MicroRNAs, Long Non-Coding RNAs, and CircRNAs in Cardiovascular Diseases.

Based on recent research, the non-coding genome is essential for controlling genes and genetic programming during development, as well as for health and cardiovascular diseases (CVDs). The microRNAs (miRNAs), lncRNAs (long ncRNAs), and circRNAs (circular RNAs) with significant regulatory and structural roles make up approximately 99% of the human genome, which does not contain proteins. Non-coding RNAs (ncRNA) have been discovered to be essential novel regulators of cardiovascular risk factors and cellular processes, making them significant prospects for advanced diagnostics and prognosis evaluation. Cases of CVDs are rising due to limitations in the current therapeutic approach; most of the treatment options are based on the coding transcripts that encode proteins. Recently, various investigations have shown the role of nc-RNA in the early diagnosis and treatment of CVDs. Furthermore, the development of novel diagnoses and treatments based on miRNAs, lncRNAs, and circRNAs could be more helpful in the clinical management of patients with CVDs. CVDs are classified into various types of heart diseases, including cardiac hypertrophy (CH), heart failure (HF), rheumatic heart disease (RHD), acute coronary syndrome (ACS), myocardial infarction (MI), atherosclerosis (AS), myocardial fibrosis (MF), arrhythmia (ARR), and pulmonary arterial hypertension (PAH). Here, we discuss the biological and clinical importance of miRNAs, lncRNAs, and circRNAs and their expression profiles and manipulation of non-coding transcripts in CVDs, which will deliver an in-depth knowledge of the role of ncRNAs in CVDs for progressing new clinical diagnosis and treatment.

Structure-based identification of potential inhibitors of ribosomal protein S6 kinase 1, targeting cancer therapy: a combined docking and molecular dynamics simulations approach.

Ribosomal protein S6 kinase 1 (S6K1), commonly known as P70-S6 kinase 1 (p70S6), is a key protein kinase involved in cellular signaling pathways that regulate cell growth, proliferation, and metabolism. Its significant role is reported in the PIK3/mTOR signaling pathway and is associated with various complex diseases, including diabetes, obesity, and different types of cancer. Due to its involvement in various physiological and pathological conditions, S6K1 is considered as an attractive target for drug design and discovery. One way to target S6K1 is by developing small molecule inhibitors that specifically bind to its ATP-binding site, preventing its activation and thus inhibiting downstream signaling pathways necessary for cell growth and survival. In this study, we have conducted a multitier virtual screening of a pool of natural compounds to identify potential S6K1 inhibitors. We performed molecular docking on IMPPAT 2.0 library and selected top hits based on their binding affinity, ligand efficiency, and specificity towards S6K1. The selected hits were further assessed based on different filters of drug-likeliness where two compounds (Hecogenin and Glabrene) were identified as potential leads for S6K1 inhibition. Both compounds showed appreciable affinity, ligand efficiency and specificity towards S6K1 binding pocket, drug-like properties, and stable protein-ligand complexes in molecular dynamics (MD) simulations. Finally, our study has suggested that Hecogenin and Glabrene can be potential S6K1 inhibitors which are presumably implicated in the therapeutic management of associated diseases such as diabetes, obesity, and varying types of cancer.Communicated by Ramaswamy H. Sarma.

Recent Clinical Advances on Long Non-Coding RNAs in Triple-Negative Breast Cancer.

Triple-negative breast cancer (TNBC) is a more aggressive type of breast cancer due to its heterogeneity and complex molecular mechanisms. TNBC has a high risk for metastasis, and it is difficult to manage clinical conditions of the patients. Various investigations are being conducted to overcome these challenges using RNA, DNA, and proteins for early diagnosis and treatment. Recently, long non-coding RNAs (lncRNAs) have emerged as a novel target to treat the multistep process of TNBC. LncRNAs regulate epigenetic expression levels, cell proliferation and apoptosis, and tumour invasiveness and metastasis. Thus, lncRNA-based early diagnosis and treatment options could be helpful, especially for patients with severe TNBC. lncRNAs are expressed in a highly specific manner in cells and tissues and are involved in TNBC progression and development. lncRNAs could be used as sensitive and specific targets for diagnosis, treatment, and monitoring of patients with TNBC. Therefore, the exploration of novel diagnostic and prognostic biomarkers is of extreme importance. Here, we discuss the molecular advances on lncRNA regulation of TNBC and lncRNA-based early diagnosis, treatment, and drug resistance.