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Evaluation of 64 Cu-Based Radiopharmaceuticals that Target Aβ Peptide Aggregates as Diagnostic Tools for Alzheimer’s Disease
Positron emission tomography (PET) imaging agents that detect amyloid plaques containing amyloid beta (Aβ) peptide aggregates in the brain of Alzheimer’s disease (AD) patients have been successfully developed and recently approved by the FDA for clinical use. However, the short half-lives of the currently used radionuclides 11 C (20.4 min) and 18 F (109.8 min) may limit the widespread use of these imaging agents. Therefore, we have begun to evaluate novel AD diagnostic agents that can be radiolabeled with 64 Cu, a radionuclide with a half-life of 12.7 h, ideal for PET imaging. Described here in this paper are a series of bifunctional chelators (BFCs), L 1 –L 5 , that were designed to tightly bind 64 Cu and shown to interact with Aβ aggregates both in vitro and in transgenic AD mouse brain sections. Importantly, biodistribution studies show that these compounds exhibit promising brain uptake and rapid clearance in wild-type mice, and initial microPET imaging studies of transgenic AD mice suggest that these compounds could serve as lead compounds for the development of improved diagnostic agents for AD.
Synthesis and antitumor activity of cyclic octapeptide, samoamide A, and its derivatives
Using 2-chloro-trityl chloride resin as a solid phase carrier, a linear peptide was synthesized by Fmoc solid phase synthesis followed by liquid phase cyclization. After separation and purification by high-performance liquid chromatography (HPLC), cyclic octapeptide samoamide A was prepared. The synthesis yield was 54.5%. The structure of cyclic octapeptide samoamide A was characterized by electrospray ionization–mass spectrometry (ESI-MS) and nuclear magnetic resonance (NMR) spectrometry. The biological activity was evaluated by the CCK-8 assay and DPP4 enzyme activity inhibition assay. This compound exhibited high antitumor activity. Using samoamide A as a lead compound, eight cyclic octapeptide samoamide A derivatives (a, b, c, d, e, f, g, and h) were designed and synthesized using the alanine scanning method. The molecular weight and chemical structure of these derivatives were verified by ESI-MS and NMR, and the antitumor activity of the derivatives was analyzed. The antitumor activity of compound f was similar to that of samoamide A, and its replacement site is the non-active site of samoamide A, providing a theoretical basis for further modification and transformation of samoamide A.
Synthesis and electrophysical properties of some rare-earth molybdates with fluorite-like structure of the Nd{sub 5}Mo{sub 3}O{sub 16} type
Polycrystalline samples of PbLn{sub 4}Mo{sub 3}O{sub 16} (Ln = La, Pr, Nd, or Sm), CdLn{sub 4}Mo{sub 3}O{sub 16} (Ln = La, Nd, Sm, Eu, or Tm), and PbLa{sub 4–x}Nd{sub x}Mo{sub 3}O{sub 16} (0 ≤ x ≤ 3) with the cubic fluorite-like structure and sp. gr. Pn n have been obtained by solid-phase synthesis in air. The specific conductivity of lead compounds is established to reach 10{sup –2} S/cm (which is an order of magnitude higher than that for cadmium compounds). The conductivity value is shown to reach a maximum at a concentration ratio of rare-earth elements of Nd: La = 1: 1.
Synthesis, structural characterization, and cytotoxic evaluation of chalcone derivatives
Chalcones containing amino or acetamide groups on ring A and electron donating/withdrawing groups on ring B have been shown to have great cytotoxic potential against human cancer cell lines. In this work, a series of twenty chalcones, including nine 1-(4′-aminophenyl)-3-(substituted aryl)-2-propen-1-ones (1–9), nine 1-(4′-acetamidophenyl)-3-(substituted aryl)-2-propen-1-ones (1a–9a), and two 1-(3′-methoxy-4′-hydroxyphenyl)-3-(substituted aryl)-2-propen-1-ones (10, 11), were synthesized and submitted for initial biological screening using HCT-116 cells. Among the evaluated compounds, chalcone 6a showed strong and selective activity against HCT-116 cells (IC{sub 50} = 2.37 ± 0.73 µM). The preliminary structure–activity relationship analysis indicated that the cytotoxic effect of these compounds might be attributed to the combined effect of two electron withdrawing groups: the nitro group (NO{sub 2}) at the meta-position of ring B and the acetyl group at the para-position of ring A. Moreover, chalcone 6a was able to induce G2/M cell cycle arrest and apoptosis at a concentration of 10 µM after 24 h of incubation. These data reinforce that compound 6a could be a promising lead compound for the future exploration of selective anti-colon carcinoma cancer agents.
Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions
Alchemical relative binding free energy calculations have recently found important applications in drug optimization. A series of congeneric compounds are generated from a preidentified lead compound, and their relative binding affinities to a protein are assessed in order to optimize candidate drugs. While methods based on equilibrium thermodynamics have been extensively studied, an approach based on nonequilibrium methods has recently been reported together with claims of its superiority. However, these claims pay insufficient attention to the basis and reliability of both methods. Here we report a comparative study of the two approaches across a large data set, comprising more than 500 ligand transformations spanning in excess of 300 ligands binding to a set of 14 diverse protein targets. Ensemble methods are essential to quantify the uncertainty in these calculations, not only for the reasons already established in the equilibrium approach but also to ensure that the nonequilibrium calculations reside within their domain of validity. If and only if ensemble methods are applied, we find that the nonequilibrium method can achieve accuracy and precision comparable to those of the equilibrium approach. Compared to the equilibrium method, the nonequilibrium approach can reduce computational costs but introduces higher computational complexity and longer wall clock times. There are, however, cases where the standard length of a nonequilibrium transition is not sufficient, necessitating a complete rerun of the entire set of transitions. This significantly increases the computational cost and proves to be highly inconvenient during large-scale applications. Our findings provide a key set of recommendations that should be adopted for the reliable implementation of nonequilibrium approaches to relative binding free energy calculations in ligand-protein systems.
Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19
The SARS-CoV-2 3CL protease is a critical drug target for small molecule COVID-19 therapy, given its likely druggability and essentiality in the viral maturation and replication cycle. Based on the conservation of 3CL protease substrate binding pockets across coronaviruses and using screening, we identified four structurally distinct lead compounds that inhibit SARS-CoV-2 3CL protease. After evaluation of their binding specificity, cellular antiviral potency, metabolic stability, and water solubility, we prioritized the GC376 scaffold as being optimal for optimization. We identified multiple drug-like compounds with <10nM potency for inhibiting SARS-CoV-2 3CL and the ability to block SARS-CoV-2 replication in human cells, obtained co-crystal structures of the 3CL protease in complex with these compounds, and determined that they have pan-coronavirus activity. We selected one compound, termed coronastat, as an optimized lead and characterized it in pharmacokinetic and safety studies in vivo. Coronastat represents a new candidate for a small molecule protease inhibitor for the treatment of SARS-CoV-2 infection for eliminating pandemics involving coronaviruses.
Mannose-conjugated platinum complexes reveals effective tumor targeting mediated by glucose transporter 1
Despite numerous studies that report the glucose derived glycoconjugates as antitumor candidates, using mannose as sugar motif for specific tumor targeting remains less studied. In this research, two novel mannose-conjugated platinum complexes 4a and 4b that target the Warburg effect were designed, synthesized and evaluated for their antitumor activities in vitro and in vivo. Compared with oxaliplatin, both complexes exhibited substantial enhancement in water solubility as well as excellent or comparative cytotoxicity in six human cancer cell lines. Cytotoxicity assessments on Glucose transporter 1 (GLUT1) down-regulated or overexpressed cells and platinum accumulation study demonstrated that cellular uptake of compound 4a was regulated by GLUT1. In particular, 4a induced apoptosis in HT29 cells by suppressing expression of Bcl-2 and Bcl-XL, which preliminary explained the mechanism origin of antitumor effect. As indicated by its maximum tolerated dose-finding assay and in vivo anticancer activity, compound 4a exhibits better safety and efficacy profile than oxaliplatin. The findings of this study indicate the possibility of subjecting mannose-conjugated platinum complexes as lead compounds for further preclinical evaluation. - Highlights: • Mannose-conjugated platinum complexes were designed and synthesized to target glucose transporter 1(GLUT1). • Mannose-conjugated platinum complex 4a transport across cancer cells through GLUT1. • Mannose-conjugated platinum complex 4a induce apoptosis in HT29 cells. • Mannose-conjugated platinum complex 4a antitumor activities were more potent than those of oxaliplatin.
Synthesis, in vitro antifungal evaluation and docking studies of novel derivatives of imidazoles and benzimidazoles
A series of imidazole and benzimidazole derivatives was designed and prepared in good yields via convenient and efficient two steps synthetic route using readily available starting materials. The structures of the synthesized compounds and their intermediates were characterized by IR, {sup 1}H-NMR, {sup 13}C-NMR spectroscopy, and MS spectra. The in vitro antifungal activities of the targeted compounds were evaluated against Candida Albicans, Cryptococcus neoformans, Aspergillus niger, and Microsporum gypseum. The results showed that some of these azole-derivatives exhibited good to excellent antifungal activities against the used strains especially C. neoformans and A. niger. For example, compound 6b, 1-[2-Phenyl-2-(3-phenyl-propoxy)-ethyl]-1H-imidazole, was quite effective on the C. neoformans, A. niger, and M. gypseum with MIC 1.95 µg mL{sup −1}. The in silico molecular docking study was also done on the synthesized compounds and the results showed they have minimum binding energy and relatively good affinity toward cytochrome P450. According to the in vitro antifungal results and molecular docking studies, the compounds 6a–d can be selected as lead compounds for further pharmaceutical investigations.
Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers
The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottleneck screening the vast number of potential small molecules to shortlist lead compounds for antiviral drug development. New opportunities to accelerate drug discovery lie at the interface between machine learning methods, in this case, developed for linear accelerators, and physics-based methods. The two in silico methods, each have their own advantages and limitations which, interestingly, complement each other. Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery. The scale of the potential resulting workflow is such that it is dependent on supercomputing to achieve extremely high throughput. We have demonstrated the viability of this workflow for the study of inhibitors for four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead antiviral compounds through repurposing on a variety of supercomputers.
Structure-activity relationships of novel dithiocarbamates containing α,β-unsaturated ketone fragment as potent anticancer agents
Based on the structure of novel lead compound 8 discovered by our group, systematic structural modification was carried out. A series of compound 8’s derivatives were synthesized and evaluated for their activities against human non-small cell lung cancer cell line H460. Among them, twelve compounds showed significant proliferation inhibition activities with IC{sub 50} values <1 μM and compound 12r was the most potent one. Further study on compound 12r revealed that it has significant inhibitory effect on the growth of eight kinds of cancer cell lines with IC{sub 50} values <1 μM. Especially for cell lines A375 and HCT116, the IC{sub 50} values of 12r achieved 63 nM and 66 nM, respectively. Meanwhile, our research results also revealed the following structure-activity relationships: (a) different substitutions on the benzene ring or heteroaromatic rings greatly effect on the activity; (b) the presence of α,β-unsaturated ketone fragment is favorable for the activity; (c) the receptor cavity binding with amine moiety might be a relatively small hydrophobic cavity. These results will be valuable for the further development of this novel kind of dithiocarbamates.
Origin of resistivity anomaly in p-type leads chalcogenide multiphase compounds
The electrical resistivity curves for binary phase compounds of p-type lead chalcogenide (PbTe){sub (0.9−x)}(PbSe){sub 0.1}(PbS){sub x,} (x = 0.15, 0.2, 0.25), which contain PbS-rich secondary phases, show different behaviour on heating and cooling between 500-700 K. This is contrast to single phase compounds which exhibit similar behaviour on heating and cooling. We correlate these anomalies in the electrical resistivities of multiphase compounds to the variation in phase composition at high temperatures. The inhomogeneous distribution of dopants between the matrix and secondary phase is found to be crucial in the electronic transport properties of the multiphase compounds. These results can lead to further advances in designing composite Pb-chalcogenides with high thermoelectric performance.
Inhibition of Acinetobacter -Derived Cephalosporinase: Exploring the Carboxylate Recognition Site Using Novel β-Lactamase Inhibitors
Boronic acids are attracting a lot of attention as β-lactamase inhibitors, and in particular, compound S02030 (K i = 44 nM) proved to be a good lead compound against ADC-7 (Acinetobacter-derived cephalosporinase), one of the most significant resistance determinants in A. baumannii. The atomic structure of the ADC-7/S02030 complex highlighted the importance of critical structural determinants for recognition of the boronic acids. Herein, to elucidate the role in recognition of the R2-carboxylate, which mimics the C 3 /C 4 found in β-lactams, we designed, synthesized, and characterized six derivatives of S02030 (3a). Out of the six compounds, the best inhibitors proved to be those with an explicit negative charge (compounds 3a–c, 3h, and 3j, K i = 44–115 nM), which is in contrast to the derivatives where the negative charge is omitted, such as the amide derivative 3d (K i = 224 nM) and the hydroxyamide derivative 3e (K i = 155 nM). To develop a structural characterization of inhibitor binding in the active site, the X-ray crystal structures of ADC-7 in a complex with compounds 3c, SM23, and EC04 were determined. All three compounds share the same structural features as in S02030 but only differ in the carboxy-R2 side chain, thereby providing the opportunity of exploring the distinct binding mode of the negatively charged R2 side chain. This cephalosporinase demonstrates a high degree of versatility in recognition, employing different residues to directly interact with the carboxylate, thus suggesting the existence of a “carboxylate binding region” rather than a binding site in ADC enzymes. As a result, this class of compounds was tested against resistant clinical strains of A. baumannii and are effective at inhibiting bacterial growth in conjunction with a β-lactam antibiotic.
Identification of Selective Dual ROCK1 and ROCK2 Inhibitors Using Structure-Based Drug Design
A HTS campaign identified compound 1, an excellent hit-like molecule to initiate medicinal chemistry efforts to optimize a dual ROCK1 and ROCK2 inhibitor. Substitution (2-Cl, 2-NH 2 , 2-F, 3-F) of the pyridine hinge binding motif or replacement with pyrimidine afforded compounds with a clean CYP inhibition profile. Cocrystal structures of an early lead compound were obtained in PKA, ROCK1, and ROCK2. This provided critical structural information for medicinal chemistry to drive compound design. The structural data indicated the preferred configuration at the central benzylic carbon would be $(R)$, and application of this information to compound design resulted in compound 16. This compound was shown to be a potent and selective dual ROCK inhibitor in both enzyme and cell assays and efficacious in the retinal nerve fiber layer model after oral dosing. This tool compound has been made available through the AbbVie Compound Toolbox. Finally, the cocrystal structures also identified that aspartic acid residues 176 and 218 in ROCK2, which are glutamic acids in PKA, could be targeted as residues to drive both potency and kinome selectivity. Introduction of a piperidin-3-ylmethanamine group to the compound series resulted in compound 58, a potent and selective dual ROCK inhibitor with excellent predicted drug-like properties.
Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis
Malaria and cryptosporidiosis, caused by apicomplexan parasites, remain major drivers of global child mortality. New drugs for the treatment of malaria and cryptosporidiosis, in particular, are of high priority; however, there are few chemically validated targets. The natural product cladosporin is active against blood- and liver-stage Plasmodium falciparum and Cryptosporidium parvum in cell-culture studies. Target deconvolution in P. falciparum has shown that cladosporin inhibits lysyl-tRNA synthetase (PfKRS1). Here, we report the identification of a series of selective inhibitors of apicomplexan KRSs. Following a biochemical screen, a small-molecule hit was identified and then optimized by using a structure-based approach, supported by structures of both PfKRS1 and C. parvum KRS (CpKRS). In vivo proof of concept was established in an SCID mouse model of malaria, after oral administration (ED 90 = 1.5 mg/kg, once a day for 4 d). Furthermore, we successfully identified an opportunity for pathogen hopping based on the structural homology between PfKRS1 and CpKRS. This series of compounds inhibit CpKRS and C. parvum and Cryptosporidium hominis in culture, and our lead compound shows oral efficacy in two cryptosporidiosis mouse models. X-ray crystallography and molecular dynamics simulations have provided a model to rationalize the selectivity of our compounds for PfKRS1 and CpKRS vs. (human) HsKRS. Our work validates apicomplexan KRSs as promising targets for the development of drugs for malaria and cryptosporidiosis.
Structure-Guided In Vitro to In Vivo Pharmacokinetic Optimization of Propargyl-Linked Antifolates
Pharmacokinetic/pharmacodynamic properties are strongly correlated with the in vivo efficacy of antibiotics. Propargyl-linked antifolates, a novel class of antibiotics, demonstrate potent antibacterial activity against both Gram-positive and Gram-negative pathogenic bacteria, including multidrug-resistant Staphylococcus aureus. Here, we report our efforts to optimize the pharmacokinetic profile of this class to best match the established pharmacodynamic properties. High-resolution crystal structures were used in combination with in vitro pharmacokinetic models to design compounds that not only are metabolically stable in vivo but also retain potent antibacterial activity. The initial lead compound was prone to both N-oxidation and demethylation, which resulted in an abbreviated in vivo half-life (~20 minutes) in mice. Stability of leads toward mouse liver microsomes was primarily used to guide medicinal chemistry efforts so robust efficacy could be demonstrated in a mouse disease model. Structure-based drug design guided mitigation of N-oxide formation through substitutions of sterically demanding groups adjacent to the pyridyl nitrogen. Additionally, deuterium and fluorine substitutions were evaluated for their effect on the rate of oxidative demethylation. The resulting compound was characterized and demonstrated to have a low projected clearance in humans with limited potential for drug-drug interactions as predicted by cytochrome P450 inhibition as well as an in vivo exposure profile that optimizes the potential for bactericidal activity, highlighting how structural data, merged with substitutions to introduce metabolic stability, are a powerful approach to drug design.
Fluorophenols bearing nitrogenated heterocycle moieties, a class of novel Keap1-Nrf2 protein-protein interaction inhibitors: synthesis, antioxidant stress screening and molecular docking
In the present study, we introduced the nitrogenated heterocycles and fluorine atoms into the 2,5′-dibromo-4,5,2′-trihydroxyl diphenylmethanone (LM49), a bromophenol analog previously reported for its strong antioxidant ability involving in the Keap1–Nrf2 pathway. Twenty-seven fluorophenols 6a–6g, 8a–8k, 10a–10g, and 12a–12b were prepared, evaluated for their antioxidant activity in EA.hy926 cells, and investigated their interacted approach and probable mode of action with key protein Keap1 by molecular docking. Fluorophenols 6f, 8d, 8f, 8h, and 8i with EC{sub 50} values ranging from 0.82 to 6.71 µM were found to be more active compared with the standard control quercetin (EC{sub 50} = 18 µM). Among them, compound 8h with an EC{sub 50} value of 0.82 µM showed the identical activity to lead compound LM49 (EC{sub 50} = 0.7 µM). Moreover, the preferable water solubility and forming salt possibility of 8h contribute to its druggability. Further molecular docking of the optimal compound 8h with key protein Keap1 indicated that 8h stably bonded to the receptor protein by the formation of hydrogen bonds, the conjugated six-membered ring was close to the key residue Arg-415 attached to the Nrf2 on Keap1-Kelch, affecting its properties, and the change leaded to the dissociation of Nrf2 from the junction with Keap1-Kelch into the nucleus exerting its antioxidant protective effect. This study introduced a class of fluorophenols containing nitrogenated heterocycles for the development of novel Keap1-Nrf2 protein–protein interaction (PPI) inhibitors. Keap1-Kelch is suggested the most potential target protein for such class of halophenols.
Discovery of first-in-class inhibitors of ASH1L histone methyltransferase with anti-leukemic activity
ASH1L histone methyltransferase plays a crucial role in the pathogenesis of different diseases, including acute leukemia. While ASH1L represents an attractive drug target, developing ASH1L inhibitors is challenging, as the catalytic SET domain adapts an inactive conformation with autoinhibitory loop blocking the access to the active site. Here, by applying fragment-based screening followed by medicinal chemistry and a structure-based design, we developed first-in-class small molecule inhibitors of the ASH1L SET domain. The crystal structures of ASH1L-inhibitor complexes reveal compound binding to the autoinhibitory loop region in the SET domain. When tested in MLL leukemia models, our lead compound, AS-99, blocks cell proliferation, induces apoptosis and differentiation, downregulates MLL fusion target genes, and reduces the leukemia burden in vivo. This work validates the ASH1L SET domain as a druggable target and provides a chemical probe to further study the biological functions of ASH1L as well as to develop therapeutic agents.