First report on predictive chemometric modeling, 3D-toxicophore mapping and in silico screening of in vitro basal cytotoxicity of diverse organic chemicals

Histone deacetylase 8 in focus: Decoding structural prerequisites for innovative epigenetic intervention beyond hydroxamates

Histone deacetylase 8 (HDAC8) inhibitors play a pivotal role in epigenetic regulation. Numerous HDAC8 inhibitors (HDAC8is), that are non-hydroxamates have been identified to date, and a few of them exhibit antiproliferative activity that is on par with hydroxamates. While many non-hydroxamate-based HDAC8is have demonstrated selectivity, hydroxamate-based HDAC8is, like Vorinostat and TSA, have a tendency of non-specificity among the different HDAC isoforms. Moreover, because of the unfavorable toxic side effects, there are significant concerns surrounding the use of hydroxamate derivatives as therapeutic agents in cancer as well as other chronic diseases. Consequently, the research on non-hydroxamate-based HDAC8is is of utmost priority. In the present study, a comprehensive study was presented to unravel the structural requirements of non-hydroxamate-based HDAC8is from a diverse set of 866 compounds. The study utilized Classification-based Quantitative Structure-Activity Relationship (QSAR) analysis, incorporating Bayesian classification, Recursive partitioning, and other machine learning methods to pinpoint the key structural features essential for HDAC8 inhibition. To underscore and gain deeper insights into the identified structural features, molecular docking, and molecular dynamic (MD) simulation studies were conducted. The integration of these computational approaches unveiled key structural motifs essential for potent HDAC8 inhibitory activity, shedding light on the molecular basis of HDAC8 inhibition using non-hydroxamates.

A fragment-based exploration of diverse MMP-9 inhibitors through classification-dependent structural assessment

Matrix metalloproteinases (MMPs) are belonging to the Zn2+-dependent metalloenzymes. These can degenerate the extracellular matrix (ECM) that is entailed with various biological processes. Among the MMP family members, MMP-9 is associated with several pathophysiological circumstances. Apart from wound healing, remodeling of bone, inflammatory mechanisms, and rheumatoid arthritis, MMP-9 has also significant roles in tumor invasion and metastasis. Therefore, MMP-9 has been in the spotlight of anticancer drug discovery programs for more than a decade. In this present study, classification-based QSAR techniques along with fragment-based data mining have been carried out on divergent MMP-9 inhibitors to point out the important structural attributes. This current study may be able to elucidate the importance of several pivotal molecular fragments such as sulfonamide, hydroxamate, i-butyl, and ethoxy functions for imparting potential MMP-9 inhibition. These observations are in correlation with the ligand-bound co-crystal structures of MMP-9. Therefore, these findings are beneficial for the design and discovery of effective MMP-9 inhibitors in the future.

First structure-activity relationship analysis of SARS-CoV-2 virus main protease (Mpro) inhibitors: an endeavor on COVID-19 drug discovery

Main protease (Mpro) of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) intervenes in the replication and transcription processes of the virus. Hence, it is a lucrative target for anti-viral drug development. In this study, molecular modeling analyses were performed on the structure activity data of recently reported diverse SARS-CoV-2 Mpro inhibitors to understand the structural requirements for higher inhibitory activity. The classification-based quantitative structure-activity relationship (QSAR) models were generated between SARS-CoV-2 Mpro inhibitory activities and different descriptors. Identification of structural fingerprints to increase or decrease in the inhibitory activity was mapped for possible inclusion/exclusion of these fingerprints in the lead optimization process. Challenges in ADME properties of protease inhibitors were also discussed to overcome the problems of oral bioavailability. Further, depending on the modeling results, we have proposed novel as well as potent SARS-CoV-2 Mpro inhibitors.

First Report on the Validated Classification-Based Chemometric Modeling of Human Rhinovirus 3C Protease (HRV 3Cpro) Inhibitors

Human rhinoviruses (HRVs), a major cause of common cold and upper respiratory infections, may trigger severe respiratory complications like asthma and COPD. To date, no drugs are available in the market which are designed as novel HRV inhibitors despite the involvement of some pharmaceutical companies' due to economical and clinical constraints. HRV 3C protease may be a potential target for drug design as it plays crucial role in viral RNA replication and virion assembly process. Therefore, designing novel HRV 3Cpro inhibitors is necessary and demanding in the field of antiviral drug design. In this article, statistically significant and validated classification-based QSARs of a series of HRV 3Cpro inhibitors were performed for the first time as per the authors' knowledge. Results suggest that oxopyrrolidine and piperidinone rings are favored whereas carboxybenzyl and unsubstituted benzyl functions may be unfavorable. Moreover, this group, along with cyclic alkyl or aryl ring structures may favor HRV 3Cpro inhibition. These observations may be utilized for the design of a higher active anti-HRV agent in future.

The rm2 metrics and regression through origin approach: reliable and useful validation tools for predictive QSAR models (Commentary on 'Is regression through origin useful in external validation of QSAR models?')

Quantitative structure-activity relationship (QSAR) is an in silico technique which can be used in drug discovery, environmental fate modeling, property and toxicity prediction of chemical entities and regulatory toxicology. The predictive potential of a QSAR model is judged from various validation metrics in order to evaluate how well it is capable to predict endpoint values of new untested compounds. The rm2 group of metrics is one of the stringent validation metrics currently used by the QSAR fraternity in different reports. We scrutinized a recently published paper which raised an issue that the constructed criteria based on regression through origin (RTO) are not optimal and there is a significant difference in the rm2 metrics values computed from different statistical software packages. According to our point of view, the conclusion drawn in this paper appears to be misleading. Any inconsistency in the software algorithms has nothing to do with the calculation of rm2 metrics, as such computation is not limited by the use of any specific software, rather it depends only on fundamental mathematical formulae that are well established. However, it is a concern to the QSAR users that Excel and SPSS can return different results for the metrics using the RTO method. Thus, a proper validation of the software tool is required before its use for computation of any validation metric.

Exploring QSTR modeling and toxicophore mapping for identification of important molecular features contributing to the chemical toxicity in Escherichia coli

Biodiversity deprivation can affect functions and services of the ecosystem. Changes in biodiversity alter ecosystem processes and change the resilience of ecosystems to ecological changes. Bacterial communities are the main form of biomass in the ecosystem and one of largest populations on the planet. Bacterial communities provide important services to biodiversity. They break down pollutants, municipal waste and ingested food, and they are the primary route for recycling of organic matter to plants and other autotrophs, conversion of inorganic matter into new biological tissue using sunlight, management of energy crisis through use of biofuel. In the present study, computational chemistry and statistical modeling have been used to develop mathematical equations which can be applied to calculate toxicity of new/unknown chemicals/biofuels/metabolites in Escherichia coli. 2D and 3D descriptors were generated from molecular structure of compounds and mathematical models have been developed using genetic function approximation followed by multiple linear regression (GFA-MLR) method. Model validity was checked through defined internal (R(2)=0.751 and Q(2)=0.711), and external (Rpred(2)=0.773) statistical parameters. Molecular features responsible for toxicity were also assessed through 3D toxicophore study. The toxicophore-based model was validated (R=0.785) using qualitative statistical metrics and randomization test (Fischer validation).