HT_PREDICT: a machine learning-based computational open-source tool for screening HDAC6 inhibitors.

Histone deacetylase 6 (HDAC6) is a promising drug target for the treatment of human diseases such as cancer, neurodegenerative diseases (in particular, Alzheimer's disease), and multiple sclerosis. Considerable attention is paid to the development of selective non-toxic HDAC6 inhibitors. To this end, we successfully form a set of 3854 compounds and proposed adequate regression QSAR models for HDAC6 inhibitors. The models have been developed using the PubChem, Klekota-Roth, 2D atom pair fingerprints, and RDkit descriptors and the gradient boosting, support vector machines, neural network, and k-nearest neighbours methods. The models are integrated into the developed HT_PREDICT application, which is freely available at https://htpredict.streamlit.app/. In vitro studies have confirmed the predictive ability of the proposed QSAR models integrated into the HT_PREDICT web application. In addition, the virtual screening performed with the HT_PREDICT web application allowed us to propose two promising inhibitors for further investigations.

HDAC6 detector: online application for evaluating compounds as potential histone deacetylase 6 inhibitors.

The HDAC6 (histone deacetylase 6) enzyme plays a key role in many biological processes, including cell division, apoptosis, and immune response. To date, HDAC6 inhibitors are being developed as effective drugs for the treatment of various diseases. In this work, adequate QSAR models of HDAC6 inhibitors are proposed. They are integrated into the developed application HDAC6 Detector, which is freely available at https://ovttiras-hdac6-detector-hdac6-detector-app-yzh8y5.streamlit.app/. The web application HDAC6 Detector can be used to perform virtual screening of HDAC6 inhibitors by dividing the compounds into active and inactive ones relative to the reference vorinostat compound (IC50 = 10.4 nM). The web application implements a structural interpretation of the developed QSAR models. In addition, the application can evaluate the compliance of a compound with Lipinski's rule. The developed models are used for virtual screening of a series of 12 new hydroxamic acids, namely, the derivatives of 3-hydroxyquinazoline-4(3H)-ones and 2-aryl-2,3-dihydroquinazoline-4(1H)-ones. In vitro evaluation of the inhibitory activity of this series of compounds against HDAC6 allowed us to confirm the results of virtual screening and to select promising compounds V-6 and V-11, the IC50 of which is 0.99 and 0.81 nM, respectively.

HDAC1 PREDICTOR: a simple and transparent application for virtual screening of histone deacetylase 1 inhibitors.

Histone deacetylases play an important role in regulating gene expression by modifying histones and changing chromatin conformation. HDAC dysregulation is involved in many diseases, such as cancer, autoimmune and neurodegenerative diseases. Histone deacetylase 1 (HDAC1) inhibitors represent an important class of drugs. Quantitative Structure-Activity Relationship (QSAR) classification models were developed using 2D RDKit molecular descriptors; ECPF4 (Extended Connectivity Fingerprint) circular fingerprints; and the Random Forest, Gradient Boosting, and Support Vector Machine methods. The developed models were integrated into the HDAC1 PREDICTOR application, which is freely available at the link https://ovttiras-hdac1-inhibitors-hdac1-predictor-app-z3mrbr.streamlitapp.com. The HDAC1 PREDICTOR web application allows one to reveal the compounds for which the predicted activity to inhibit HDAC1 is higher than that of the reference Vorinostat compound (IC50 = 11.08 nM). The algorithm implemented in HDAC1 PREDICTOR for determining the contributions of molecular fragments to the inhibitory activity can be used to find the molecule segments that increase or decrease the activity, enabling the researcher to conduct a rational molecular design of new highly active HDAC1 inhibitors. The developed QSAR models and the code for their construction in the Python programming language are freely available on the GitHub platform at https://github.com/ovttiras/HDAC1-inhibitors.

QSAR analysis and experimental evaluation of new quinazoline-containing hydroxamic acids as histone deacetylase 6 inhibitors.

Histone deacetylase inhibitors represent the most important class of drugs for the treatment of human cancer and other diseases due to their influence on cell growth, differentiation, and apoptosis. Among the well-known eighteen histone deacetylases, histone deacetylase 6 (HDAC6), which is involved in oncogenesis, cell survival, and cancer cell metastasis, is of great importance. Using the CDK and alvaDesc molecular descriptors and the Random Forest and EXtreme Gradient Boosting methods, we propose a number of adequate QSAR classification models, which are integrated into a consensus model and are freely available on the OCHEM web platform (https://ochem.eu). The consensus QSAR model is used for virtual screening of a series of seven new compounds, the derivatives of N-((hydroxyamino)-oxoalkyl)-2-(quinazoline-4-ilamino)-benzamides, the synthesis schemes of which are also presented in this work. In vitro evaluation of the inhibitory activity (IC50) of this series of compounds against HDAC6 allowed us to confirm the results of virtual screening and to reveal promising compounds V-2 and V-4, IC50 of which is 3.25 nM and 0.04 nM, respectively. The subsequent in silico evaluation of the main ADMET properties of active compounds V-2 and V-4 allowed us to find that they have acceptable pharmacokinetic parameters and level of acute toxicity.

[Mechanisms of cytotoxic action of a series of directionally synthesized heterocyclic hydroxamic acids]. / Mekhanizmy tsitotoksicheskogo deistviia riada tsiklicheskikh gidroksamovykh kislot.

Cyclic hydroxamic acids based on quinazoline-4(3H)-one and dihydroquinazoline-4(1H)-one have been synthesized. The antioxidant and iron-chelating properties of these compounds, their effect on the activity of the histone deacetylase enzyme, and their cytotoxic effect on cells of various tumor lines have been investigated. We have identified two compounds-hits, which exhibit the multipharmacological type of the antineoplastic activity. Their cytotoxic effect on cells of human lung carcinoma A549 and breast adenocarcinoma MCF-7 is obviously associated with their ability to modulate the level of reactive oxygen species and to chelate Fe(II) ions, as well as to inhibit the metalloenzymes, histone deacetylases, involved in the epigenetic regulation of tumor genesis. Thus, the synthesized hydroxamic acids may be considered as a promising basis for creating potential oncolytics.