Fragment-Based Drug Discovery of Inhibitors of Phosphopantetheine Adenylyltransferase from Gram-Negative Bacteria

In Silico and In Vitro Identification of 1,8-Dihydroxy-4,5-dinitroanthraquinone as a New Antibacterial Agent against Staphylococcus aureus and Enterococcus faecalis

Increasing rates of bacterial resistance to antibiotics are a growing concern worldwide. The search for potential new antibiotics has included several natural products such as anthraquinones. However, comparatively less attention has been given to anthraquinones that exhibit functional groups that are uncommon in nature. In this work, 114 anthraquinones were evaluated using in silico methods to identify inhibitors of the enzyme phosphopantetheine adenylyltransferase (PPAT) of Staphylococcus aureus, Enterococcus faecalis, and Escherichia coli. Virtual screenings based on molecular docking and the pharmacophore model, molecular dynamics simulations, and free energy calculations pointed to 1,8-dihydroxy-4,5-dinitroanthraquinone (DHDNA) as the most promising inhibitor. In addition, these analyses highlighted the contribution of the nitro group to the affinity of this anthraquinone for the nucleotide-binding site of PPAT. Furthermore, DHDNA was active in vitro towards Gram-positive bacteria with minimum inhibitory concentration (MIC) values of 31.25 µg/mL for S. aureus and 62.5 µg/mL for E. faecalis against both antibiotic-resistant isolates and reference strains but was ineffective against E. coli. Experiments on kill-time kinetics indicated that, at the tested concentrations, DHDNA produced bacteriostatic effects on both Gram-positive bacteria. Overall, our results present DHDNA as a potential PPAT inhibitor, showing antibacterial activity against antibiotic-resistant isolates of S. aureus and E. faecalis, findings that point to nitro groups as key to explaining these results.

The Magic Methyl and Its Tricks in Drug Discovery and Development

One of the key scientific aspects of small-molecule drug discovery and development is the analysis of the relationship between its chemical structure and biological activity. Understanding the effects that lead to significant changes in biological activity is of paramount importance for the rational design and optimization of bioactive molecules. The "methylation effect", or the "magic methyl" effect, is a factor that stands out due to the number of examples that demonstrate profound changes in either pharmacodynamic or pharmacokinetic properties. In many cases, this has been carried out rationally, but in others it has been the product of serendipitous observations. This paper summarizes recent examples that provide an overview of the current state of the art and contribute to a better understanding of the methylation effect in bioactive small-molecule drug candidates.

Chemical Validation of Mycobacterium tuberculosis Phosphopantetheine Adenylyltransferase Using Fragment Linking and CRISPR Interference

The coenzyme A (CoA) biosynthesis pathway has attracted attention as a potential target for much-needed novel antimicrobial drugs, including for the treatment of tuberculosis (TB), the lethal disease caused by Mycobacterium tuberculosis (Mtb). Seeking to identify inhibitors of Mtb phosphopantetheine adenylyltransferase (MtbPPAT), the enzyme that catalyses the penultimate step in CoA biosynthesis, we performed a fragment screen. In doing so, we discovered three series of fragments that occupy distinct regions of the MtbPPAT active site, presenting a unique opportunity for fragment linking. Here we show how, guided by X-ray crystal structures, we could link weakly-binding fragments to produce an active site binder with a K D <20 μM and on-target anti-Mtb activity, as demonstrated using CRISPR interference. This study represents a big step toward validating MtbPPAT as a potential drug target and designing a MtbPPAT-targeting anti-TB drug.

Chemical Validation of Mycobacterium tuberculosis Phosphopantetheine Adenylyltransferase Using Fragment Linking and CRISPR Interference

The coenzyme A (CoA) biosynthesis pathway has attracted attention as a potential target for much-needed novel antimicrobial drugs, including for the treatment of tuberculosis (TB), the lethal disease caused by Mycobacterium tuberculosis (Mtb). Seeking to identify inhibitors of Mtb phosphopantetheine adenylyltransferase (MtbPPAT), the enzyme that catalyses the penultimate step in CoA biosynthesis, we performed a fragment screen. In doing so, we discovered three series of fragments that occupy distinct regions of the MtbPPAT active site, presenting a unique opportunity for fragment linking. Here we show how, guided by X-ray crystal structures, we could link weakly-binding fragments to produce an active site binder with a KD <20 μM and on-target anti-Mtb activity, as demonstrated using CRISPR interference. This study represents a big step toward validating MtbPPAT as a potential drug target and designing a MtbPPAT-targeting anti-TB drug.

Fragment-Based Lead Discovery Strategies in Antimicrobial Drug Discovery

Fragment-based lead discovery (FBLD) is a powerful application for developing ligands as modulators of disease targets. This approach strategy involves identification of interactions between low-molecular weight compounds (100-300 Da) and their putative targets, often with low affinity (K_D ~0.1-1 mM) interactions. The focus of this screening methodology is to optimize and streamline identification of fragments with higher ligand efficiency (LE) than typical high-throughput screening. The focus of this review is on the last half decade of fragment-based drug discovery strategies that have been used for antimicrobial drug discovery.

Modified Electrostatic Complementary Score Function and Its Application Boundary Exploration in Drug Design

In recent years, machine learning (ML) models have been found to quickly predict various molecular properties with accuracy comparable to high-level quantum chemistry methods. One such example is the calculation of electrostatic potential (ESP). Different ESP prediction ML models were proposed to generate surface molecular charge distribution. Electrostatic complementarity (EC) can apply ESP data to quantify the complementarity between a ligand and its binding pocket, leading to the potential to increase the efficiency of drug design. However, there is not much research discussing EC score functions and their applicability domain. We propose a new EC score function modified from the one originally developed by Bauer and Mackey, and confirm its effectiveness against the available Pearson's R correlation coefficient. Additionally, the applicability domain of the EC score and two indices used to define the EC score application scope will be discussed.

Vitamin in the Crosshairs: Targeting Pantothenate and Coenzyme A Biosynthesis for New Antituberculosis Agents

Despite decades of dedicated research, there remains a dire need for new drugs against tuberculosis (TB). Current therapies are generations old and problematic. Resistance to these existing therapies results in an ever-increasing burden of patients with disease that is difficult or impossible to treat. Novel chemical entities with new mechanisms of action are therefore earnestly required. The biosynthesis of coenzyme A (CoA) has long been known to be essential in Mycobacterium tuberculosis (Mtb), the causative agent of TB. The pathway has been genetically validated by seminal studies in vitro and in vivo. In Mtb, the CoA biosynthetic pathway is comprised of nine enzymes: four to synthesize pantothenate (Pan) from l-aspartate and α-ketoisovalerate; five to synthesize CoA from Pan and pantetheine (PantSH). This review gathers literature reports on the structure/mechanism, inhibitors, and vulnerability of each enzyme in the CoA pathway. In addition to traditional inhibition of a single enzyme, the CoA pathway offers an antimetabolite strategy as a promising alternative. In this review, we provide our assessment of what appear to be the best targets, and, thus, which CoA pathway enzymes present the best opportunities for antitubercular drug discovery moving forward.

Phosphopantetheine Adenylyltransferase: A promising drug target to combat antibiotic resistance

Phosphopantetheine Adenylyltransferase (PPAT) is an enzyme that catalyzes the penultimate step in the biosynthesis of Coenzyme A (CoA), which is the active and physiologically functional form of dietary Vitamin B5. CoA serves as a cofactor for numerous metabolic reactions which makes it essential for cellular survival. This enzyme is also subject to feedback inhibition by CoA to maintain its cellular concentration. The steps of the CoA biosynthesis pathway remain conserved from prokaryotes to eukaryotes, with humans and pathogenic micro-organisms showing significant diversity on a sequence, structure and mechanistic level. This suggests that the development of selective inhibitors of microbial CoA biosynthesis should be possible using these enzymes as targets for drug development. Bacterial PPAT shows significant mechanistic difference from its human counterpart CoA synthase, which is a dual protein carrying the activity of both PPAT and next step in the pathway catalyzed by the enzyme Dephospho CoA kinase (DPCK). This review covers the detailed description of the mechanistic, structural and functional aspects of this enzyme. Also, all the attempts to design high efficiency inhibitors of this enzyme using the approach of structure based drug design have been discussed in detail. This comprehensive structural and functional discussion of PPAT will help in further exploiting it as a drug target.

Comprehensive and High-Throughput Exploration of Chemical Space Using Broadband 19 F NMR-Based Screening

Fragment-based lead discovery has become a fundamental approach to identify ligands that efficiently interact with disease-relevant targets. Among the numerous screening techniques, fluorine-detected NMR has gained popularity owing to its high sensitivity, robustness, and ease of use. To effectively explore chemical space, a universal NMR experiment, a rationally designed fragment library, and a sample composition optimized for a maximal number of compounds and minimal measurement time are required. Here, we introduce a comprehensive method that enabled the efficient assembly of a high-quality and diverse library containing nearly 4000 fragments and screening for target-specific binders within days. At the core of the approach is a novel broadband relaxation-edited NMR experiment that covers the entire chemical shift range of drug-like ¹⁹ F motifs in a single measurement. Our approach facilitates the identification of diverse binders and the fast ligandability assessment of new targets.

Fragment-to-Lead Medicinal Chemistry Publications in 2018

This Perspective, the fourth in an annual series, summarizes fragment-to-lead (F2L) success stories published during 2018. Topics such as target class, screening methods, physicochemical properties, and ligand efficiency are discussed for the 2018 examples as well as for the combined 111 F2L examples covering 2015-2018. While the overall properties of fragments and leads have remained constant, a number of new trends are noted, for example, broadening of target class coverage and application of FBDD to covalent inhibitors. Moreover, several studies make use of fragment hits that were previously described in the literature, illustrating that fragments are versatile starting points that can be optimized to structurally diverse leads. By focusing on success stories, the hope is that this Perspective will identify and inform best practices in fragment-based drug discovery.

Essential ingredients for rational drug design

This short review focuses on three aspects of rational drug design that we consider of utmost importance: the conformation of small molecules in solid form, the conformation of small molecules in solution and lesser studied interactions in protein-ligand complexes. Using examples from recent literature, we will illustrate these different aspects and how they have contributed to the discovery of potent modulators.

The coenzyme A biosynthetic pathway: A new tool for prodrug bioactivation

Prodrugs account for more than 5% of pharmaceuticals approved worldwide. Over the past decades several prodrug design strategies have been firmly established; however, only a few functional groups remain amenable to this approach. The aim of this overview is to highlight the use of coenzyme A (CoA) biosynthetic enzymes as a recently explored bioactivation scheme and provide information about its scope of utility. This emerging tool is likely to have a strong impact on future medicinal and biological studies as it offers promiscuity, orthogonal selectivity, and the capability of assembling exceptionally large molecules.

Computational investigations of gram-negative bacteria phosphopantetheine adenylyltransferase inhibitors using 3D-QSAR, molecular docking and molecular dynamic simulations

Phosphopantetheine adenylyltransferase (PPAT) has been recognized as a promising target to develop novel antimicrobial agents, which is a hexameric enzyme that catalyzes the penultimate step in coenzyme A biosynthesis. In this work, molecular modeling study was performed with a series of PPAT inhibitors using molecular docking, three-dimensional qualitative structure-activity relationship (3D-QSAR) and molecular dynamic (MD) simulations to reveal the structural determinants for their bioactivities. Molecular docking study was applied to understand the binding mode of PPAT with its inhibitors. Subsequently, 3D-QSAR model was constructed to find the features required for different substituents on the scaffolds. For the best comparative molecular field analysis (CoMFA) model, the Q² and R² values of which were calculated as 0.702 and 0.989, while they were calculated as 0.767 and 0.983 for the best comparative molecular similarity index analysis model. The statistical data verified the significance and accuracy of our 3D-QSAR models. Furthermore, MD simulations were carried out to evaluate the stability of the receptor-ligand contacts in physiological conditions, and the results were consistent with molecular docking studies and 3D-QSAR contour map analysis. Binding free energy was calculated with molecular mechanics generalized born surface area approach, the result of which coincided well with bioactivities and demonstrated that van der Waals accounted for the largest portion. Overall, our study provided a valuable insight for further research work on the recognition of potent PPAT inhibitors.Communicated by Ramaswamy H. Sarma.

Probing a dipeptide-based supramolecular assembly as an efficient camptothecin delivering carrier for cancer therapy: computational simulations and experimental validations

Short peptide-based supramolecular assemblies have drawn much attention in the field of drug delivery. However, the progress still remains limited owing to the inefficient drug loading capacity of conventional short peptide-based materials. In this study, based on coordinated intramolecular π-π stacking, we customize a dipeptide-based rhein derivative (rhein-diphenylalanine peptide, RDP), which could spontaneously form spherical nanoassemblies for drug delivery. A structure-based virtual screening of a library of small molecules is conducted to identify the suitable compounds which could be effectively delivered by this nanocarrier. Sorted by binding energy results, fifteen superior and five inferior molecules are found. Subsequently, the co-assembly capacity of high-affinity molecules (camptothecin, CPT) and low-affinity molecules (norcantharidin, NCTD) with the dipeptide-based carrier is predicted via dissipative particle dynamics (DPD) simulation. Consistent with computational results, the in vitro experimental results show that CPT-encapsulated nanoassemblies have significant advantages in the particle size distribution and recrystallization-inhibitory effect compared with NCTD. Furthermore, in vivo experiments were conducted to determine whether CPT is precisely delivered to tumor sites by using the dipeptide-based nanoassemblies. The CPT-loaded nanoassemblies show better effects in terms of drug biodistribution and in vivo anti-tumor efficacy compared to free CPT. The cooperative computational and experimental strategies (in vitro and in vivo) used in this work lay a good foundation to systematically understand short peptide-based assemblies for precise drug delivery.

Addressing Antimicrobial Resistance through New Medicinal and Synthetic Chemistry Strategies

Over the past century, a multitude of derivatives of structural scaffolds with established antimicrobial potential have been prepared and tested, and a variety of new scaffolds have emerged. The effectiveness of antibiotics, however, is in sharp decline because of the emergence of drug-resistant microorganisms. The prevalence of drug resistance, both in clinical and community settings, is a consequence of bacterial ingenuity in altering pathways and/or cell morphology, making it a persistent threat to human health. The fundamental ability of pathogens to survive in a multitude of habitats can be triggered by recognition of chemical signals that warn organisms of exposure to a potentially harmful environment. Host immune defenses, including reactive oxygen intermediates and antibacterial substances, are among the multitude of chemical signals that can subsequently trigger expression of phenotypes better adapted for survival in that hostile environment. Thus, resistance development appears to be unavoidable, which leads to the conclusion that developing an alternative perspective for treatment options is vital. This review will discuss emerging medicinal chemistry approaches for addressing the global multidrug resistance in the 21st century.