Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent Reorganization

The first- and second-generation clinically used HIV-1 integrase (IN) strand transfer inhibitors (INSTIs) are key components of antiretroviral therapy (ART), which work by blocking the integration step in the HIV-1 replication cycle that is catalyzed by a nucleoprotein assembly called an intasome. However, resistance to even the latest clinically used INSTIs is beginning to emerge. Developmental third-generation INSTIs, based on naphthyridine scaffolds, are promising candidates to combat drug-resistant viral variants. Among these novel INSTIs, compound 4f exhibits two distinct conformations when binding with intasomes from HIV-1 and the closely related prototype foamy virus (PFV) despite the high structural similarity of their INSTI binding pockets. The molecular mechanism and the key active site residues responsible for these differing binding modes in closely related intasomes remain elusive. To unravel the molecular determinants governing the two distinct binding modes, we applied a novel molecular dynamics-based free energy method that utilizes alchemical pathways to overcome the sampling challenges associated with transitioning between the two bound conformations of ligand 4f within the crowded environments of the INSTI binding pockets in these intasomes. The calculated conformational free energies successfully recapitulate the experimentally observed binding mode preferences in the two viral intasomes. Analysis of the simulated structures suggests that the observed binding mode preferences are caused by amino acid residue differences in both the front and the central catalytic sub-pocket of the INSTI binding site in HIV-1 and PFV. Additional free energy calculations on mutants of HIV-1 and PFV revealed that while both sub-pockets contribute to binding mode selection, the central sub-pocket plays a more important role. These results highlight the importance of both side chain and solvent reorganization, as well as the conformational entropy in determining the ligand binding mode, and will help inform the development of more effective INSTIs for combatting drug-resistant viral variants.

Oxidative Addition and β-Hydride Elimination by a Macrocyclic Dinickel Complex: Observing Bimetallic Elementary Reactions

The dinickel(I) complex Ni2 (tBu PONNOPONNO), featuring a planar macrocyclic diphosphoranide ligand tBu PONNOPONNO, offers a unique architectural platform for observing bimetallic elementary reactions. Oxidative addition reactions of alkyl halides produce dinickel(II) complexes of the type Ni2 (μ-R)(μ-X)(tBu PONNOPONNO). However, when R=Et β-hydride elimination is observed to form a dinickel monohydride, with the rate dependent on the nature of X. DFT studies suggest a new mechanism for bimetallic β-hydride elimination, where the rate dependence arises from the steric pressure imposed by the X group on the opposing trans face of the dinickel macrocycle. This work enhances understanding of bimetallic elementary reactions, particularly β-hydride elimination, which have not been well-explored for dinuclear systems.

Design, Synthesis, Anticancer Evaluation, and Molecular Docking Studies of Oxazole-Incorporated Naphthyridine Derivatives

A novel series of oxazole incorporated naphthyridine (21 a-j) derivatives were designed and, synthesized followed by screening of their anticancer activity profiles against human breast cancer (MCF-7), human lung cancer (A549) and human prostate (PC3 & DU-145) cancer cell lines by employing MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide] assay using etoposide as the positive control. Of these compounds, N-(6-chloro-3-(4-(3,4,5-trimethoxyphenyl)oxazol-2-yl)-1,5-naphthyridin-4-yl)oxazol-2-amine with 3,4,5-trimethoxy substituent on the aryl moiety attached to oxazole ring showed potent anticancer activity against PC3, A549, MCF-7, and DU-145 cell lines with IC50 values of 0.13±0.095 μM; 0.10±0.084 μM; 0.18±0.087 μM and 0.15±0.076 μM respectively. Apart from this, compounds N-(6-chloro-3-(4-(3,5-dimethoxyphenyl)oxazol-2-yl)-1,5-naphthyridin-4-yl)oxazol-2-amine, N-(6-chloro-3-(4-(4-methoxyphenyl)oxazol-2-yl)-1,5-naphthyridin-4-yl)oxazol-2-amine, and N-(6-chloro-3-(4-(3,5-dimethylphenyl)oxazol-2-yl)-1,5-naphthyridin-4-yl)oxazol-2-amine also showed better anticancer activities against four cancer cell lines screened for. These activities were also validated through the molecular docking simulations, which further indicated demonstration of better interaction energy and profile by these compounds.

Discovery of a Potent and Selective Naphthyridine-Based Chemical Probe for Casein Kinase 2

Naphthyridine-based inhibitors were synthesized to yield a potent and cell-active inhibitor of casein kinase 2 (CK2). Compound 2 selectively inhibits CK2α and CK2α' when profiled broadly, thereby making it an exquisitely selective chemical probe for CK2. A negative control that is structurally related but lacks a key hinge-binding nitrogen (7) was designed on the basis of structural studies. Compound 7 does not bind CK2α or CK2α' in cells and demonstrates excellent kinome-wide selectivity. Differential anticancer activity was observed when compound 2 was profiled alongside a structurally distinct CK2 chemical probe: SGC-CK2-1. This naphthyridine-based chemical probe (2) represents one of the best available small molecule tools with which to interrogate biology mediated by CK2.

Bimetallic Nickel Complexes Supported by a Planar Macrocyclic Diphosphoranide Ligand

Metal-metal cooperativity is emerging as an important strategy in catalysis. This requires appropriate ligand scaffolds that can support two metals in close proximity. Here we report nickel-promoted formation of a dinucleating planar macrocyclic ligand that can support bimetallic dinickel(II) and dinickel(I) complexes. Reaction outcomes can be tuned by variation of the substituents and reaction conditions to favour dinucleating macrocyclic, mononucleating macrocyclic or conventional pincer architectures.

Power Efficiency Enhancement of Organic Light-Emitting Diodes Due to the Favorable Horizontal Orientation of a Naphthyridine-Based Thermally Activated Delayed Fluorescence Luminophore

Four emitters based on the naphthyridine acceptor moiety and various donor units exhibiting thermally activated delayed fluorescence (TADF) were designed and synthesized. The emitters exhibited excellent TADF properties with a small ΔE _ST and a high photoluminescence quantum yield. A green TADF organic light-emitting diode based on 10-(4-(1,8-naphthyridin-2-yl)phenyl)-10H-phenothiazine exhibited a maximum external quantum efficiency of 16.4% with Commission Internationale de L'éclairage coordinates of (0.368, 0.569) as well as a high current and power efficiency of 58.6 cd/A and 57.1 lm/W, respectively. The supreme power efficiency is a record-high value among the reported values of devices with naphthyridine-based emitters. This results from its high photoluminescence quantum yield, efficient TADF, and horizontal molecular orientation. The molecular orientations of the films of the host and the host doped with the naphthyridine emitter were explored by angle-dependent photoluminescence and grazing-incidence small-angle X-ray scattering (GIWAXS). The orientation order parameters (Θ_ADPL) were found to be 0.37, 0.45, 0.62, and 0.74 for the naphthyridine dopants with dimethylacridan, carbazole, phenoxazine, and phenothiazine donor moieties, respectively. These results were also proven by GIWAXS measurement. The derivative of naphthyridine and phenothiazine was shown to be more flexible to align with the host and to show the favorable horizontal molecular orientation and crystalline domain size, benefiting the outcoupling efficiency and contributing to the device efficiency.

Applications of Isosteres of Piperazine in the Design of Biologically Active Compounds: Part 1

Piperazine and homopiperazine are well-studied heterocycles in drug design that have found gainful application as scaffolds and terminal elements and for enhancing the aqueous solubility of a molecule. The optimization of drug candidates that incorporate these heterocycles in an effort to refine potency, selectivity, and developability properties has stimulated the design and evaluation of a wide range of bioisosteres that can offer advantage. In this review, we summarize the design and application of bioisosteres of piperazine and homopiperazine that have almost exclusively been in the drug design arena. While there are ∼100 approved drugs that incorporate a piperazine ring, only a single marketed agricultural product is built on this heterocycle. As part of the review, we discuss some of the potential reasons underlying the relatively low level of importance of this heterocycle to the design of agrochemicals and highlight the potential opportunities for their use in contemporary research programs.

Enhancement of Antibiotic Activity by 1,8-Naphthyridine Derivatives against Multi-Resistant Bacterial Strains

The search for new antibacterial agents has become urgent due to the exponential growth of bacterial resistance to antibiotics. Nitrogen-containing heterocycles such as 1,8-naphthyridine derivatives have been shown to have excellent antimicrobial properties. Therefore, the purpose of this study was to evaluate the antibacterial and antibiotic-modulating activities of 1,8-naphthyridine derivatives against multi-resistant bacterial strains. The broth microdilution method was used to determine the minimum inhibitory concentration (MIC) of the following compounds: 7-acetamido-1,8-naphthyridin-4(1H)-one and 3-trifluoromethyl-N-(5-chloro-1,8-naphthyridin-2-yl)-benzenesulfonamide. The antibiotic-modulating activity was analyzed using subinhibitory concentrations (MIC/8) of these compounds in combination with norfloxacin, ofloxacin, and lomefloxacin. Multi-resistant strains of Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus were used in both tests. Although the compounds had no direct antibacterial activity (MIC ≥ 1.024 µg/mL), they could decrease the MIC of these fluoroquinolones, indicating synergism was obtained from the association of the compounds. These results suggest the existence of a structure-activity relationship in this group of compounds with regard to the modulation of antibiotic activity. Therefore, we conclude that 1,8-naphthyridine derivatives potentiate the activity of fluoroquinolone antibiotics against multi-resistant bacterial strains, and thereby interesting candidates for the development of drugs against bacterial infections caused by multidrug resistant strains.

Diphosphino-Functionalized 1,8-Naphthyridines: a Multifaceted Ligand Platform for Boranes and Diboranes

A 1,8‐naphthyridine diphosphine (NDP) reacts with boron‐containing Lewis acids to generate complexes featuring a number of different naphthyridine bonding modes. When exposed to diborane B₂Br₄, NDP underwent self‐deprotonation to afford [NDP‐B₂Br₃]Br, an unsymmetrical diborane comprised of four fused rings. The reaction of two equivalents of monoborane BBr₃ and NDP in a non‐polar solvent provided the simple phosphine‐borane adduct [NDP(BBr₃)₂], which then underwent intramolecular halide abstraction to furnish the salt [NDP‐BBr₂][BBr₄], featuring a different coordination mode from that of [NDP‐B₂Br₃]Br. Direct deprotonation of NDP by KHMDS or PhCH₂K generates mono‐ and dipotassium reagents, respectively. The monopotassium reagent reacts with one or half an equivalent of B₂(NMe₂)₂Cl₂ to afford NDP‐based diboranes with three or four amino substituents.

Coordination Chemistry of Ru(II) Complexes of an Asymmetric Bipyridine Analogue: Synergistic Effects of Supporting Ligand and Coordination Geometry on Reactivities

The reactivities of transition metal coordination compounds are often controlled by the environment around the coordination sphere. For ruthenium(II) complexes, differences in polypyridyl supporting ligands affect some types of reactivity despite identical coordination geometries. To evaluate the synergistic effects of (i) the supporting ligands, and (ii) the coordination geometry, a series of dicarbonyl-ruthenium(II) complexes that contain both asymmetric and symmetric bidentate polypyridyl ligands were synthesized. Molecular structures of the complexes were determined by X-ray crystallography to distinguish their steric configuration. Structural, computational, and electrochemical analysis revealed some differences between the isomers. Photo- and thermal reactions indicated that the reactivities of the complexes were significantly affected by both their structures and the ligands involved.

A novel approach to analogues of pyridoacridine alkaloids

Readily available 4-bromobenzo[c][2,7]naphthyridine undergoes regioselective direct ring metalation at C-5 with TMPMgCl∙LiCl at −40 °C. Quenching with various electrophiles gives a broad range of 5-substituted products, which are building blocks for the synthesis of heterocyclic natural products and analogues thereof. In combination with a Parham-type cyclization a novel approach to pyrido[4,3,2-mn]acridones has been worked out.

Spectroscopic investigations on DNA binding profile of two new naphthyridine carboxamides and their application as turn-on fluorescent DNA staining probes

Two new 10-methoxydibenzo[b,h][1,6]naphthyridine-2-carboxamide derivatives (R1 and R2) have been synthesized and characterized using different spectral techniques. The binding of these probes with DNA was investigated using spectral (Electronic, fluorescence, ¹H NMR and circular dichroism) and molecular docking studies. These probes exhibited a strong fluorescence around 440 nm upon excitation around 380 nm. Electronic and competitive fluorescence titration studies, in HEPES [(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)] buffer/dimethyl sulfoxide (pH 7.4) medium, suggest that these probes bind strongly to DNA, which is substantiated by ¹H NMR study. The binding constants are calculated to be 5.3 × 10⁷ and 6.8 × 10⁶ M^-1 for R1 and R2, respectively. From the results of spectral studies, it is proposed that the mechanism of binding of these probes with DNA is through minor groove binding mode, which is further confirmed by circular dichroism and molecular docking studies. Initial cell viability screening using MTT (3-[4,5-methylthiazol-2-yl]-2,5-diphenyl-tetrazolium bromide) assay shows that normal Vero cells are viable towards these probes at nano molar concentration, which is the concentration range employed in the present study for DNA staining (IC₅₀ in the order of 0.023 mM). The enhancement in fluorescence intensity of these probes upon binding with DNA enables the staining of DNA in agarose gel in gel electrophoresis experiment. The sensitivity of these probes is comparable with that of ethidium bromide and DNA amounts as low as 4 nano gram are detectable.Communicated by Ramaswamy H. Sarma.

Zn-, Mg-, and Li-TMP Bases for the Successive Regioselective Metalations of the 1,5-Naphthyridine Scaffold (TMP=2,2,6,6-Tetramethylpiperidyl)

A set of successive regioselective metalations and functionalizations of the 1,5-naphthyridine scaffold are described. A combination of Zn-, Mg-, and Li-TMP (TMP=2,2,6,6-tetramethylpiperidyl) bases and the presence or absence of a Lewis acid (BF₃ ⋅OEt₂ ) allows the introduction of up to three substituents to the 1,5-naphthyridine core. Also, a novel "halogen dance" reaction was discovered upon metalation of an 8-iodo-2,4-trifunctionalized 1,5-naphthyridine allowing a fourth regioselective functionalization. Additionally, reactions leading to key 1,5-naphthyridines for the preparation of OLED materials and a potential antibacterial agent were performed.

Structure-Based Design of GNE-495, a Potent and Selective MAP4K4 Inhibitor with Efficacy in Retinal Angiogenesis

Diverse biological roles for mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) have necessitated the identification of potent inhibitors in order to study its function in various disease contexts. In particular, compounds that can be used to carry out such studies in vivo would be critical for elucidating the potential for therapeutic intervention. A structure-based design effort coupled with property-guided optimization directed at minimizing the ability of the inhibitors to cross into the CNS led to an advanced compound 13 (GNE-495) that showed excellent potency and good PK and was used to demonstrate in vivo efficacy in a retinal angiogenesis model recapitulating effects that were observed in the inducible Map4k4 knockout mice.