Proteochemometric Modeling of the Interaction Space of Carbonic Anhydrase and its Inhibitors: An Assessment of Structure-based and Sequence-based Descriptors

Proteochemometric Method for pIC50 Prediction of Flaviviridae

Viruses remain an area of concern despite constant development of antiviral drugs and therapies. One of the contributors is the Flaviviridae family of viruses causing diseases that need attention. Among other anitviral methods, antiviral peptides are being studied as viable candidates. Although antiviral peptides (AVPs) are emerging as potential therapeutics, it is important to assess the efficacy of a given peptide in terms of its bioactivity. Experimental identification of the bioactivity of each potential peptide is an expensive and time consuming task. Computational methods like proteochemometric modeling (PCM) is a promising method for prediction of bioactivity (pIC50) based on peptide and target sequence pair. In this study, we propose a prediction of pIC50 of AVP against the Flaviviridae family that may help make the decision to choose a peptide with desired efficacy. The peptides data was collected from a public database and target sequences were manually curated from literature. Features are calculated using peptide and target sequence PCM descriptors which consist of individual and cross-term features of peptide and respective target. The resultant R² and MAPE values are 0.85 and 8.44%, respectively, for prediction of pIC50 value of AVPs.

New insights into the selective inhibition of the β-carbonic anhydrases of pathogenic bacteria Burkholderia pseudomallei and Francisella tularensis: a proteochemometrics study

Nowadays, antibiotic resistance has turned into one of the most important worldwide health problems. Biological end point of critical enzymes induced by potent inhibitors is recently being considered as a highly effective and popular strategy to defeat antibiotic-resistant pathogens. For instance, the simple but critical β-carbonic anhydrase has recently been in the center of attention for anti-pathogen drug discoveries. However, no β-carbonic anhydrase selective inhibitor has yet been developed. Available β-carbonic anhydrase inhibitors are also highly potent with regard to human carbonic anhydrases, leading to severe inevitable side effects in case of usage. Therefore, developing novel inhibitors with high selectivity against pathogenic β-carbonic anhydrases is of great essence. Herein, for the first time, we have conducted a proteochemometric study to explore the structural and the chemical aspects of the interactions governed by bacterial β-carbonic anhydrases and their inhibitors. We have found valuable information which can lead to designing novel inhibitors with better selectivity for bacterial β-carbonic anhydrases.

Probing the chemical interaction space governed by 4-aminosubstituted benzenesulfonamides and carbonic anhydrase isoforms

Isoform diversity, critical physiological roles and involvement in major diseases/disorders such as glaucoma, epilepsy, Alzheimer's disease, obesity, and cancers have made carbonic anhydrase (CA), one of the most interesting case studies in the field of computer aided drug design. Since applying non-selective inhibitors can result in major side effects, there have been considerable efforts so far to achieve selective inhibitors for different isoforms of CA. Using proteochemometrics approach, the chemical interaction space governed by a group of 4-amino-substituted benzenesulfonamides and human CAs has been explored in the present study. Several validation methods have been utilized to assess the validity, robustness and predictivity power of the proposed proteochemometric model. Our model has offered major structural information that can be applied to design new selective inhibitors for distinct isoforms of CA. To prove the applicability of the proposed model, new compounds have been designed based on the offered discriminative structural features.

Exploring the origin of phosphodiesterase inhibition via proteochemometric modeling

A proteochemometric study of a set of phosphodiesterase 4B and 4D inhibitors sheds light on the origin of their inhibition and selectivities.