Discovery of covalent prolyl oligopeptidase boronic ester inhibitors

The Rise of Boron-Containing Compounds: Advancements in Synthesis, Medicinal Chemistry, and Emerging Pharmacology

Boron-containing compounds (BCC) have emerged as important pharmacophores. To date, five BCC drugs (including boronic acids and boroles) have been approved by the FDA for the treatment of cancer, infections, and atopic dermatitis, while some natural BCC are included in dietary supplements. Boron's Lewis acidity facilitates a mechanism of action via formation of reversible covalent bonds within the active site of target proteins. Boron has also been employed in the development of fluorophores, such as BODIPY for imaging, and in carboranes that are potential neutron capture therapy agents as well as novel agents in diagnostics and therapy. The utility of natural and synthetic BCC has become multifaceted, and the breadth of their applications continues to expand. This review covers the many uses and targets of boron in medicinal chemistry.

Computational and biophysical methods for the discovery and optimization of covalent drugs

Drugs that act by covalently attaching to their targets have been used to treat human diseases for over a hundred years. However, the deliberate design of covalent drugs was discouraged due to concerns of toxicity and off-target effects. Recent successes in covalent drug discovery have sparked fresh interest in this field. New screening and testing methods aimed at covalent inhibitors can play pivotal roles in facilitating the discovery process. This feature article focuses on computational and biophysical advances originating from our labs over the past decade and how these approaches have contributed to the design of prolyl oligopeptidase (POP) and SARS-CoV-2 3CLpro covalent inhibitors.

Docking Ligands into Flexible and Solvated Macromolecules. 8. Forming New Bonds─Challenges and Opportunities

Over the years, structure-based design programs and specifically docking small molecules to proteins have become prominent in drug discovery. However, many of these computational tools have been developed to primarily dock enzyme inhibitors (and ligands to other protein classes) relying heavily on hydrogen bonds and electrostatic and hydrophobic interactions. In reality, many drug targets either feature metal ions, can be targeted covalently, or are simply not even proteins (e.g., nucleic acids). Herein, we describe several new features that we have implemented into Fitted to broaden its applicability to a wide range of covalent enzyme inhibitors and to metalloenzymes, where metal coordination is essential for drug binding. This updated version of our docking program was tested for its ability to predict the correct binding mode of drug-sized molecules in a large variety of proteins. We also report new datasets that were essential to demonstrate areas of success and those where additional efforts are required. This resource could be used by other program developers to assess their own software.

Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CLpro covalent inhibitors

Severe diseases such as the ongoing COVID-19 pandemic, as well as the previous SARS and MERS outbreaks, are the result of coronavirus infections and have demonstrated the urgent need for antiviral drugs to combat these deadly viruses. Due to its essential role in viral replication and function, 3CLpro (main coronaviruses cysteine-protease) has been identified as a promising target for the development of antiviral drugs. Previously reported SARS-CoV 3CLpro non-covalent inhibitors were used as a starting point for the development of covalent inhibitors of SARS-CoV-2 3CLpro. We report herein our efforts in the design and synthesis of submicromolar covalent inhibitors when the enzymatic activity of the viral protease was used as a screening platform.

Investigation of interaction between boronic acids and sugar: effect of structural change of sugars on binding affinity using steady state and time resolved fluorescence spectroscopy and molecular docking

Binding interactions of boronic acid derivatives viz. 2-Methylphenylboronic acid (B1) and 3-Methoxyphenylboronic acid (B2) with mono saccharides (arabinose, fructose and galactose) and disaccharides (sucrose, lactose and maltose) in aqueous condition at pH 7.4 by means of fluorescence spectroscopy is reported in the present investigation. Sugar sensing as well as continuous glucose monitoring (CGM) plays a significant role in diabetes regulation. Sugar sensors mediated through enzymes have their own drawbacks, which led to encouragement to search for designing new sensors through alternate approaches. Among many, fluorescence-based sensors are drawing more attention. Boronic acid-based fluorescence sensors have the capacity to bind reversibly with diols, which makes their demand high in applications. Addition of sugar reduces fluorescence intensities. Change in intensities is associated to cleavage of intermolecular hydrogen bonding which leads in reduced stability of boronate ester. Lineweaver-Burk and Benesi-Hildebrand equation is used for analysing data. Mono sugars are estimated to have higher binding constants. Mutarotation leads to structural changes in saccharides which play a key role in binding interactions. Sugars in furanose form are found to be highly favoured for binding. Molecular docking of B1 and B2 with proteins with PDB ID: 2IPL and 2IPM being periplasmic was done with the help of Schrodinger Maestro 11.2 version. GLIDE scores terms are used for expressing binding affinity.

Understanding the binding interaction between phenyl boronic acid P1 and sugars: determination of association and dissociation constants using S-V plots, steady-state spectroscopic methods and molecular docking

Continuous monitoring of glucose and sugar sensing plays a vital role in diabetes control. The drawbacks of the present enzyme-based sugar sensors have encouraged the investigation into alternate approaches to design new sensors. The popularity of fluorescence sensors is due to their ability to bind reversibly to compounds containing diol. In this study we investigated the binding ability of phenyl boronic acid P1 for monosaccharides and disaccharides (sugars) in aqueous medium at physiological pH 7.4 using steady-state fluorescence and absorbance. P1 fluorescence was quenched due to formation of esters with sugars. Absorbance and fluorescence measurements led to results that indicated that the sugars studied could be ordered in terms of their affinity to P1, as stated: sucrose > lactose > galactose > xylose > ribose > arabinose. In each case, the slope of modified Stern-Volmer plots was nearly 1, indicating the presence of only a single binding site in boronic acids for sugars. Docking studies were carried out using Schrodinger Maestro v.11.2 software. The binding affinity of phenyl boronic acid P1 with periplasmic protein (PDB ID 2IPM and 2IPL) was estimated using GlideScore.

Ferrocene-containing hybrids as potential anticancer agents: Current developments, mechanisms of action and structure-activity relationships

Cancer is one of the most fatal threatens to human health throughout the world. The major challenges in the control and eradication of cancers are the continuous emergency of drug-resistant cancer and the low specificity of anticancer agents, creating an urgent need to develop novel anticancer agents. Organometallic compounds especially ferrocene derivatives possess remarkable structural and mechanistic diversity, inherent stability towards air, heat and light, low toxicity, low cost, reversible redox, ligand exchange, and catalytic properties, making them promising drug candidates for cancer therapy. Ferrocifen, a ferrocene-phenol hybrid, has demonstrated promising anticancer properties on drug-resistant cancers. Currently, Ferrocifen is in pre-clinical trial against cancers. Obviously, ferrocene moiety is a useful template for the development of novel anticancer agents. This review will provide an overview of ferrocene-containing hybrids with potential application in the treatment of cancers covering articles published between 2010 and 2020. The mechanisms of action, the critical aspects of design and structure-activity relationships are also discussed.