Development of New Inhibitors of HDAC1-3 Enzymes Aided by In Silico Design Strategies

Chemical-based epigenetic reprogramming to advance pluripotency and totipotency

Reprogramming technology, breaking the inherent limitations of cellular identity and turning somatic cells into pluripotent cells with more developmental potential, holds great promise for cell therapy and regenerative medicine. Compared with traditional methods based on overexpressing transcription factors, chemical reprogramming with small molecules exhibits substantial advantages in safety and convenience, thus being the leading edge. Over the past decade, a notable focus has been reshaping cellular pluripotency and totipotency using pure small-molecule systems. Here, we provide a concise Review comparing the chemical approaches that have emerged to date and discussing the epigenetic regulatory mechanisms involved in chemical reprogramming. This Review highlights the remarkable potential of small-molecule potions to reformulate cell fate through epigenetic reprogramming and newly discovered actions. We aim to offer insights into chemically controlled cell manipulation and key challenges and future application prospects of chemical reprogramming.

Computational insights in repurposing a cardiovascular drug for Alzheimer's disease: the role of aromatic amino acids in stabilizing the drug through π-π stacking interaction

Alzheimer's disease (AD) is a neurological condition that worsens over time and causes linguistic difficulties, cognitive decline, and memory loss. Since AD is a complicated, multifaceted illness, it is critical to identify drugs to combat this degenerative condition. Histone deacetylase 2 (HDAC2) represents a promising epigenetic target for neurodegenerative diseases. So, for this study, we chose HDAC2 as the targeted protein. Repurposing drugs has many advantages, including reduced costs and high profits. There is a lower probability of malfunction because the unique drug candidate has previously completed numerous investigations. In this study, we have taken 58 clinically approved food and drug administration (FDA) drugs utilized in clinical trials for AD. Molecular docking was carried out for the 58 compounds. The telmisartan drug has the highest binding score of -9.4 kcal mol-1. The angiotensin II receptor blocker (ARB) telmisartan has demonstrated some promise in AD research as of the last update in January 2022. However, its exact significance in treating or preventing AD is still being studied. Molecular dynamics (MD) and molecular mechanics with generalized born and surface area solvation (MM-GBSA)/interaction entropy (IE) calculations were carried out to study the structural stability of the complexes. Umbrella sampling (US) techniques are a cutting-edge drug development method to understand more about the interactions between protein and ligand. π-π stacking interactions play a major role in helping the ligand to bind in the zinc bounding domain of the protein. From these analyses, we conclude that telmisartan, which is a cardiovascular drug, is more potent than the other drugs to treat AD. The anti-inflammatory, neuroprotective, and blood-brain barrier-crossing qualities of telmisartan make it a promising therapeutic agent for AD; however, more research, including larger clinical trials, is needed to determine the drug's precise role in treating AD.

Pharmacophore modeling, 3D-QSAR, and MD simulation-based overture for the discovery of new potential HDAC1 inhibitors

Histone deacetylases (HDACs) are important epigenetic regulators that modulate the activity of histone and non-histone proteins leading to various cancers. Histone deacetylase 1 (HDAC1) is a member of class 1 HDAC family related to different cancers. However, the nonselective profile of existing HDAC1 inhibitors restricted their clinical utility. Therefore, the identification of new HDAC1 selective inhibitors may be fruitful against cancer therapy. In this present work, a pharmacophore model was built using 60 benzamide-based known HDAC1 selective inhibitors and it was used further to filter the large epigenetic molecular database of small molecules. Further, the 3D-QSAR model was built using the best common pharmacophore hypothesis consisting of higher PLS statistics of R2 of 0.89, Q2 of 0.83, variance ratio (F) of 65.7 and Pearson-r value of 0.94 revealing the model reliability and its high predictive power. The screened hits of the pharmacophore model were then subjected to molecular docking against HDAC1 to identify high-affinity lead molecules. The top 10 hits were ranked from the docking studies using docking scores for lead optimization. The potential hit molecules M1 and M2 identified from the study showed promising interaction during HDAC1 docking and MD simulation studies with acceptable ADME properties. Also, the newly designed lead compounds M11 and M12 may be considered highly potential inhibitors against HDAC1. The 3D-QSAR analysis, conformational requirements, and observations noticed in the MD simulations study will enable the optimization of lead molecules and to design of novel effective, and selective HDAC1 inhibitors in the future.

Key structural requirements of benzamide derivatives for histone deacetylase inhibition: design, synthesis and biological evaluation

Background: Histone deacetylase inhibitors (HDACIs) are important as anticancer agents. Objective: This study aimed to investigate some key structural features of HDACIs via the design, synthesis and biological evaluation of novel benzamide-based derivatives. Methods: Novel structures, designed using a molecular modification approach, were synthesized and biologically evaluated. Results: The results indicated that a subset of molecules with CH3/NH2 at R2 position possess selective antiproliferative activity. However, only those with an NH2 group showed HDACI activity. Importantly, the shorter the molecule length, the stronger HDACI. Among all, 7j was the most potent HDAC1-3 inhibitor and antiproliferative compound. Conclusion: The results of the present investigation could provide valuable structural knowledge applicable for the development of the HDACIs and benzamide-based antiproliferative agents in the future.

Exploration of novel hydroxamate zinc binding group inhibitors against HDAC-1-3 enzymes by AI-based virtual screening: atomistic insights from steered molecular dynamics

Overexpression of histone deacetylase (HDAC) enzymes is linked to a wide variety of illnesses, including malignancies and neurological disorders, which makes HDAC inhibitors potentially therapeutic. However, most HDAC inhibitors lack subclass or isoform selectivity, which can be dangerous. Featuring both enhanced selectivity and toxicity profiles, slow-binding HDAC inhibitors offer promising treatment options for a variety of disorders. Diseases like cardiac, neurodegenerative disorders and diabetes are mainly associated with the HDAC1, HDAC2 and HDAC3 enzymes. The AI-based virtual screening tool PyRMD is implemented to identify the potential inhibitors from ∼2 million compounds. Based on the IC50 values, the top 10 compounds were selected for molecular docking. From the docking and ADMET study, the top-ranked three compounds were selected for molecular dynamics (MD) simulations. Further, to get more insights into the binding/unbinding mechanism of the ligand, we have employed the steered molecular dynamics (SMD) simulations. This study assists in developing Amber force field parameters for the HDAC1, HDAC2 and HDAC3 proteins and sheds light on the discovery of a potent drug. Our study suggests that hydroxamic acid derivative (i.e. referred to as Comp-1, CHEMBL600072) is the potential inhibitor for the series of HDAC-related diseases.

Herbicidal Activity of Beflubutamid Analogues as PDS Inhibitors and SAR Analysis and Degradation Dynamics in Wheat

In this work, a series of beflubutamid (BF) analogues' postemergent herbicidal activity was evaluated, and the structure-activity relationship (SAR) was discussed. At a dosage of 300 g ai/ha, compounds (Rac)-6h and (Rac)-6q showed excellent herbicidal activity against Amaranthus retroflexus, Abutilon theophrasti, and Medicago sativa, with inhibition rates of 90, 100, and 80% and 100, 100, and 100%, respectively, comparable to that of commercial herbicide BF, which showed inhibition rates of 90, 100, and 100%, respectively. Notably, at dosages of 150 and 300 g ai/ha, the chiral compounds (S)-6h and (S)-6q exhibited higher herbicidal activities than their racemates. Molecular docking results indicated that compounds (S)-BF and (S)-6h have stronger binding affinities with Oryza sativa phytoene desaturase (OsPDS), resulting in a higher herbicidal activity. Additionally, the degradation dynamics half-life of (S)-BF in wheat was determined to be 77.02 h. Consequently, compounds (S)-6h and (S)-6q are promising lead candidates for the development of highly effective herbicides.

Phenylacetyl-/Trolox- Amides: Synthesis, Sigma-1, HDAC-6, and Antioxidant Activities

In search of novel multi-mechanistic approaches for treating Alzheimer's disease (AD), we have embarked on synthesizing single small molecules for probing contributory roles of the following combined disease targets: sigma-1 (σ-1), class IIb histone deacetylase-6 (HDAC-6), and oxidative stress (OS). Herein, we report the synthesis and partial evaluation of 20 amides (i.e., phenylacetic and Trolox or 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid derivatives). Target compounds were conveniently synthesized via amidation by either directly reacting acyl chlorides with amines or condensing acids with amines in the presence of coupling agents 1-[bis(dimethylamino)methylene]-1H-1,2,3-triazolo [4,5-b] pyridinium 3-oxide hexafluorophosphate (HATU) or 1,1'-carbonyldiimidazole (CDI). Overall, this project afforded compound 8 as a promising lead with σ-1 affinity (Ki = 2.1 μM), HDAC-6 (IC50 = 17 nM), and antioxidant (1.92 Trolox antioxidant equivalents or TEs) activities for optimization in ensuing structure-activity relationship (SAR) studies.

Recent updates in click and computational chemistry for drug discovery and development

Drug discovery is a costly and time-consuming process with a very high failure rate. Recently, click chemistry and computer-aided drug design (CADD) represent popular areas for new drug development. Herein, we summarized the recent updates in click and computational chemistry for drug discovery and development including clicking to effectively synthesize druggable candidates, synthesis and modification of natural products, targeted delivery systems, and computer-aided drug discovery for target identification, seeking out and optimizing lead compounds, ADMET prediction as well as compounds synthesis, hopefully, inspires new ideas for novel drug development in the future.

Current trends in development of HDAC-based chemotherapeutics

BACKGROUND

Histone deacetylases (HDACs) are one of the essential epigenetic targets in cancer treatment. These enzymes play key roles in post-translation modification (PTM) and gene expression, and consequently, their inhibitors are about to find their place in pharmacotherapy. Most of the currently approved HDAC inhibitors (HDACIs) are wide-spectrum with poor clinical outcomes and numerous side effects. Therefore, new generations of HDAC-based chemotherapeutics with better clinical outcomes are emerging, e.g., isoform-selective inhibitors, multitargeted HDACIs, as well as HDAC degraders.

AIM

The review intended to introduce drug design approaches which were used for designing novel agents which can be beneficial in the process of finding new and more effective HDACI-based therapeutics.

METHODS

PubMed and other databases were searched for literature regarding the structure-function of HDAC isoforms, and strategies used to design HDAC inhibitors. Also, all clinical trials available from the ClinicalTrials site for years 2021-2022 were investigated.

KEY FINDINGS

It is expected that the future of drug discovery projects in HDAC field will concentrate mostly on issues such as isoform-selectivity, multitargeted HDAC inhibitors and HDAC degraders. Deeper knowledge of the 3D structure of HDACs complexed with inhibitors and extensive delineation of biological roles of HDACs are needed for efficient investigations leading to the discovery of novel potent inhibitors.

SIGNIFICANCE

Histone deacetylases (HDACs) are one of the important epigenetic targets in cancer treatment drug discovery. Comprehending the structure of HDAC isoforms along with applied drug design strategies can inspire new ideas.