Metal-Binding Isosteres as New Scaffolds for Metalloenzyme Inhibitors

Homoleptic coordination polymers and complexes of transition metals with 2-(1,2,4-1H-triazol-3-yl) pyridine and tuning towards white-light emission

Twelve coordination compounds ranging from polymers to complexes based on divalent ions of the 3d-transition metals Mn to Zn, and Cd together with the ligand 2-(1,2,4-1H-triazol-3-yl)pyridine (Hpt) were synthesised and fully characterised. The main products are homoleptic, one-dimensional coordination polymers 1∞[M(pt)2] (M = Mn-Zn, and Cd, pt = 3-(pyridin-2-yl)-1,2,4-triazolate), 1∞[Cu(pt)2]·0.5Py, besides complexes [MX2(Hpt)2] from MnCl2, FeCl2, CoCl2, CoBr2, ZnCl2, and Hpt = 2-(1,2,4-1H-triazol-3-yl)pyridine. In addition to these series, single crystalline by-products of the reactions were identified and their structures determined. The obtained products were investigated with single-crystal (SCXRD) and powder X-ray diffraction (PXRD), including temperature-dependent PXRD, physisorption experiments, UV-Vis, IR, and photoluminescence spectroscopy (PL), simultaneous thermal analysis, and elemental analysis. Based on 1∞[Zn(pt)2], it was possible to generate a white light-emitting compound by addition of Eu3+ and Tb3+. It follows the RGB concept with blue ligand-based emission of the coordination polymer and red/green emission of lanthanide ions and shows excitation dependent tuneable character of emission colour from blue to practically perfect white.

Non-Hydroxamate Inhibitors of IspC Enzyme in the MEP Pathway: Structural Insights and Drug Development Potential

1-Deoxy-D-xylulose-5-phosphate reductoisomerase (IspC) is a key enzyme in the MEP pathway, essential for many bacteria, human pathogens, and plants, thus being an attractive drug target. Fosmidomycin, a potent IspC inhibitor with hydroxamate metal-binding pharmacophores (MBPs), has entered clinical trials for malaria but is hampered by pharmacokinetic and toxicity issues of the hydroxamate fragment. This has led to increased interest in non-hydroxamate inhibitors. This review focuses on the crystal structure and active-site binding mode of IspC, and the structural types, inhibitory activities, and structure-activity relationships of non-hydroxamate IspC inhibitors. Early attempts to design such inhibitors involved direct removal or replacement of the hydroxamate MBPs, with varying results. Lipophilic inhibitors, bisubstrate inhibitors, and those developed for herbicidal applications have shown promise. However, challenges remain due to the sensitivity of the enzyme active site to ligand interactions. Future research could draw from other metalloenzyme studies to develop novel and efficient non-hydroxamate IspC inhibitors.

Computational approaches for the identification of novel metal-binding pharmacophores: advances and challenges

Metalloenzymes are important therapeutic targets for a variety of human diseases. Computational approaches have recently emerged as effective tools to understand metal-ligand interactions and expand the structural diversity of both metalloenzyme inhibitors (MIs) and metal-binding pharmacophores (MBPs). In this review, we highlight key advances in currently available fine-tuning modeling methods and data-driven cheminformatic approaches. We also discuss major challenges to the recognition of novel MBPs and MIs. The evidence provided herein could expedite future computational efforts to guide metalloenzyme-based drug discovery.

Replacement of the hydroxamic acid group in the selective HDAC8 inhibitor PCI-34051

PCI-34051 is a valuable tool to interrogate the therapeutic effects of selective inhibition of HDAC8. However, it has not advanced to clinical trials, perhaps due to poor PK or off-target effects. We hypothesized that the presence of a hydroxamic acid (HA) group in PCI-34051 contributed to its lack of advancement. Therefore, we replaced the HA in the PCI-34051 scaffold with a series of moieties that have the potential to bind to Zn and evaluated their activity in a HDAC8 assay. Surprisingly, none of the replacements effectively mimicked the HA, and analogs lost significant potency. Evaluation of the analogs' affinity to Zn indicated that none had affinity for Zn within the same range as the HA. These studies point to the difficulty in the application of bioisosteric replacements for Zn binding motifs.

Discovery of Novel Metalloenzyme Inhibitors Based on Property Characterization: Strategy and Application for HDAC1 Inhibitors

Metalloenzymes are ubiquitously present in the human body and are relevant to a variety of diseases. However, the development of metalloenzyme inhibitors is limited by low specificity and poor drug-likeness associated with metal-binding fragments (MBFs). A generalized drug discovery strategy was established, which is characterized by the property characterization of zinc-dependent metalloenzyme inhibitors (ZnMIs). Fifteen potential Zn2+-binding fragments (ZnBFs) were identified, and a customized pharmacophore feature was defined based on these ZnBFs. The customized feature was set as a required feature and applied to a search for novel inhibitors for histone deacetylase 1 (HDAC1). Ten potential HDAC1 inhibitors were recognized, and one of them (compound 9) was a known potent HDAC1 inhibitor. The results demonstrated the effectiveness of our strategy to identify novel inhibitors for zinc-dependent metalloenzymes.

BRD4354 Is a Potent Covalent Inhibitor against the SARS-CoV-2 Main Protease

Numerous organic molecules are known to inhibit the main protease (MPro) of SARS-CoV-2, the pathogen of Coronavirus Disease 2019 (COVID-19). Guided by previous research on zinc-ligand inhibitors of MPro and zinc-dependent histone deacetylases (HDACs), we identified BRD4354 as a potent inhibitor of MPro. The in vitro protease activity assays show that BRD4354 displays time-dependent inhibition against MPro with an IC50 (concentration that inhibits activity by 50%) of 0.72 ± 0.04 μM after 60 min of incubation. Inactivation follows a two-step process with an initial rapid binding step with a KI of 1.9 ± 0.5 μM followed by a second slow inactivation step, kinact,max of 0.040 ± 0.002 min-1. Native mass spectrometry studies indicate that a covalent intermediate is formed where the ortho-quinone methide fragment of BRD4354 forms a covalent bond with the catalytic cysteine C145 of MPro. Based on these data, a Michael-addition reaction mechanism between MPro C145 and BRD4354 was proposed. These results suggest that both preclinical testing of BRD4354 and structure-activity relationship studies based on BRD4354 are warranted to develop more effective anti-COVID therapeutics.

Control of metalloenzyme activity using photopharmacophores

Metalloenzymes are responsible for numerous physiological and pathological processes in living organisms; however, there are very few FDA-approved metalloenzyme-targeting therapeutics (only ~ 67 FDA-approved metalloenzyme inhibitors as of 2020, less than ~ 5 % of all FDA-approved therapeutics). Most metalloenzyme inhibitors have been developed to target the catalytic metal centers in metalloenzymes via the incorporation of metal-binding groups. Light-controlled inhibition of metalloenzymes has been used as a means to specifically activate and inactivate inhibitor engagement at a desired location and time via light irradiation, allowing for precise spatiotemporal control over metalloenzyme activity. In this review, we summarize the strategies that have been employed to develop biocompatible light-sensitive inhibitors for metalloenzymes via the incorporation of different photo-activatable moieties (including photoswitchable and photocleavable groups), and the application of photo-activateable inhibitors both in vitro and in vivo. We also discuss the photophysical mechanisms of different photo-activatable groups, their action under physiological conditions, and the different modes of interaction between inhibitors and proteins (i.e., inhibition mechanisms) in the presence and absence of light. Finally, we discuss considerations for the future development of light-responsive metalloenzyme inhibitors and the challenges limiting their application in vivo.

Inhibiting HCMV pUL89-C Endonuclease with Metal-Binding Compounds

Human cytomegalovirus (HCMV) infects individuals of all ages and establishes a lifelong latency. Current antiviral drugs are suboptimal in efficacy and safety and ineffective against resistant/refractory HCMV. Therefore, there is an unmet clinical need for efficacious, safe, and mechanistically novel HCMV drugs. The recent Food and Drug Administration (FDA) approval of letermovir (LTV) validated the HCMV terminase complex as a new target for antiviral development. LTV targets terminase subunit pUL56 but not the main endonuclease enzymatic function housed in the C terminus of subunit pUL89 (pUL89-C). Structurally and mechanistically, pUL89-C is an RNase H-like viral endonuclease entailing two divalent metal ions at the active site. In recent years, numerous studies have extensively explored pUL89-C inhibition using metal-chelating chemotypes, an approach previously used for inhibiting HIV ribonuclease H (RNase H) and integrase strand transfer (INST). Collectively, the work summarized herein validates the use of metal-binding scaffolds for designing potent and specific pUL89-C inhibitors.

Carboxylic Acid Isostere Derivatives of Hydroxypyridinones as Core Scaffolds for Influenza Endonuclease Inhibitors

Among the most important influenza virus targets is the RNA-dependent RNA polymerase acidic N-terminal (PA_N) endonuclease, which is a critical component of the viral replication machinery. To inhibit the activity of this metalloenzyme, small-molecule inhibitors employ metal-binding pharmacophores (MBPs) that coordinate to the dinuclear Mn²⁺ active site. In this study, several metal-binding isosteres (MBIs) were examined where the carboxylic acid moiety of a hydroxypyridinone MBP is replaced with other groups to modulate the physicochemical properties of the compound. MBIs were evaluated for their ability to inhibit PA_N using a FRET-based enzymatic assay, and their mode of binding in PA_N was determined using X-ray crystallography.

Current medicinal chemistry strategies in the discovery of novel HIV-1 ribonuclease H inhibitors

During HIV-1 genome replication, the viral reverse transcriptase-associated ribonuclease H (RT-associated RNase H) activity hydrolyzes the RNA strand of RNA/DNA heteroduplex intermediates. As of today, HIV-1 RNase H inhibitors (RHIs) remain at an investigational level, although none of them reached clinical trials. Therefore, RNase H remains as an attractive target for drug design and development. In this paper, we review the current status of medicinal chemistry strategies aimed at the discovery of novel RHIs, while discussing problems encountered in their characterization and further development, thereby providing an update on recent progress in the field.

Medicinal inorganic chemistry - challenges, opportunities and guidelines to develop the next generation of radioactive, photoactivated and active site inhibiting metal-based medicines

Medicinal inorganic chemistry is a burgeoning subfield of medicinal chemistry that focuses on the development of metal-based diagnostic and therapeutic agents. This tutorial review aims to provide an introductory primer, present a timely overview of recent discoveries and identify current challenges and opportunities of the field. Three specific areas of discovery are highlighted herein. The first part focuses on metal-based radiopharmaceuticals for diagnostic and therapeutic purposes and specific design criteria for the development of radiopharmaceuticals that combine fundamental aqueous coordination chemistry with elucidation of pharmacokinetics. The second part describes approaches to photodynamic therapy with metal complexes. Here, photophysical characterization, combined with the challenge of careful control of the chemical behavior and selective biological deposition of transition metals with significant off-target toxicity, is discussed. In the third part, we summarize emerging strategies to modulate enzyme inhibition with coordination chemistry, while also highlighting the utility of the unique properties of metal ions for the characterization of mechanisms of action of these emerging diagnostic and therapeutic agents.

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.

Thietanes and derivatives thereof in medicinal chemistry

Unlike the oxetane ring, which, as evidenced by numerous studies, is known to play an increasingly important role in medicinal chemistry, the thietane ring has thus far received comparatively limited attention. Nonetheless, a growing number of reports now indicate that this 4-membered ring heterocycle may provide opportunities in analog design. In the present review article, we discuss the possible use and utility of the thietane fragment in medicinal chemistry and provide an overview of its properties and recent applications with a focus on isosteric replacements.

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.

Targeting Metalloenzymes by Boron-Containing Metal-Binding Pharmacophores

Metalloenzymes have critical roles in a wide range of biological processes and are directly involved in many human diseases; hence, they are considered as important targets for therapeutic intervention. The specific characteristics of metal ion(s)-containing active sites make exploitation of metal-binding pharmacophores (MBPs) critical to inhibitor development targeting metalloenzymes. This Perspective focuses on boron-containing MBPs, which display unique binding modes with metalloenzyme active sites, particularly via mimicking native substrates or tetrahedral transition states. The design concepts regarding boron-containing MBPs are highlighted through the case analyses on five distinct classes of clinically relevant nucleophilic metalloenzymes from medicinal chemistry perspectives. The challenges (e.g., selectivity) faced by some boron-containing MBPs and possible strategies (e.g., bioisosteres) for metalloenzyme inhibitor transformation are also discussed.

Synthesis of tetranuclear rhenium(I) tricarbonyl metallacycles

Re(I) tricarbonyl complexes have received much attention due to their attractive photochemical, electrochemical, and biological properties. Beyond simple mononuclear complexes, multinuclear assemblies offer greater structural diversity and properties. Despite previous reports on the preparation of di-, tri-, or tetranuclear Re(I) tricarbonyl assemblies, the synthesis of these supramolecular structures remains challenging due to overall low yields or tedious purification protocols. Herein, the facile preparation and characterization of tetranuclear Re(I) tricarbonyl metallacycles with a square geometry is reported using a tetrazole-based ligand. The synthesis of the metallacycle was optimized using different metal precursors, solvents, temperatures, and reagent concentrations. Finally, the scope of suitable tetrazole-based ligands was explored to produce several tetranuclear Re(I) tricarbonyl-based metallacycles.

Evaluating Metal-Ligand Interactions of Metal-Binding Isosteres Using Model Complexes

Bioisosteres are a useful approach to address pharmacokinetic liabilities and improve drug-like properties. Specific to developing metalloenzyme inhibitors, metal-binding pharmacophores (MBPs) have been combined with bioisosteres, to produce metal-binding isosteres (MBIs) as alternative scaffolds for use in fragment-based drug discovery (FBDD). Picolinic acid MBIs have been reported and evaluated for their metal-binding ability, pharmacokinetic properties, and enzyme inhibitory activity. However, their structural, electronic, and spectroscopic properties with metal ions other than Zn(II) have not been reported, which might reveal similarities and differences between MBIs and the parent MBPs. To this end, [M(TPA)(MBI)]⁺ (M = Ni(II) and Co(II), TPA = tris(2-pyridylmethyl)amine) is presented as a bioinorganic model system for investigating picolinic acid, four heterocyclic MBIs, and 2,2'-bipyridine. These complexes were characterized by X-ray crystallography as well as NMR, IR, and UV-vis spectroscopies, and their magnetic moments were accessed. In addition, [(Tp^Ph,Me)Co(MBI)] (Tp^Ph,Me = hydrotris(3,5-phenylmethylpyrazolyl)borate) was used as a second model compound, and the limitations and attributes of the two model systems are discussed. These results demonstrate that bioinorganic model complexes are versatile tools for metalloenzyme inhibitor design and can provide insights into the broader use of MBIs.

An E. coli-Based Biosynthetic Platform Expands the Structural Diversity of Natural Benzoxazoles

Benzoxazoles are frequently found in synthetic pharmaceuticals and medicinally active natural products. To facilitate benzoxazole-based drug development, an eco-friendly and rapid platform for benzoxazole production is required. In this study, we have completed the biosynthesis of benzoxazoles in E. coli by coexpressing the minimal set of enzymes required for their biosynthesis. Moreover, by coupling this E. coli-based platform with precursor-directed biosynthesis, we have shown that the benzoxazole biosynthetic system is highly promiscuous in incorporating fluorine, chlorine, nitrile, picolinic, and alkyne functionalities into the scaffold. Our E. coli-based system thus paves the way for straightforward generation of novel benzoxazole analogues through future protein engineering and combinatorial biosynthesis.

Recent Developments in the Practical Application of Novel Carboxylic Acid Bioisosteres

BACKGROUND

The carboxylic acid is an important functional group which features in the pharmacophore of some 450 drugs. Unfortunately, some carboxylic acid-containing drugs have been withdrawn from market due to unforeseen toxicity issues. Other issues associated with the carboxylate moiety include reduced metabolic stability or limited passive diffusion across biological membranes. Medicinal chemists often turn to bioisosteres to circumvent such obstacles.

OBJECTIVE

The aim of this review is to provide a summary of the various applications of novel carboxylic acid bioisosteres which have appeared in the literature since 2013.

RESULTS

We have summarised the most recent developments in carboxylic acid bioisosterism. In particular, we focus on the changes in bioactivity, selectivity or physiochemical properties brought about by these substitutions, as well as the advantages and disadvantages of each isostere.

CONCLUSION

The topics discussed herein highlight the continued interest in carboxylate bioisosteres. The development of novel carboxylic acid substitutes which display improved pharmacological profiles is testament to the innovation and creativity required to overcome the challenges faced in modern drug design.

MolOpt: A Web Server for Drug Design using Bioisosteric Transformation

BACKGROUND

Bioisosteric replacement is widely used in drug design for lead optimization. However, the identification of a suitable bioisosteric group is not an easy task.

METHODS

In this work, we present MolOpt, a web server for in silico drug design using bioisosteric transformation. Potential bioisosteric transformation rules were derived from data mining, deep generative machine learning and similarity comparison. MolOpt tries to assist the medicinal chemist in his/her search for what to make next.

RESULTS AND DISCUSSION

By replacing molecular substructures with similar chemical groups, MolOpt automatically generates lists of analogues. MolOpt also evaluates forty important pharmacokinetic and toxic properties for each newly designed molecule. The transformed analogues can be assessed for possible future study.

CONCLUSION

MolOpt is useful for the identification of suitable lead optimization ideas. The MolOpt Server is freely available for use on the web at http://xundrug.cn/molopt.

Development of 2-Morpholino-N-hydroxybenzamides as anti-proliferative PC-PLC inhibitors

Phosphatidylcholine-specific phospholipase C (PC-PLC) is a key enzyme involved in the metabolism of the mammalian phospholipid phosphatidylcholine into secondary messengers diacylglycerol (DAG) and phosphocholine. DAG and phosphocholine have been identified to amplify various cellular processes involved in oncogenesis such as proliferation, cell-cycle activation, differentiation and motility, therefore making PC-PLC a potential target for novel anti-cancer treatments. The current literature standard for PC-PLC inhibition, tricyclodecan-9-yl-potassium xanthate (D609), has been shown to arrest proliferation in multiple cancer cell lines, however, it is not drug-like resulting in low aqueous stability, making it a poor drug candidate. 2-Morpholinobenzoic acids have been shown to have improved PC-PLC inhibitory activity compared to D609, with molecular modelling identifying chelation of the carboxylic acid to catalytic Zn²⁺ ions in the PC-PLC active site being a key interaction. In this study, the carboxylic acid motif was replaced with a hydroxamic acid to strengthen the Zn²⁺ interaction. It was found that the hydroxamic acid derivatives displayed PC-PLC inhibitory activity similar, or better, than D609. Furthermore, these novel inhibitors had potent anti-proliferative activity in MDA-MB-231 and HCT-116 cancer cell lines, far greater than D609 and previous 2-morpholinobenzoic acids.

Using NMR Spectroscopy in the Fragment-Based Drug Discovery of Small-Molecule Anticancer Targeted Therapies

Against the challenge of providing personalized cancer care, the development of targeted therapies stands as a promising approach. The discovery of these agents can benefit from fragment-based drug discovery (FBDD) methods that help guide ligand design and provide key structural information on the targets of interest. In particular, nuclear magnetic resonance spectroscopy is a promising biophysical tool in fragment discovery due to its detection capabilities and versatility. This review provides an overview of FBDD, describes the basis of NMR-based fragment screening, summarizes some exciting technical advances reported over the past decades, and closes with a discussion of selected case studies where this technique has been used as part of drug discovery campaigns to produce lead compounds towards the design of anti-cancer targeted therapies.

Non-hydroxamate inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR): A critical review and future perspective

1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) catalyzes the second step of the non-mevalonate (or MEP) pathway that functions in several organisms and plants for the synthesis of isoprenoids. DXR is essential for the survival of multiple pathogenic bacteria/parasites, including those that cause tuberculosis and malaria in humans. DXR function is inhibited by fosmidomycin (1), a natural product, which forms a chelate with the active site divalent metal (Mg²⁺/Mn²⁺) through its hydroxamate metal-binding group (MBG). Most of the potent DXR inhibitors are structurally similar to 1 and retain hydroxamate despite the unfavourable pharmacokinetic and toxicity profile of the latter. We provide our perspective on the lack of non-hydroxamate DXR inhibitors. We also highlight the fundamental flaws in the design of MBG in these molecules, primarily responsible for their failure to inhibit DXR. We also suggest that for designing next-generation non-hydroxamate DXR inhibitors, approaches followed for other metalloenzymes targets may be exploited.

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.

MeLAD: an integrated resource for metalloenzyme-ligand associations

MOTIVATION

Metalloenzymes are attractive targets for therapeutic intervention owing to their central roles in various biological processes and pathological situations. The fast-growing body of structural data on metalloenzyme-ligand interactions is facilitating efficient drug discovery targeting metalloenzymes. However, there remains a shortage of specific databases that can provide centralized, interconnected information exclusive to metalloenzyme-ligand associations.

RESULTS

We created a Metalloenzyme-Ligand Association Database (MeLAD), which is designed to provide curated structural data and information exclusive to metalloenzyme-ligand interactions, and more uniquely, present expanded associations that are represented by metal-binding pharmacophores (MBPs), metalloenzyme structural similarity (MeSIM) and ligand chemical similarity (LigSIM). MeLAD currently contains 6086 structurally resolved interactions of 1416 metalloenzymes with 3564 ligands, of which classical metal-binding, non-classical metal-binding, non-metal-binding and metal water-bridging interactions account for 63.0%, 2.3%, 34.4% and 0.3%, respectively. A total of 263 monodentate, 191 bidentate and 15 tridentate MBP chemotypes were included in MeLAD, which are linked to different active site metal ions and coordination modes. 3726 and 52 740 deductive metalloenzyme-ligand associations by MeSIM and LigSIM analyses, respectively, were included in MeLAD. An online server is provided for users to conduct metalloenzyme profiling prediction for small molecules of interest. MeLAD is searchable by multiple criteria, e.g. metalloenzyme name, ligand identifier, functional class, bioinorganic class, metal ion and metal-containing cofactor, which will serve as a valuable, integrative data source to foster metalloenzyme related research, particularly involved in drug discovery targeting metalloenzymes.

AVAILABILITY AND IMPLEMENTATION

MeLAD is accessible at https://melad.ddtmlab.org.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Proteomics for cancer drug design

Introduction: Signal transduction cascades drive cellular proliferation, apoptosis, immune, and survival pathways. Proteins have emerged as actionable drug targets because they are often dysregulated in cancer, due to underlying genetic mutations, or dysregulated signaling pathways. Cancer drug development relies on proteomic technologies to identify potential biomarkers, mechanisms-of-action, and to identify protein binding hot spots. Areas covered: Brief summaries of proteomic technologies for drug discovery include mass spectrometry, reverse phase protein arrays, chemoproteomics, and fragment based screening. Protein-protein interface mapping is presented as a promising method for peptide therapeutic development. The topic of biosimilar therapeutics is presented as an opportunity to apply proteomic technologies to this new class of cancer drug. Expert opinion: Proteomic technologies are indispensable for drug discovery. A suite of technologies including mass spectrometry, reverse phase protein arrays, and protein-protein interaction mapping provide complimentary information for drug development. These assays have matured into well controlled, robust technologies. Recent regulatory approval of biosimilar therapeutics provides another opportunity to decipher the molecular nuances of their unique mechanisms of action. The ability to identify previously hidden protein hot spots is expanding the gamut of potential drug targets. Proteomic profiling permits lead compound evaluation beyond the one drug, one target paradigm.

Emerging Opportunities To Manipulate Metal Trafficking for Therapeutic Benefit

The indispensable requirement for metals in life processes has led to the evolution of sophisticated mechanisms that allow organisms to maintain dynamic equilibria of these ions. This dynamic control of the level, speciation, and availability of a variety of metal ions allows organisms to sustain biological processes while avoiding toxicity. When functioning properly, these mechanisms allow cells to return to their metal homeostatic set points following shifts in the metal availability or other stressors. These periods of transition, when cells are in a state of flux in which they work to regain homeostasis, present windows of opportunity to pharmacologically manipulate targets associated with metal-trafficking pathways in ways that could either facilitate a return to homeostasis and the recovery of cellular function or further push cells outside of homeostasis and into cellular distress. The purpose of this Viewpoint is to highlight emerging opportunities for chemists and chemical biologists to develop compounds to manipulate metal-trafficking processes for therapeutic benefit.

Investigation of Dipicolinic Acid Isosteres for the Inhibition of Metallo-β-Lactamases

New Delhi metallo-β-lactamase-1 (NDM-1) poses an immediate threat to our most effective and widely prescribed drugs, the β-lactam-containing class of antibiotics. There are no clinically relevant inhibitors to combat NDM-1, despite significant efforts toward their development. Inhibitors that use a carboxylic acid motif for binding the Zn^II ions in the active site of NDM-1 make up a large portion of the >500 inhibitors reported to date. New and structurally diverse scaffolds for inhibitor development are needed urgently. Herein we report the isosteric replacement of one carboxylate group of dipicolinic acid (DPA) to obtain DPA isosteres with good inhibitory activity against NDM-1 (and related metallo-β-lactamases, IMP-1 and VIM-2). It was determined that the choice of carboxylate isostere influences both the potency of NDM-1 inhibition and the mechanism of action. Additionally, we show that an isostere with a metal-stripping mechanism can be re-engineered into an inhibitor that favors ternary complex formation. This work provides a roadmap for future isosteric replacement of routinely used metal binding motifs (i.e., carboxylic acids) for the generation of new entities in NDM-1 inhibitor design and development.