Ligand Side Chain Research Articles

Optimization of the polishing process by integrating experimental design and high-throughput screening

Complex bispecific antibody formats tend to form more product-related impurities than monoclonal antibodies. The primary constraints are yield and purity in the polishing stage. The purpose of this study was to enhance the understanding of the optimal working window for four mixed-mode resins and to reduce the burden of resin screening and parameter optimization during process development. This study optimized the loading and elution conditions of four different mixed-mode cationic resins to enhance the yield and purity by integrating Design of Experiments with High-Throughput Screening. It was observed that despite being weakly acidic mixed-mode cationic resins, these four resins exhibited significant differences in their adsorption and elution performances and varied tolerances to salt concentrations. Capto MMC demonstrated strong hydrophobicity, while the performance profiles of MX-Trp-650 M and Nuvia cPrime were similar, with Nuvia cPrime showing superior purification effects. Eshmuno CMX, by extending its side chain ligand, achieved higher binding efficiency and capacity. Through the optimization of salt concentrations or the application of dual-gradient elution strategies, the target protein with high yield (77 %) and purity over 99 % was successfully obtained. This research not only provides in-depth insights into the application of mixed-mode chromatography in the biopharmaceutical field but also offers practical optimization strategies for the industrial-scale purification of bispecific antibodies.

Iron-Based nanoporous Metal-Organic frameworks with Side-Chain amino substituents for Efficiency-Regulated oxygen evolution reaction

Nanoporous iron-based MOFs, possessing notable attributes such as adjustable structure, considerable porosity, and large surface area, exhibit considerable promise for various applications in the field of photocatalysis. However, the effect of the ligand substitution ratio on the photocatalytic reaction process is currently unknown. In the current investigation, a series of iron-based MOFs MIL-101(Fe)-X with various ratios of amino substituents (X = H: NH2 = 1:0, 1:0.5, 1:1, 1:2, 1:4, 0:1) were synthesized using the solvothermal method. The morphology and structure were characterized using SEM, TEM, XRD, XPS, BET, FT-IR, etc. Their efficacy as water oxidation catalysts under AM1.5G (solar light) irradiation was investigated. The findings of the study indicated that MIL-101(Fe) with an X value of 1:2 exhibited the highest surface area of 380.4 m2/g. This resulted in the exposure of a greater number of active sites, leading to enhanced charge separation efficiency and exceptional oxygen evolution activity when illuminated by simulated sunlight. The oxygen evolution rate under solar light was measured to be 11.7 mmol·h−1·g−1. This research confirmed the effect of substituent variation on the oxygen evolution rate by modulating the substitution ratio of side-chain ligands on MOFs, thereby altering their microstructure and charge distribution. The incorporation of a suitable quantity of amino groups, that act as strong electron-donating groups, facilitated the effective separation of electron-hole pairs generated during the photocatalytic process. However, an excessive introduction of amino groups can result in a reduction in both pore structure and surface area, thereby impeding the efficiency of the photocatalytic oxygen evolution reaction.

Molecular Selectivity in the Binding of Alkali Metals, Alkaline Earth Metals, First-Row Transition Metals, and Lanthanides with Cyclic Depsipeptides.

Beauvericin (BEA) and enniatins (ENN) are cyclic hexadepsipeptide mycotoxins known for their ionophoric activities across cell membranes. While their ability to selectively bind alkali ions to form binary complexes has been studied, their interaction with multivalent metal ions to form higher-order complexes remains less explored. We report the unique characteristics of the 1:2, Mn+:BEA or ENN complexes with monovalent, divalent, and trivalent metal ions. A thorough IMS-MS analysis underscores the substantial interplay among ionic radii, coordination numbers, and their impact on conformational selection within higher-order complexes that is pertinent to ion transport. Transition metals offer insights into the effects of ion radii and ligand side chains on conformational selection, while lanthanide complexes enable a direct evaluation of coordination chemistry. An intriguing finding concerning the lanthanide complexes involves an unexpected C-H bond activation, wherein water ligands may catalyze the deprotonation of the cyclic peptides.

Ligand‐engineered Zr‐MOF membranes with fast water transport channels for alcohol–water separation

AbstractMetal–organic framework (MOF) membranes with rich functionality and a tunable pore system are promising for molecular separation. However, an inadequate pore microenvironment and low water stability may hamper the extension of their use in gas separation to liquid separation (e.g., organic solvent dehydration). In this study, we report a high‐valence Zr‐MOF membrane with high stability and tunable pore microenvironment, prepared using a mixed‐ligand strategy based on fumarate (fum) and 2‐methylfumarate (mes) ligands for the pervaporation dehydration of alcohols. The introduction of a methyl group in the ligand side chain narrowed the aperture size while balancing the hydrophilicity, thus facilitating the fast and selective permeation of water over alcohol molecules. The resulting mes/fum‐Zr‐MOF membrane with a mes content of 30% displayed excellent butanol/water separation performance with total flux of 5226 g−1·m−2·h−1, separation factor of 1281, and water content of 99.3% in the permeate, transcending the upper‐bound of state‐of‐the‐art MOF and polymer membranes, thereby exhibiting immense potential for alcohols dehydration.

Rapid Rescoring and Refinement of Ligand-Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir.

Virtual screening (VS) involves generation of poses for a library of ligands and ranking using simplified energy functions and limited flexibility. Top-scored poses are used to rank and prioritize ligands. Here, we adapt the reservoir replica exchange molecular dynamics (res-REMD) method to rerank poses generated through VS. REMD simulations are carried out but with occasional Monte Carlo jumps to alternate VS-generated poses using a Metropolis criterion. The simulations converge within 10 ns for all systems, generating populations of alternate poses in the context of fully flexible ligand and protein side chains. The protocol is applied to four model protein-ligand complexes, where DOCK resulted in two successes and two scoring failures. In all four systems, the most populated cluster from the final ensemble exhibits high similarity to the crystallographic pose with ligand RMSD values under 2.0 Å. Both DOCK failures were rescued. For one DOCK success, the protocol identified the correct pose but also sampled an alternate pose at equal probability. Opportunities for future improvements and extensions are discussed.

Spectroscopy evidence of interaction of 1,5 disubstituted piperidino-amido anthraquinone derivative with human telomeric G-quadruplex DNA: Basis of anticancer action

The binding of ligands to G-quadruplex (G4) structures at the ends of human telomeric DNA induces thermal stabilization, which interferes with telomere maintenance by disrupting the association of telomeres with the telomerase enzyme—an important marker for cancer. Understanding the binding mode of the ligand-G quadruplex DNA complex is imperative for evaluating the relative efficacy and specificity of their interaction. We focused on the interaction of 1,5-Bis(3-piperidino propionamido) anthracene-9,10-dione with human telomeric DNA sequences using surface plasmon resonance, absorbance, fluorescence (steady-state and lifetime), and circular dichroism spectroscopy techniques. The ligand binding with HTel22 (Kb = 8.4 × 105 M−1) induced cell toxicity with an IC50 value of ∼ 8.64 µM in MCF-7 cancer cell lines. Significant hypochromism (59 %), fluorescence quenching (97 %), no change in fluorescence lifetime and absence of induced Circular Dichroism (CD) band upon addition of G4 DNA to ligand, suggest a groove/external binding mode. CD spectral changes reflect rearrangement in parallel and antiparallel strands to accommodate the ligand. Docking results reveal specific short contacts of the ligand's side chain, including 9CO, 13N, 14NH, and 11CO, with the grooves of the G4 DNA, without making any contact with the loops, favoring an energetically more favorable conformation. Thermal denaturation profiles, obtained by Differential Scanning Calorimetry and CD, show the stabilization of wHTel26 and HTel22 G4 DNA in K+ and Na+ rich solutions by 21.2 and 17.6 °C, respectively, which may restrict the access of telomerase to telomeres. The findings indicate the potential of modifying anthraquinone substituent groups for therapeutic applications.

Chemical features and machine learning assisted predictions of protein-ligand short hydrogen bonds

There are continuous efforts to elucidate the structure and biological functions of short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms reside more than 0.3 Å closer than the sum of their van der Waals radii. In this work, we evaluate 1070 atomic-resolution protein structures and characterize the common chemical features of SHBs formed between the side chains of amino acids and small molecule ligands. We then develop a machine learning assisted prediction of protein-ligand SHBs (MAPSHB-Ligand) model and reveal that the types of amino acids and ligand functional groups as well as the sequence of neighboring residues are essential factors that determine the class of protein-ligand hydrogen bonds. The MAPSHB-Ligand model and its implementation on our web server enable the effective identification of protein-ligand SHBs in proteins, which will facilitate the design of biomolecules and ligands that exploit these close contacts for enhanced functions.

Linker regulation of iron-based MOFs for highly effective Fenton-like degradation of refractory organic contaminants

Iron-based MOFs with tunable structure, large surface area along with attractive diversity have been often used in heterogeneous Fenton-like reactions to generate hydroxyl groups for the degradation of new pollutants. It is unclear how linker substituents of MIL-101 with MTN-typed topology influence the heterogeneous Fenton. Solvothermal methods were used to successfully synthesize a series of MIL-101-X(Fe) with various substituents (X = -H, –NH2, –OH and –OCH3) in the side chains of organic ligands. Their physicochemical properties are fully investigated by various characterizations, which confirmed that changes in the substituents affected crystal morphology and thus catalytic efficiency. In the Fenton system, MIL-101-X showed significant differences in antibiotics removal. Particularly, the MIL-101-NH2 exhibited 100 % removal of SMX within 70 mins, with a rate of 30.06 times faster than MIL-101-H. This was related to the change in the active surface, following ligand functionalization, which greatly facilitates the dissociation of H2O2 and accelerates the iron cycling process. Therefore, this study provides the first mechanistic foresight on the regulation of Fenton-like reactions through modifying the substituents in the side chain of MOFs to alter their particle morphology and active surface.

ACES: Optimized Alchemically Enhanced Sampling.

We present an alchemical enhanced sampling (ACES) method implemented in the GPU-accelerated AMBER free energy MD engine. The methods hinges on the creation of an "enhanced sampling state" by reducing or eliminating selected potential energy terms and interactions that lead to kinetic traps and conformational barriers while maintaining those terms that curtail the need to otherwise sample large volumes of phase space. For example, the enhanced sampling state might involve transforming regions of a ligand and/or protein side chain into a noninteracting "dummy state" with internal electrostatics and torsion angle terms turned off. The enhanced sampling state is connected to a real-state end point through a Hamiltonian replica exchange (HREMD) framework that is facilitated by newly developed alchemical transformation pathways and smoothstep softcore potentials. This creates a counterdiffusion of real and enhanced-sampling states along the HREMD network. The effect of a differential response of the environment to the real and enhanced-sampling states is minimized by leveraging the dual topology framework in AMBER to construct a counterbalancing HREMD network in the opposite alchemical direction with the same (or similar) real and enhanced sampling states at inverted end points. The method has been demonstrated in a series of test cases of increasing complexity where traditional MD, and in several cases alternative REST2-like enhanced sampling methods, are shown to fail. The hydration free energy for acetic acid was shown to be independent of the starting conformation, and the values for four additional edge case molecules from the FreeSolv database were shown to have a significantly closer agreement with experiment using ACES. The method was further able to handle different rotamer states in a Cdk2 ligand identified as fractionally occupied in crystal structures. Finally, ACES was applied to T4-lysozyme and demonstrated that the side chain distribution of V111χ1 could be reliably reproduced for the apo state, bound to p-xylene, and in p-xylene→ benzene transformations. In these cases, the ACES method is shown to be highly robust and superior to a REST2-like enhanced sampling implementation alone.

High-affinity binding at quadruplex-duplex junctions: rather the rule than the exception.

Quadruplex-duplex (Q-D) junctions constitute unique structural motifs in genomic sequences. Through comprehensive calorimetric as well as high-resolution NMR structural studies, Q-D junctions with a hairpin-type snapback loop coaxially stacked onto an outer G-tetrad were identified to be most effective binding sites for various polycyclic quadruplex ligands. The Q-D interface is readily recognized by intercalation of the ligand aromatic core structure between G-tetrad and the neighboring base pair. Based on the thermodynamic and structural data, guidelines for the design of ligands with enhanced selectivity towards a Q-D interface emerge. Whereas intercalation at Q-D junctions mostly outcompete stacking at the quadruplex free outer tetrad or intercalation between duplex base pairs to varying degrees, ligand side chains considerably contribute to the selectivity for a Q-D target over other binding sites. In contrast to common perceptions, an appended side chain that additionally interacts within the duplex minor groove may confer only poor selectivity. Rather, the Q-D selectivity is suggested to benefit from an extension of the side chain towards the exposed part of the G-tetrad at the junction. The presented results will support the design of selective high-affinity binding ligands for targeting Q-D interfaces in medicinal but also technological applications.

Complexes of copper(II) with tetradentate S,O-ligands: Synthesis, characterization, DNA/albumin interactions, molecular docking simulations and antitumor activity

Four new complexes of copper(II) with S,O-tetradentate ligands, derivatives of thiosalicylic acid, encompassing an ethylene-, propylene-, butylene- and pentylene- bridge, were synthesized and characterized by microanalysis, molecular conductance and infrared (IR) spectra. The structures were assumed based on the previously mentioned analyses and confirmed with the results of electron paramagnetic resonance (EPR) spectra. The reactivity of complexes towards L-methionine (L-Met), L-cysteine (L-Cys) and guanosine-5′-monophosphate (5’-GMP) was also examined. Complex C1 ([Cu(S,O-ethylene-thiosalicylic acid)(H2O)2]) containing two inert methylene groups in the side chain of ligand shows the highest reactivity, while the least reactive is complex C4 ([Cu(S,O-pentylene-thiosalicylic acid)(H2O)2]) with five methylene groups. All complexes showed the highest reactivity towards L-Met and the lowest reactivity towards 5’-GMP. The interactions of complexes C1-C4 with calf thymus DNA (ct-DNA) were examined by ultraviolet-visible (UV–Vis) absorption and fluorescence spectral studies, revealing good DNA interaction abilities. All synthesized complexes C1-C4 show to interact with human serum albumin (HSA) with high values of binding constants. Complexes interaction with DNA/HSA was also confirmed using molecular docking simulations. All synthesized complexes reduce viability of human colon, breast and lung cancer cells, evaluated by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) colorimetric technique. The complex [Cu(S,O-pentylene- thiosalicylic acid)(H2O)2] showed the highest binding affinity constants to DNA/HSA and highest cytotoxicity, thus presenting a good candidate for further pharmacological research in the field of colon, breast and lung cancer therapy.

Tuning the coordination properties of chiral pseudopeptide bis(2-picolyl)amine and iminodiacetamide ligands in Zn(II) and Cu(II) complexes.

Seven bis(2-picolyl)amine (bpa) and five iminodiacetamide (imda) ligands were prepared with different modifications in their side chain structure. The coordination properties of the ligands (L) were influenced by changes in the aliphatic linker length (C1, C2, or C3), amide group isomers and type of chiral terminal group. Complexation with Cu(II) afforded two polymorphs of a ML complex which features tetradentate coordination of a ligand with C2 linkers, while crystal structures of three trans-fac ML2 complexes with Cu(II) and Ni(II) show tridentate coordination of ligands with a C3 linker. The stoichiometry and stereochemistry of Zn(II) and Cu(II) complexes was further studied in solution by NMR and UV-Vis spectroscopy. DFT calculations gave an insight into the relative stability of isomers, as well as potential hydrogen bonding between two ligands in a ML2 complex. Furthermore, ML complexes of Cu(II) exhibited DNA cleavage activity.

Structured Waters Mediate Small Molecule Binding to G-Quadruplex Nucleic Acids.

The role of G-quadruplexes in human cancers is increasingly well-defined. Accordingly, G-quadruplexes can be suitable drug targets and many small molecules have been identified to date as G-quadruplex binders, some using computer-based design methods and co-crystal structures. The role of bound water molecules in the crystal structures of G-quadruplex-small molecule complexes has been analyzed in this study, focusing on the water arrangements in several G-quadruplex ligand complexes. One is the complex between the tetrasubstituted naphthalene diimide compound MM41 and a human intramolecular telomeric DNA G-quadruplex, and the others are in substituted acridine bimolecular G-quadruplex complexes. Bridging water molecules form most of the hydrogen-bond contacts between ligands and DNA in the parallel G-quadruplex structures examined here. Clusters of structured water molecules play essential roles in mediating between ligand side chain groups/chromophore core and G-quadruplex. These clusters tend to be conserved between complex and native G-quadruplex structures, suggesting that they more generally serve as platforms for ligand binding, and should be taken into account in docking and in silico studies.

Role of low-energy electrons in the solubility switch of Zn-based oxocluster photoresist for extreme ultraviolet lithography.

The electron-induced chemistry of a resist material for extreme ultraviolet lithography (EUVL) consisting of Zn oxoclusters with methacrylate (MA) and trifluoroacetate (TFA) ligands (Zn(MA)(TFA)) has been studied. Electron energies of 80 eV and 20 eV mimic the effect of photoelectrons released by the absorption of EUV photons and low-energy secondary electrons (LESEs) produced by those photoelectrons. The chemical conversion of the resist is studied by mass spectrometry to monitor the volatile species that desorb during electron irradiation, combined with reflection absorption infrared spectra (RAIRS) measured before and after irradiation. The observed reactions are closely related to those initiated upon EUV absorption. Also, the conversion of the Zn(MA)(TFA) resist layer that is required in EUVL is achieved by a similar energy input upon electron irradiation. The dominant component of the desorbing gas is CO2, but CO detection also suggests Zn oxide formation during electron irradiation. In contrast, species deriving from the ligand side chains predominantly remain within the resist layer. RAIRS gives direct evidence that, during electron irradiation, C Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> C bonds of the MA ligands are more rapidly consumed than the carboxylate groups. This supports that chain reactions occur and contribute to the solubility switch in the resist in EUVL. Remarkably, 20 eV electrons still evolve roughly 50% of the amount of the gas that is observed at 80 eV for the same electron dose. The present results thus provide complementary and new insight to the EUV-induced chemistry in the Zn(MA)(TFA) resist and point towards the important contribution of low-energy electrons therein.

Broad Specificity of Amino Acid Chemoreceptor CtaA of Pseudomonas fluorescens Is Afforded by Plasticity of Its Amphipathic Ligand-Binding Pocket.

Motile bacteria follow gradients of nutrients or other environmental cues. Many bacterial chemoreceptors that sense exogenous amino acids contain a double Cache (dCache; calcium channels and chemotaxis receptors) ligand-binding domain (LBD). A growing number of studies suggest that broad-specificity dCache-type receptors that sense more than one amino acid are common. Here, we present an investigation into the mechanism by which the dCache LBD of the chemoreceptor CtaA from a plant growth-promoting rhizobacterium, Pseudomonas fluorescens, recognizes several chemically distinct amino acids. We established that amino acids that signal by directly binding to the CtaA LBD include ones with aliphatic (l-alanine, l-proline, l-leucine, l-isoleucine, l-valine), small polar (l-serine), and large charged (l-arginine) side chains. We determined the structure of CtaA LBD in complex with different amino acids, revealing that its ability to recognize a range of structurally and chemically distinct amino acids is afforded by its easily accessible plastic pocket, which can expand or contract according to the size of the ligand side chain. The amphipathic character of the pocket enables promiscuous interactions with both polar and nonpolar amino acids. The results not only clarify the means by which various amino acids are recognized by CtaA but also reveal that a conserved mobile lid over the ligand-binding pocket adopts the same conformation in all complexes, consistent with this being an important and invariant part of the signaling mechanism.

Construction of a polyMOF using a polymer ligand bearing the benzenedicarboxylic acid moiety in the side chain

Here we report a new synthetic strategy of a polyMOF consisting of a side chain ligand polymer. The polyMOF was consisting of a crystalline MOF-like structure in the polymer despite its film form.

Co(II)-salen catalyzed stereoselective cyclopropanation of fluorinated styrenes.

Three cis-selective Co(II)-salen complexes have been developed for the asymmetric cyclopropanation of para-fluorinated styrenes with ethyl diazoacetate. Increasing the steric reach of the C2 -symmetric ligand side chains improved the enantiomeric ratio of the reaction from 28:1 to 66:1. The methodology was exemplified by the gram-scale synthesis of a lead compound for the treatment of castration-resistant prostate cancer (CRPC), as well as a structurally related analog.

Tuning the Aggregation of N^N^C Pt(II) Complexes by Varying the Aliphatic Side Chain and Auxiliary Halide Ligand: 1H and 195Pt NMR Investigation

A series of six tridentate cyclometallated N^N^C Pt(II) complexes with different halide auxiliary ligands and different aliphatic side chains have been prepared. All complexes show concentration‐dependent NMR spectra. Their self‐association was studied by a dilution method monitoring both the 1H as well as 195Pt nuclei. Both techniques show similar results validating that 195Pt NMR is an important methodology to study self‐association of potentially any Pt complex regardless of the nature of the ligands. Experimental data allowed to predict the most probable geometry of the dimers and to get insight into the structural and thermodynamic specificity of the aggregation. The in‐depth analysis of the data suggests that the halide auxiliary ligand has no significant influence on self‐association while the effect of the aliphatic side chain depends on the length and the structure of the chain.

Binding Mechanism of Thrombin-Ligand Systems Investigated by a Polarized Protein-Specific Charge Force Field and Interaction Entropy Method.

In this study, 2 groups of 10 modified ligand systems with modified P3 and P2 side chains are used to study the binding mechanism with thrombin. Experimental results show that the binding affinity is enhanced by complex ligand side chains. The binding free energy obtained from the polarized protein-specific charge (PPC) force field combined with the newly developed interaction entropy (IE) method is consistent with the experimental values with a high correlation coefficient. On the contrary, poor correlation is obtained using the traditional normal mode (Nmode) method for calculating the entropy change. Furthermore, the binding free energy and hot-spot residue energy are decomposed, and the common hot-spot residues in the two groups of systems are Trp50, Leu96, Ile179, Asp199, Cyx201, Ser226, Trp227, Gly228, and Gly230. The electrostatic and van der Waals interaction energies were found to be the main contributors in the binding energy difference. CH-π and CH-CH interactions of Leu96 ligands are significantly related to the energy change due to the modified side chain, and the hydrogen bond between Asp199 and the ligand provides a strong electrostatic interaction, contributing to the binding free energy. Investigating the B-factor, principal component, and binding pocket also explains the change in the binding affinity caused by the modified side chains in ligands from the viewpoint of conformational change. This study demonstrates that the new IE method is superior to the Nmode method in the predicting binding free energy and emphasizes the importance of electronic polarization in molecular dynamics simulation. Moreover, from the viewpoint of energy and structure analysis, this study reveals the origin of the change in binding free energy in modified ligands with different binding sites.

Exploring the PROTAC degron candidates: OBHSA with different side chains as novel selective estrogen receptor degraders (SERDs)

As the mutant estrogen receptor (ER) continues to be characterized, breast cancer is becoming increasingly difficult to cure when treated with hormone therapy. In this regard, a strategy to selectively and effectively degrade the ER might be an effective alternative to endocrine therapy for breast cancer. In a previous study, we identified a novel series of 7-oxabicyclo[2.2.1]heptene sulfonamide (OBHSA) compounds as full ER antagonists while lacking the prototypical ligand side chain that has been widely used to induce antagonism of ERα. Further crystal structure studies and phenotypic assays revealed that these compounds are selective estrogen receptor degraders (SERDs) with a new mechanism of action. However, from a drug discovery point of view, there still is room to improve the potency of these OBHSA compounds. In this study, we have developed new classes of SERDs that contain the OBHSA core structure and different side chains, e.g., basic side chains, long alkyl acid side chains, and glycerol ether side chains, to simply mimic the degrons of proteolysis targeting chimera (PROTAC) and then investigated the structure-activity relationships of these PROTAC-like hybrid compounds. These novel SERDs could effectively inhibit MCF-7 cell proliferation and demonstrated good ERα degradation efficacy. Among the SERDs, compounds 17d, 17e and 17g containing a basic side chain with a N-trifluoroethyl substituent and a para methoxyl group at the phenyl group of the sulfonamide turned out to be the best candidates for ER degraders. A further docking study of these compounds with ERα elucidates their structure-activity relationships, which provides guidance to design new PROTAC degrons targeting ER for breast cancer therapy. Lastly, easy modification of these PROTAC-like SERDs enables further fine-tuning of their pharmacokinetic properties, including oral availability.