Identifying chelators for metalloprotein inhibitors using a fragment-based approach

Discovery of matrix metalloproteinase inhibitors as anti-skin photoaging agents

Photodamage is the result of prolonged exposure of the skin to sunlight. This exposure causes an overexpression of matrix metalloproteinases (MMPs), leading to the abnormal degradation of collagen in the skin tissue and resulting in skin aging and damage. This review presents a detailed overview of MMPs as a potential target for addressing skin aging. Specifically, we elucidated the precise mechanisms by which MMP inhibitors exert their anti-photoaging effects. Furthermore, we comprehensively analyzed the current research progress on MMP inhibitors that demonstrate significant inhibitory activity against MMPs and anti-skin photoaging effects. The review also provides insights into the structure-activity relationships of these inhibitors. Our objective in conducting this review is to provide valuable practical information to researchers engaged in investigations on anti-skin photoaging.

Pomegranate extract on eroded dentin: antioxidant action, bond strength and morphology of the adhesive interface after aging

Objectives

This study aimed to evaluate the effect of pomegranate solution (Punica granatum) on eroded dentin through antioxidant action, shear bond strength (SBS) and interface morphology.

Materials and Methods

The 10% pomegranate peel extract was prepared by the lyophilization method. Punicalagin polyphenol was confirmed by high-performance liquid chromatography. Antioxidant activity was evaluated by capturing the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical. For the SBS, 48 dentin fragments were divided into sound or eroded, and subdivided according to the pretreatment (n = 12): water or P. granatum. The surfaces were restored with self-etch adhesive and a bulk-fill resin (Ecosite; DMG). The SBS was done immediately (24 hours) and after thermal cycling + water storage (12 months). For scanning electron microscopy, 48 dentin fragments (24 sound and 24 eroded) received the same treatments as for SBS (n = 6), and they were analyzed after 24 hours and 12 months.

Results

The P. granatum had antioxidant action similar (p = 0.246) to the phenolic standard antioxidants. After 24 hours, eroded dentin had lower SBS than sound dentin (p < 0.001), regardless of the pretreatment. After 12 months, P. granatum maintained the SBS of sound dentin (13.46 ± 3.42 MPa) and eroded dentin (10.96 ± 1.90 MPa) statistically similar. The lowest values were found on eroded dentin treated with water (5.75 ± 1.65 MPa) (p < 0.001). P. granatum on eroded dentin caused peritubular demineralization and hybrid layer with resin tags.

Conclusions

The pomegranate extract had antioxidant action and preserved the adhesive interface of the eroded dentin.

Antiviral Compounds to Address Influenza Pandemics: An Update from 2016-2022

In recent decades, the world has gained experience of the dangerous effects of pandemic events caused by emerging respiratory viruses. In particular, annual epidemics of influenza are responsible for severe illness and deaths. Even if conventional influenza vaccines represent the most effective tool for preventing virus infections, they are not completely effective in patients with severe chronic disease and immunocompromised and new small molecules have emerged to prevent and control the influenza viruses. Thus, the attention of chemists is continuously focused on the synthesis of new antiviral drugs able to interact with the different molecular targets involved in the virus replication cycle. To date, different classes of influenza viruses inhibitors able to target neuraminidase enzyme, hemagglutinin protein, Matrix-2 (M2) protein ion channel, nucleoprotein or RNAdependent RNA polymerase have been synthesized using several synthetic strategies comprising the chemical modification of currently used drugs. The best results, in terms of inhibitory activity, are in the nanomolar range and have been obtained from the chemical modification of clinically used drugs such as Peramivir, Zanamivir, Oseltamir, Rimantadine, as well as sialylated molecules, and hydroxypyridinone derivatives. The aim of this review is to report, covering the period 2016-2022, the most recent routes related to the synthesis of effective influenza virus inhibitors.

Steady-state kinetic analysis of reversible enzyme inhibitors: A case study on calf intestine alkaline phosphatase

Enzymes are important drug targets and inhibition of enzymatic activity is an important therapeutic strategy. Enzyme assays measuring catalytic activity are utilized in both the discovery and development of new drugs. Colorimetric assays based on the release of 4-nitrophenol from substrates are commonly used. 4-Nitrophenol is only partly ionized to 4-nitrophenolate under typical assay conditions (pH 7-9) leading to under-estimation of product formation rates due to the much lower extinction coefficient of 4-nitrophenol compared to 4-nitrophenolate. Determination of 4-nitrophenol pKa values based on absorbance at 405 nm as a function of experimental pH values is reported, allowing for calculation of a corrected extinction coefficient at the assay pH. Characterization of inhibitor properties using steady-state enzyme kinetics is demonstrated using calf intestine alkaline phosphatase and 4-nitrophenyl phosphate as substrate at pH ∼8.2. The following kinetic parameters were determined: Km= 40±3 µM; Vmax= 72.8±1.2 µmolmin-1mg protein-1; kcat= 9.70±0.16 s-1; kcat/Km= 2.44±0.16 × 105 M-1s-1 (mean± SEM, N = 4). Sodium orthovanadate and EDTA were used as model inhibitors and the following pIC50 values were measured using dose-response curves: 6.61±0.08 and 3.07±0.03 (mean±SEM, N = 4). Rapid dilution experiments determined that inhibition was reversible for sodium orthovanadate and irreversible for EDTA. A Ki value for orthovanadate of 51±8 nM (mean±SEM, N = 3) was determined. Finally, data analysis and statistical design of experiments are discussed.

Understanding the Structure-Activity Relationship through Density Functional Theory: A Simple Method Predicts Relative Binding Free Energies of Metalloenzyme Fragment-like Inhibitors

Despite being involved in several human diseases, metalloenzymes are targeted by a small percentage of FDA-approved drugs. Development of novel and efficient inhibitors is required, as the chemical space of metal binding groups (MBGs) is currently limited to four main classes. The use of computational chemistry methods in drug discovery has gained momentum thanks to accurate estimates of binding modes and binding free energies of ligands to receptors. However, exact predictions of binding free energies in metalloenzymes are challenging due to the occurrence of nonclassical phenomena and interactions that common force field-based methods are unable to correctly describe. In this regard, we applied density functional theory (DFT) to predict the binding free energies and to understand the structure-activity relationship of metalloenzyme fragment-like inhibitors. We tested this method on a set of small-molecule inhibitors with different electronic properties and coordinating two Mn²⁺ ions in the binding site of the influenza RNA polymerase PA_N endonuclease. We modeled the binding site using only atoms from the first coordination shell, hence reducing the computational cost. Thanks to the explicit treatment of electrons by DFT, we highlighted the main contributions to the binding free energies and the electronic features differentiating strong and weak inhibitors, achieving good qualitative correlation with the experimentally determined affinities. By introducing automated docking, we explored alternative ways to coordinate the metal centers and we identified 70% of the highest affinity inhibitors. This methodology provides a fast and predictive tool for the identification of key features of metalloenzyme MBGs, which can be useful for the design of new and efficient drugs targeting these ubiquitous proteins.

Matrix Metalloproteinases in Oral Health-Special Attention on MMP-8

Matrix metalloproteinases (MMPs) are a large family of Ca²⁺ and Zn²⁺ dependent proteolytic enzymes, able to cleave the various components of the extracellular matrix (ECM), as well as a range of other regulatory molecules. Several reports have proven the important role of both MMPs and their endogenous inhibitors, TIPMs, in oral health, the initial development of the tooth, and during enamel maturation. In this mini-review, we aim to summarize the literature information about the functions of MMPs, paying more attention to MMP-8 (collagenase-2 or neutrophil collagenase) in the development and progression of periodontitis, peri-implantitis, and carious lesions. We also emphasize the role of particular gene variants in MMP8 as predisposing factors for some oral diseases.

Utilizing genetic code expansion to modify N-TIMP2 specificity towards MMP-2, MMP-9, and MMP-14

Matrix metalloproteinases (MMPs) regulate the degradation of extracellular matrix (ECM) components in biological processes. MMP activity is controlled by natural tissue inhibitors of metalloproteinases (TIMPs) that non-selectively inhibit the function of multiple MMPs via interaction with the MMPs' Zn2+-containing catalytic pocket. Recent studies suggest that TIMPs engineered to confer MMP specificity could be exploited for therapeutic purposes, but obtaining specific TIMP-2 inhibitors has proved to be challenging. Here, in an effort to improve MMP specificity, we incorporated the metal-binding non-canonical amino acids (NCAAs), 3,4-dihydroxyphenylalanine (L-DOPA) and (8-hydroxyquinolin-3-yl)alanine (HqAla), into the MMP-inhibitory N-terminal domain of TIMP2 (N-TIMP2) at selected positions that interact with the catalytic Zn2+ ion (S2, S69, A70, L100) or with a structural Ca2+ ion (Y36). Evaluation of the inhibitory potency of the NCAA-containing variants towards MMP-2, MMP-9 and MMP-14 in vitro revealed that most showed a significant loss of inhibitory activity towards MMP-14, but not towards MMP-2 and MMP-9, resulting in increased specificity towards the latter proteases. Substitutions at S69 conferred the best improvement in selectivity for both L-DOPA and HqAla variants. Molecular modeling provided an indication of how MMP-2 and MMP-9 are better able to accommodate the bulky NCAA substituents at the intermolecular interface with N-TIMP2. The models also showed that, rather than coordinating to Zn2+, the NCAA side chains formed stabilizing polar interactions at the intermolecular interface with MMP-2 and MMP-9. Our findings illustrate how incorporation of NCAAs can be used to probe-and possibly exploit-differential tolerance for substitution within closely related protein-protein complexes as a means to improve specificity.

A Superior Corrosion Protection of Mg Alloy via Smart Nontoxic Hybrid Inhibitor-Containing Coatings

The increase of corrosion resistance of magnesium and its alloys by forming the smart self-healing hybrid coatings was achieved in this work in two steps. In the first step, using the plasma electrolytic oxidation (PEO) treatment, a ceramic-like bioactive coating was synthesized on the surface of biodegradable MA8 magnesium alloy. During the second step, the formed porous PEO layer was impregnated with a corrosion inhibitor 8-hydroxyquinoline (8-HQ) and bioresorbable polymer polycaprolactone (PCL) in different variations to enhance the protective properties of the coating. The composition, anticorrosion, and antifriction properties of the formed coatings were studied. 8-HQ allows controlling the rate of material degradation due to the self-healing effect of the smart coating. PCL treatment of the inhibitor-containing layer significantly improves the corrosion and wear resistance and retains an inhibitor in the pores of the PEO layer. It was revealed that the corrosion inhibitor incorporation method (including the number of steps, impregnation, and the type of solvent) significantly matters to the self-healing mechanism. The hybrid coatings obtained by a 1-step treatment in a dichloromethane solution containing 6 wt.% polycaprolactone and 15 g/L of 8-HQ are characterized by the best corrosion resistance. This coating demonstrates the lowest value of corrosion current density (3.02 × 10−7 A cm−2). The formation of the hybrid coating results in the corrosion rate decrease by 18 times (0.007 mm year−1) as compared to the blank PEO layer (0.128 mm year−1). An inhibitor efficiency was established to be 83.9%. The mechanism of corrosion protection of Mg alloy via smart hybrid coating was revealed.

Developing Metal-Binding Isosteres of 8-Hydroxyquinoline as Metalloenzyme Inhibitor Scaffolds

The use of metal-binding pharmacophores (MBPs) in fragment-based drug discovery has proven effective for targeted metalloenzyme drug development. However, MBPs can still suffer from pharmacokinetic liabilities. Bioisostere replacement is an effective strategy utilized by medicinal chemists to navigate these issues during the drug development process. The quinoline pharmacophore and its bioisosteres, such as quinazoline, are important building blocks in the design of new therapeutics. More relevant to metalloenzyme inhibition, 8-hydroxyquinoline (8-HQ) and its derivatives can serve as MBPs for metalloenzyme inhibition. In this report, 8-HQ isosteres are designed and the coordination chemistry of the resulting metal-binding isosteres (MBIs) is explored using a bioinorganic model complex. In addition, the physicochemical properties and metalloenzyme inhibition activity of these MBIs were investigated to establish drug-like profiles. This report provides a new group of 8-HQ-derived MBIs that can serve as novel scaffolds for metalloenzyme inhibitor development with tunable, and potentially improved, physicochemical properties.

Recent Advances of Pyridinone in Medicinal Chemistry

Pyridinones have been adopted as an important block in medicinal chemistry that could serve as hydrogen bond donors and acceptors. With the help of feasible synthesis routes via established condensation reactions, the physicochemical properties of such a scaffold could be manipulated by adjustment of polarity, lipophilicity, and hydrogen bonding, and eventually lead to its wide application in fragment-based drug design, biomolecular mimetics, and kinase hinge-binding motifs. In addition, most pyridinone derivatives exhibit various biological activities ranging from antitumor, antimicrobial, anti-inflammatory, and anticoagulant to cardiotonic effects. This review focuses on recent contributions of pyridinone cores to medicinal chemistry, and addresses the structural features and structure–activity relationships (SARs) of each drug-like molecule. These advancements contribute to an in-depth understanding of the potential of this biologically enriched scaffold and expedite the development of its new applications in drug discovery.

Salicylate metal-binding isosteres as fragments for metalloenzyme inhibition

Metalloenzyme inhibitors typically share a common need to possess a metal-binding pharmacophore (MBP) for binding the active site metal ions. However, MBPs can suffer from physicochemical liabilities, impeding the pharmacological properties and drug-likeliness of inhibitors. To circumvent this, problematic features of the MBP can be identified and exchanged with isosteric replacements. Herein, the carboxylic and hydroxyl group of the salicylic acid MBP were replaced and a total of 27 salicylate metal-binding isosteres (MBIs) synthesized. Of these 27 MBIs, at least 12 represent previously unreported compounds, and the metal-binding abilities of >20 of the MBIs have not been previously reported. These salicylate MBIs were examined for their metal-binding features in model complexes, physicochemical properties, and biological activity. It was observed that salicylate MBIs can demonstrate a range of attractive physicochemical properties and bind to the metal in a variety of expected and unexpected binding modes. The biological activity of these novel MBIs was evaluated by measuring inhibition against two Zn2+-dependent metalloenzymes, human glyoxalase 1 (GLO1) and matrix metalloproteinase 3 (MMP-3), as well as a dinuclear Mn2+-dependent metalloenzyme, influenza H1N1 N-terminal endonuclease (PAN). It was observed that salicylate MBIs could maintain or improve enzyme inhibition and selectivity. To probe salicylate MBIs as fragments for fragment-based drug discovery (FBDD), an MBI that showed good inhibitory activity against GLO1 was derivatized and a rudimentary structure-activity relationship was developed. The resulting elaborated fragments showed GLO1 inhibition with low micromolar activity.

The Glitazone Class of Drugs as Carbonic Anhydrase Inhibitors-A Spin-Off Discovery from Fragment Screening

The approved drugs that target carbonic anhydrases (CA, EC 4.2.1.1), a family of zinc metalloenzymes, comprise almost exclusively of primary sulfonamides (R-SO2NH2) as the zinc binding chemotype. New clinical applications for CA inhibitors, particularly for hard-to-treat cancers, has driven a growing interest in the development of novel CA inhibitors. We recently discovered that the thiazolidinedione heterocycle, where the ring nitrogen carries no substituent, is a new zinc binding group and an alternate CA inhibitor chemotype. This heterocycle is curiously also a substructure of the glitazone class of drugs used in the treatment options for type 2 diabetes. Herein, we investigate and characterise three glitazone drugs (troglitazone 11, rosiglitazone 12 and pioglitazone 13) for binding to CA using native mass spectrometry, protein X-ray crystallography and hydrogen-deuterium exchange (HDX) mass spectrometry, followed by CA enzyme inhibition studies. The glitazone drugs all displayed appreciable binding to and inhibition of CA isozymes. Given that thiazolidinediones are not credited as a zinc binding group nor known as CA inhibitors, our findings indicate that CA may be an off-target of these compounds when used clinically. Furthermore, thiazolidinediones may represent a new opportunity for the development of novel CA inhibitors as future drugs.

19F-Tagged metal binding pharmacophores for NMR screening of metalloenzymes

This study demonstrates the screening of a collection of twelve 19F-tagged metal-binding pharmacophores (MBPs) against the Zn(ii)-dependent metalloenzyme human carbonic anhydrase II (hCAII) by 19F NMR. The isomorphous replacement of Zn(ii) by Co(ii) in hCAII produces enhanced sensitivity and reveals the potential of 19F NMR-based techniques for metalloenzyme ligand discovery.

Hydroxypyridinethione Inhibitors of Human Insulin-Degrading Enzyme

Insulin-degrading enzyme (IDE) is a human mononuclear Zn²⁺ -dependent metalloenzyme that is widely regarded as the primary peptidase responsible for insulin degradation. Despite its name, IDE is also critically involved in the hydrolysis of several other disparate peptide hormones, including glucagon, amylin, and the amyloid β-protein. As such, the study of IDE inhibition is highly relevant to deciphering the role of IDE in conditions such as type-2 diabetes mellitus and Alzheimer disease. There have been few reported IDE inhibitors, and of these, inhibitors that directly target the active-site Zn²⁺ ion have yet to be fully explored. In an effort to discover new, zinc-targeting inhibitors of IDE, a library of ∼350 metal-binding pharmacophores was screened against IDE, resulting in the identification of 1-hydroxypyridine-2-thione (1,2-HOPTO) as an effective Zn²⁺ -binding scaffold. Screening a focused library of HOPTO compounds identified 3-sulfonamide derivatives of 1,2-HOPTO as inhibitors of IDE (K_i values of ∼50 μM). Further structure-activity relationship studies yielded several thiophene-sulfonamide HOPTO derivatives with good, broad-spectrum activity against IDE that have the potential to be useful pharmacological tools for future studies of IDE.

Systematic Assessment of Fragment Identification for Multitarget Drug Design

Designed multitarget ligands are a popular approach to generating efficient and safe drugs, and fragment-based strategies have been postulated as a versatile avenue to discover multitarget ligand leads. To systematically probe the potential of fragment-based multiple ligand discovery, we have employed a large fragment library for comprehensive screening on five targets chosen from proteins for which multitarget ligands have been successfully developed previously (soluble epoxide hydrolase, leukotriene A4 hydrolase, 5-lipoxygenase, retinoid X receptor, farnesoid X receptor). Differential scanning fluorimetry served as primary screening method before fragments hitting at least two targets were validated in orthogonal assays. Thereby, we obtained valuable fragment leads with dual-target engagement for six out of ten target combinations. Our results demonstrate the applicability of fragment-based approaches to identify starting points for polypharmacological compound development with certain limitations.

SAR and QSAR research on tyrosinase inhibitors using machine learning methods

Tyrosinase is a key rate-limiting enzyme in the process of melanin synthesis, which is closely related to human pigmentation disorders. Tyrosinase inhibitors can down-regulate tyrosinase to effectively reduce melanin synthesis. In this work, we conducted structure-activity relationship (SAR) study on 1097 diverse mushroom tyrosinase inhibitors. We applied five kinds of machine learning methods to develop 15 classification models. Model 5B built by fully connected neural networks and ECFP4 fingerprints achieved the highest prediction accuracy of 91.36% and Matthews correlation coefficient (MCC) of 0.81 on the test set. The applicability domains (AD) of classification models were defined by d S T D - P R O method. Moreover, we clustered the 1097 inhibitors into eight subsets by K-Means to figure out inhibitors' structural features. In addition, 10 quantitative structure-activity relationship (QSAR) models were constructed by four machine learning methods based on 813 inhibitors. Model 6 J, the best QSAR model, was developed by fully connected neural networks with 50 RDKit descriptors. It resulted in a coefficient of determination (r ²) of 0.770 and a root mean squared error (RMSE) of 0.482 on the test set. The AD of Model 6 J was visualized by Williams plot. The models built in this study can be obtained from the authors.

Insights of 8-hydroxyquinolines: A novel target in medicinal chemistry

8-Hydroxyquinoline (8-HQ) is a significant heterocyclic scaffold in organic and analytical chemistry because of the properties of chromophore and is used to detect various metal ions and anions. But from the last 2 decades, this moiety has been drawn great attention of medicinal chemists due to its significant biological activities. Synthetic modification of 8-hydroxyquinoline is under exploration on large scale to develop more potent target-based broad spectrum drug molecules for the treatment of several life-threatening diseases such as anti-cancer, HIV, neurodegenerative disorders, etc. Metal chelation properties of 8-hydroxyquinoline and its derivatives also make these potent drug candidates for the treatment of various diseases. This review comprises 8-hydroxyquinoline derivatives reported in the literature in last five years (2016-2020) and we anticipate that it will assist medicinal chemists in the synthesis of novel and pharmacologically potent agents for various therapeutic targets, mainly anti-proliferative, anti-microbial, anti-fungal and anti-viral as well as for the treatment of neurodegenerative disorders.

Identification of 3-hydroxy-1,2-dimethylpyridine-4(1H)-thione as a metal-binding motif for the inhibition of botulinum neurotoxin A

Botulinum neurotoxin serotype A (BoNT/A) is an important therapeutic target owing to its extremely potent nature, but also has potential use as a biowarfare agent. Currently, no therapeutic exists to reverse the long-lasting paralysis caused by BoNT/A. Herein, we describe the identification of 3-hydroxy-1,2-dimethylpyridine-4(1H)-thione (3,4-HOPTO) as a metal binding warhead for the inhibition of BoNT/A1. An initial screen of 96 metal binding fragments identified three derivatives containing the 3,4-HOPTO scaffold to inhibit the BoNT/A1 light chain (LC) at >95% at 1 mM. Additional screening of a 3,4-HOPTO sub-library identified structure-activity relationships (SARs) between N-substituted 3,4-HOPTO derivatives and the BoNT/A1 LC. Subsequent synthesis was conducted to improve on inhibitory potency - achieving low μM biochemical IC50 values. Representative compounds were evaluated in a cellular-based assay and showed promising μM activity.

Biosynthesis of Mycotoxin Fusaric Acid and Application of a PLP-Dependent Enzyme for Chemoenzymatic Synthesis of Substituted l-Pipecolic Acids

Fusaric acid (FA) is a well-known mycotoxin that plays an important role in plant pathology. The biosynthetic gene cluster for FA has been identified, but the biosynthetic pathway remains unclarified. Here, we elucidated the biosynthesis of FA, which features a two-enzyme catalytic cascade, a pyridoxal 5'-phosphate (PLP)-dependent enzyme (Fub7), and a flavin mononucleotide (FMN)-dependent oxidase (Fub9) in synthesizing the picolinic acid scaffold. FA biosynthesis also involves an off-line collaboration between a highly reducing polyketide synthase (HRPKS, Fub1) and a nonribosomal peptide synthetase (NRPS)-like carboxylic acid reductase (Fub8) in making an aliphatic α,β-unsaturated aldehyde. By harnessing the stereoselective C-C bond-forming activity of Fub7, we established a chemoenzymatic route for stereoconvergent synthesis of a series of 5-alkyl-, 5,5-dialkyl-, and 5,5,6-trialkyl-l-pipecolic acids of high diastereomeric ratio.

Hydroxypyridinone-Based Iron Chelators with Broad-Ranging Biological Activities

Iron plays an essential role in all living cells because of its unique chemical properties. It is also the most abundant trace element in mammals. However, when iron is present in excess or inappropriately located, it becomes toxic. Excess iron can become involved in free radical formation, resulting in oxidative stress and cellular damage. Iron chelators are used to treat serious pathological disorders associated with systemic iron overload. Hydroxypyridinones stand out for their outstanding chelation properties, including high selectivity for Fe³⁺ in the biological environment, ease of derivatization, and good biocompatibility. Herein, we overview the potential for multifunctional hydroxypyridinone-based chelators to be used as therapeutic agents against a wide range of diseases associated either with systemic or local elevated iron levels.

Effect of heterocycle content on metal binding isostere coordination

Bioisostere replacement is a core concept in modern medicinal chemistry and in this work new metal-binding isosteres (MBIs) are synthesized and evaluated for use in metalloenzyme inhibitors.

Bioisostere replacement is a core concept in modern medicinal chemistry and has proven an invaluable strategy to address pharmacodynamic and pharmacokinetic limitations of therapeutics. The success of bioisostere replacement is often dependent on the scaffold that is being modified (i.e., “context dependence”). The application of bioisostere replacement to a picolinic acid fragment was recently demonstrated as a means to expand a library of metal-binding pharmacophores (MBPs) to modulate their physicochemical properties, while retaining their metal binding and metalloenzyme inhibitory activity. Here, metal binding isosteres (MBIs) with different nitrogen-containing heteroarenes is explored. This resulted in a number of new MBIs that were evaluated for their physicochemical properties and metal binding features. It was observed that the coordination behavior of an MBI is dependent on the identity and arrangement of the heteroatoms within each heteroarene. To further understand the observed coordination chemistry trends, density functional theory (DFT) calculations were performed. Theory indicates that preferences in coordination geometry are largely determined by the electronic character of the heteroarene scaffold. These results provide important insights into the development of novel MBI scaffolds that can serve to broaden the scope of scaffolds for metalloenzyme inhibitor development.

Matrix Metalloproteinases as New Targets in Alzheimer's Disease: Opportunities and Challenges

Although matrix metalloproteinases (MMPs) are implicated in the regulation of numerous physiological processes, evidence of their pathological roles have also been obtained in the last decades, making MMPs attractive therapeutic targets for several diseases. Recent discoveries of their involvement in central nervous system (CNS) disorders, and in particular in Alzheimer's disease (AD), have paved the way to consider MMP modulators as promising therapeutic strategies. Over the past few decades, diverse approaches have been undertaken in the design of therapeutic agents targeting MMPs for various purposes, leading, more recently, to encouraging developments. In this article, we will present recent examples of inhibitors ranging from small molecules and peptidomimetics to biologics. We will also discuss the scientific knowledge that has led to the development of emerging tools and techniques to overcome the challenges of selective MMP inhibition.

Dentin degradonomics - The potential role of salivary MMP-8 in dentin caries

Background

Dentin caries involves dissolution of minerals which eventually leads to degradation of organic matrix. This degradation which was thought to be by bacterial proteases is now considered to be orchestrated by endogenous collagenases such as Matrix Metalloproteinases (MMPs). This paper aims to estimate the salivary levels of MMP-8 in dental caries and also to asses the various risk factors that contribute to the formation of dental caries.

Material and Methods

A random sample of 75 adults aged 18-35 were included and categorized based on the number of caries lesions (MCL). Standard clinical examinations were performed, and stimulated saliva was collected and analyzed for concentrations of MMP-8 using enzyme-linked immunosorbent assay. Caries risk factors were assessed using a chair-side kit. Correlation of MMP-8 in varying MCL using Spearman’s correlation was done. Multiple linear regression analysis was done to asses the relationship between various caries risk factors with MMP-8 and MCL as dependent variable.

Results

The study results showed a statistically significant higher concentration of MMP-8 in carious group (MCL 1-2) and MCL ≥3 compared to non-carious group. On correlating, the levels of MMP-8 were seen to be higher in MCL ≥3 than in MCL = 0 and MCL 1-2. The mean MMP-8 of controls, MCL 1-2, and MCL ≥3 were 131.34ng/ml, 230.14ng/ml, and 391.91ng/ml respectively. Multiple linear regression analysis with MMP-8 as the dependent variable revealed caries, buffer capacity and S. mutans count as significant variables. Using MCL as the dependent variable the only significant variable was MMP-8 levels.

Conclusions

The study suggests that subjects with caries have elevated MMP-8 levels compared with subjects with no carious lesions. There is also a positive correlation between the number of carious lesions and MMP-8 levels suggesting that MMP-8 plays an important role in the degradation of dentin and causes progression of caries.

Key words:Caries, Dentin, Enzyme-linked Immunosorbent Assay, MMP-8.

Structural Requirements of N-alpha-Mercaptoacetyl Dipeptide (NAMdP) Inhibitors of Pseudomonas Aeruginosa Virulence Factor LasB: 3D-QSAR, Molecular Docking, and Interaction Fingerprint Studies

The zinc metallopeptidase Pseudomonas elastase (LasB) is a virulence factor of Pseudomonas aeruginosa (P. aeruginosa), a pathogenic bacterium that can cause nosocomial infections. The present study relates the structural analysis of 118 N-alpha-mercaptoacetyl dipeptides (NAMdPs) as LasB inhibitors. Field-based 3D-QSAR and molecular docking methods were employed to describe the essential interactions between NAMdPs and LasB binding sites, and the chemical features that determine their differential activities. We report a predictive 3D-QSAR model that was developed according to the internal and external validation tests. The best model, including steric, electrostatic, hydrogen bond donor, hydrogen bond acceptor, and hydrophobic fields, was found to depict a three-dimensional map with the local positive and negative effects of these chemotypes on the LasB inhibitory activities. Furthermore, molecular docking experiments yielded bioactive conformations of NAMdPs inside the LasB binding site. The series of NAMdPs adopted a similar orientation with respect to phosphoramidon within the LasB binding site (crystallographic reference), where the backbone atoms of NAMdPs are hydrogen-bonded to the LasB residues N112, A113, and R198, similarly to phosphoramidon. Our study also included a deep description of the residues involved in the protein-ligand interaction patterns for the whole set of NAMdPs, through the use of interaction fingerprints (IFPs).

Identification of Inhibitors against Botulinum Neurotoxins: 8-Hydroxyquinolines Hold Promise

Botulinum neurotoxins (BoNTs) are the most toxic category A biological warfare agents. There is no therapeutics available for BoNT intoxication yet, necessitating the development of a medical countermeasure against these neurotoxins. The discovery of small molecule-based drugs has revolutionized in the last two decades resulting in the identification of several small molecule inhibitors of BoNTs. However, none progressed to clinical trials. 8-Hydroxyquinolines scaffold-based molecules are important 'privileged structures' that can be exploited as inhibitors of a diverse range of targets. In this review, our study of recent reports suggests the development of 8-hydroxyquinoline derived molecules as a potential drug may be on the horizon.

Structure-based design of selective histone deacetylase 6 zinc binding groups

The binding site of the second catalytic domain of human histone deacetylase 6 (HDAC6 CDII) has structural features that differ from the other human orthologues, being also mainly responsible for the overall enzymatic activity of this isoform. Aiming to identify new fragments as a possible novel selective zinc binding group (ZBG) for HDAC6 CDII, two fragment libraries were designed: one library consisting of known chelators and a second one using the fragments of the ZINC15 database. The most promising fragments identified in a structure-based virtual screening of designed libraries were further evaluated through molecular docking and molecular dynamics simulations. An interesting benzimidazole fragment was selected from the in silico studies and presented as potential zing binding group for the development of novel HDAC6 selective inhibitors.Communicated by Ramaswamy H. Sarma.

Identification of the 2-Benzoxazol-2-yl-phenol Scaffold as New Hit for JMJD3 Inhibition

JMJD3 is a member of the KDM6 subfamily and catalyzes the demethylation of lysine 27 on histone H3 (H3K27). This protein was identified as a useful tool in understanding the role of epigenetics in inflammatory conditions and in cancer as well. Guided by a virtual fragment screening approach, we identified the benzoxazole scaffold as a new hit suitable for the development of tighter JMJD3 inhibitors. Compounds were synthesized by a microwave-assisted one-pot reaction under catalyst and solvent-free conditions. Among these, compound 8 presented the highest inhibitory activity (IC₅₀ = 1.22 ± 0.22 μM) in accordance with molecular modeling calculations. Moreover, 8 induced the cycle arrest in S-phase on A375 melanoma cells.

Metal-Binding Pharmacophore Library Yields the Discovery of a Glyoxalase 1 Inhibitor

Anxiety and depression are common, highly comorbid psychiatric diseases that account for a large proportion of worldwide medical disability. Glyoxalase 1 (GLO1) has been identified as a possible target for the treatment of anxiety and depression. GLO1 is a Zn²⁺-dependent enzyme that isomerizes a hemithioacetal, formed from glutathione and methylglyoxal, to a lactic acid thioester. To develop active inhibitors of GLO1, fragment-based drug discovery was used to identify fragments that could serve as core scaffolds for lead development. After screening a focused library of metal-binding pharmacophores, 8-(methylsulfonylamino)quinoline (8-MSQ) was identified as a hit. Through computational modeling and synthetic elaboration, a potent GLO1 inhibitor was developed with a novel sulfonamide core pharmacophore. A lead compound was demonstrated to penetrate the blood-brain barrier, elevate levels of methylglyoxal in the brain, and reduce depression-like behavior in mice. These findings provide the basis for GLO1 inhibitors to treat depression and related psychiatric illnesses.

New ternary iron(iii) aminobisphenolate hydroxyquinoline complexes as potential therapeutic agents

Fe(iii)-Aminobisphenolate hydroxyquinoline complexes are active anticancer drug candidates in the low micromolar range, displaying apoptosis as the mode of cell death.

Structure-Activity Relationships in Metal-Binding Pharmacophores for Influenza Endonuclease

Metalloenzymes represent an important target space for drug discovery. A limitation to the early development of metalloenzyme inhibitors has been the lack of established structure-activity relationships (SARs) for molecules that bind the metal ion cofactor(s) of a metalloenzyme. Herein, we employed a bioinorganic perspective to develop an SAR for inhibition of the metalloenzyme influenza RNA polymerase PA_N endonuclease. The identified trends highlight the importance of the electronics of the metal-binding pharmacophore (MBP), in addition to MBP sterics, for achieving improved inhibition and selectivity. By optimization of the MBPs for PA_N endonuclease, a class of highly active and selective fragments was developed that displays IC₅₀ values <50 nM. This SAR led to structurally distinct molecules that also displayed IC₅₀ values of ∼10 nM, illustrating the utility of a metal-centric development campaign in generating highly active and selective metalloenzyme inhibitors.

Metal-Binding Isosteres as New Scaffolds for Metalloenzyme Inhibitors

The principle of isosteres or bioisosteres in medicinal chemistry is a central and essential concept in modern drug discovery. For example, carboxylic acids are often replaced by bioisosteres to mitigate issues related to lipophilicity or acidity while retaining acidic characteristics in addition to hydrogen bond donor/acceptor abilities. Separately, the development of metal-binding pharmacophores (MBPs) for binding to the active site metal ion in metalloenzymes of therapeutic interest is an emerging area in the realm of fragment-based drug discovery (FBDD). The direct application of the bioisostere concept to MBPs has not been well-described or systematically investigated. Herein, the picolinic acid MBP is used as a case study for the development of MBP isosteres (so-called MBIs). Many of these isosteres are novel compounds, and data on their physicochemical properties, metal binding capacity, and metalloenzyme inhibition characteristics are presented. The results show that MBIs of picolinic acid generally retain metal coordinating properties and exhibit predictable metalloenzyme inhibitory activity while possessing a broad range of physicochemical properties (e.g., p Ka, log P). These findings demonstrate the use of bioisosteres results in an untapped source of metal binding functional groups suitable for metalloenzyme FBDD. These MBIs provide a previously unexplored route for modulating the physicochemical properties of metalloenzyme inhibitors and improving their drug-likeness.

Multi-target-directed ligands for treating Alzheimer's disease: Butyrylcholinesterase inhibitors displaying antioxidant and neuroprotective activities

The limited clinical efficacy of current symptomatic treatment and minute effect on progression of Alzheimer's disease has shifted the research focus from single targets towards multi-target-directed ligands. Here, a potent selective inhibitor of human butyrylcholinesterase was used as the starting point to develop a new series of multifunctional ligands. A focused library of derivatives was designed and synthesised that showed both butyrylcholinesterase inhibition and good antioxidant activity as determined by the DPPH assay. The crystal structure of compound 11 in complex with butyrylcholinesterase revealed the molecular basis for its low nanomolar inhibition of butyrylcholinesterase (Ki = 1.09 ± 0.12 nM). In addition, compounds 8 and 11 show metal-chelating properties, and reduce the redox activity of chelated Cu²⁺ ions in a Cu-ascorbate redox system. Compounds 8 and 11 decrease intracellular levels of reactive oxygen species, and are not substrates of the active efflux transport system, as determined in Caco2 cells. Compound 11 also protects neuroblastoma SH-SY5Y cells from toxic Aβ_1-42 species. These data indicate that compounds 8 and 11 are promising multifunctional lead ligands for treatment of Alzheimer's disease.

Syntheses, Crystal Structures, and Antitumor Activities of Copper(II) and Nickel(II) Complexes with 2-((2-(Pyridin-2-yl)hydrazono)methyl)quinolin-8-ol

Two transition metal complexes with 2-((2-(pyridin-2-yl)hydrazono)methyl)quinolin-8-ol (L), [Cu(L)Cl₂]₂ (1) and [Ni(L)Cl₂]·CH₂Cl₂ (2), were synthesized and fully characterized. Complex 1 exhibited high in vitro antitumor activity against SK-OV-3, MGC80-3 and HeLa cells with IC50 values of 3.69 ± 0.16, 2.60 ± 0.17, and 3.62 ± 0.12 μM, respectively. In addition, complex 1 caused cell arrest in the S phase, which led to the down-regulation of Cdc25 A, Cyclin B, Cyclin A, and CDK2, and the up-regulation of p27, p21, and p53 proteins in MGC80-3 cells. Complex 1 induced MGC80-3 cell apoptosis via a mitochondrial dysfunction pathway, as shown by the significantly decreased level of bcl-2 protein and the loss of Δψ, as well as increased levels of reactive oxygen species (ROS), intracellular Ca2+, cytochrome C, apaf-1, caspase-3, and caspase-9 proteins in MGC80-3 cells.

Virtual Fragment Screening Identification of a Quinoline-5,8-dicarboxylic Acid Derivative as a Selective JMJD3 Inhibitor

The quinoline-5,8 dicarboxylic acid scaffold has been identified by a fragment-based approach as new potential lead compound for the development of JMJD3 inhibitors. Among them, 3-(2,4-dimethoxypyrimidin-5-yl)quinoline-5,8-dicarboxylic acid (compound 3) shows low micromolar inhibitory activity against Jumonji domain-containing protein 3 (JMJD3). The experimental evaluation of inhibitory activity against seven related isoforms of JMJD3 highlighted an unprecedented selectivity toward the biological target of interest.

In vitro assessment of ribose modified two-step etch-and-rinse dentine adhesive

OBJECTIVE

Collagen fibrils aid in anchoring resin composite restorations to the dentine substrate. The aim of the study was to investigate effect of non-enzymatic glycation on bond strength and durability of demineralized dentine specimens in a modified two-step etch-and-rinse dentine adhesive.

METHODS

Dentine surfaces were etched with 37% phosphoric acid, bonded with respective in vitro ethanol and acetone adhesives modified with (m/m, 0, 1%, 2% and 3% ribose), restored with restorative composite-resin, and sectioned into resin-dentine slabs and beams to be stored for 24h or 12 months in artificial saliva. Bond-strength testing was performed with bond failure analysis. Pentosidine assay was performed on demineralized ribose modified dentine specimens with HPLC sensitive fluorescent detection. The structural variations of ribose-modified dentine were analysed using TEM and human dental pulpal cells were used for cell viability. Three-point bending test of ribose-modified dentine beams were performed and depth of penetration of adhesives evaluated with micro-Raman spectroscopy. The MMP-2 and cathepsin K activities in ribose-treated dentine powder were also quantified using ELISA. Bond strength data was expressed using two-way ANOVA followed by Tukey's test. Paired T tests were used to analyse the specimens for pentosidine crosslinks. The modulus of elasticity and dentinal MMP-2 and cathepsin K concentrations was separately analyzed using one-way ANOVA.

RESULTS

The incorporation of RB in the experimental two-step etch-and-rinse adhesive at 1% improved the adhesive bond strength without adversely affecting the degree of polymerisation. The newly developed adhesive increases the resistance of dentine collagen to degradation by inhibiting endogenous matrix metalloproteinases and cysteine cathepsins. The application of RB to acid-etched dentine helps maintain the mechanical properties.

SIGNIFICANCE

The incorporation of 1%RB can be considered as a potential candidate stabilizing resin dentine bond.

Phenotypic Screening To Discover Novel Chemical Series as Efficient Antihemorrhagic Agents

In an effort to find novel chemical series as antifibrinolytic agents, we explore α-phenylsulfonyl-α-spiropiperidines bearing different zinc-binding groups (ZBGs) to target those metalloproteinases involved in the fibrinolytic process: MMP3 and MMP10. Surprisingly, all these new chemical series were inactive against these metalloproteinases; however, several new molecules retained the antifibrinolytic activity in a phenotypic functional assay using thromboelastometry and human whole blood. Further optimization led to compound 38 as a potent antifibrinolytic agent in vivo, three times more efficacious than the current standard-of-care (tranexamic acid, TXA) at 300 times lower dose. Finally, in order to decipher the underlying mode-of-action leading to this phenotypic response, an affinity-based probe 39 was successfully designed to identify the target involved in this response: a potentially unknown mechanism-of-action in the fibrinolytic process.