Non-covalent Binding Mode Research Articles

Miniaturized Modular Click Chemistry-enabled Rapid Discovery of Unique SARS-CoV-2 Mpro Inhibitors With Robust Potency and Drug-like Profile.

The COVID-19 pandemic has required an expeditious advancement of innovative antiviral drugs. In this study, focused compound libraries are synthesized in 96- well plates utilizing modular click chemistry to rapidly discover potent inhibitors targeting the main protease (Mpro) of SARS-CoV-2. Subsequent direct biological screening identifies novel 1,2,3-triazole derivatives as robust Mpro inhibitors with high anti-SARS-CoV-2 activity. Notably, C5N17B demonstrates sub-micromolar Mpro inhibitory potency (IC50 = 0.12 µM) and excellent antiviral activity in Calu-3 cells determined in an immunofluorescence-based antiviral assay (EC50 = 0.078 µM, no cytotoxicity: CC50 > 100 µM). C5N17B shows superior potency to nirmatrelvir (EC50 = 1.95 µM) and similar efficacy to ensitrelvir (EC50 = 0.11 µM). Importantly, this compound displays high antiviral activities against several SARS-CoV-2 variants (Gamma, Delta, and Omicron, EC50 = 0.13 - 0.26 µM) and HCoV-OC43, indicating its broad-spectrum antiviral activity. It is worthy that C5N17B retains antiviral activity against nirmatrelvir-resistant strains with T21I/E166V and L50F/E166V mutations in Mpro (EC50 = 0.26 and 0.15 µM, respectively). Furthermore, C5N17B displays favorable pharmacokinetic properties. Crystallography studies reveal a unique, non-covalent multi-site binding mode. In conclusion, these findings substantiate the potential of C5N17B as an up-and-coming drug candidate targeting SARS-CoV-2 Mpro for clinical therapy.

From docking to dynamics: Unveiling the potential non-peptide and non-covalent inhibitors of Mpro from natural products

MotivationThis study aims to investigate non-covalent and non-peptide inhibitors of Mpro, a crucial protein target, by employing a comprehensive approach that integrates molecular docking, molecular dynamics simulations, and top-hits activity predictions. The focus is on elucidating the non-covalent and non-peptide binding modes of potential inhibitors with Mpro. MethodsWe employed a semi-flexible molecular docking methodology, binding score and ADME screening, which are based on structure, to screen compounds from CMNPD and HERB in silico. These methodologies allowed us to find potential candidates depending on their binding values and interactions with the binding site of main protease. To further evaluate the stability of these interactions, we conducted molecular dynamics simulations and calculated binding energies. Ultimately, a top-hits activity prediction method was employed to prioritize compounds based on their predicted inhibitory potential. ResultsThrough a combination of binding energy calculations and activity predictions, we identified six potential inhibitor molecules exhibiting promising activity against Mpro. These compounds demonstrated favorable binding interactions and stability profiles, making them attractive candidates for further experimental validation and drug development efforts targeting Mpro.

Synthesis, characterization, DNA interaction, molecular docking, and α‐glucosidase inhibition studies of 3‐(pyrimidin‐2‐ylthio) groups substituted water soluble zinc (II) phthalocyanine

In this work, 3‐(pyrimidin‐2‐ylthio)phthalonitrile (n‐MP1), non‐peripherally 3‐(pyrimidin‐2‐ylthio) groups substituted Zn (II) phthalocyanine (n‐MP2), and its water soluble derivative (n‐MP3) have been firstly synthesized and characterized with spectral data. The interaction of the n‐MP3 complex with DNA was examined in vitro using UV–visible titrimetric and thermal denaturation assays and in silico by performing molecular docking studies. In addition, the antidiabetic activity of n‐MP3 was revealed spectroscopically by studying α‐glucosidase inhibition activities. The spectroscopic results indicated that n‐MP3 effectively binds to CT‐DNA with a Kb value of 2.0 × 105 M−1 and interacts with CT‐DNA via noncovalent binding mode. Besides, docking studies divulged that n‐MP3 exhibits a stronger binding tendency (BE: −10.64 kcal/mol) with DNA than the control compounds, (7.78 kcal/mol for ethidium bromide and −6.21 kcal/mol for cisplatin). Consequently, due to its strong DNA binding activity, n‐MP3 may be suitable for antimicrobial and anticancer applications after further toxicological test systems. Also, n‐MP3 complex inhibited the activity of α‐glucosidase with the IC50 value of 1.44 ± 0.08 μM, whereas IC50 value of acarbose was 237.24 ± 1.80 μM. Therefore, it can be said that n‐MP3 is a very effective α‐glucosidase inhibitor.

De novo design and preparation, structural details, and cytotoxic response of a new water soluble (2,2′–bipy)–(phenylalaninato)–μ–chlorido–copper(II) drug candidate against resistant cancer cells

A new water soluble (2,2′–bipyridine)–(phenylalaninato)–μ–chlorido–copper(II) complex was synthesized using ancillary ligands, l-phenylalanine, and 2,2-bipyridine as a chemotherapeutic anticancer agent. The complex was characterized by employing various spectroscopic (UV–visible, FT-IR, EPR, elemental analysis) and single crystal X-ray diffraction technique which revealed the structure of crystal as monoclinic with P21 space group. The interaction studies of the complex with therapeutic drug target, ct-DNA were caried out using various complimentary biophysical techniques, and the corroborative results of these experiments revealed that complex binds avidly through non-covalent electrostatic binding mode in the groove region of DNA. The binding propensity was quantified by calculating the intrinsic binding constant values (Kb and Ksv) which were found to be 3.1 (±0.95) × 105M−1 and 0.4 (±0.05) × 103M−1, respectively. The cleavage studies of copper(II) based drug candidate 1 with pBR322 plasmid DNA were performed in concentration dependent manner and it was demonstrated that complex was capable of conversion of supercoiled form SC (Form I) into nicked form NC (Form II) upon incubation of 3 μM concentration, implicating efficient single strand cleavage of DNA helix. The mechanistic cleavage studies were also performed in the presence various activators viz., DMSO, NaN3, SOD, and H2O2 and the strong inhibition of cleavage process was observed in presence of NaN3 and SOD that suggested an oxidative pathway (Fenton's mechanism) for the Cu(II) complex. The cytotoxicity of the complex was evaluated by SRB assay against the resistant cancer cell lines, viz., Hop-62, MCF-7, AW13516, MDA-MB-231, and SiHa. The cytotoxicity activity demonstrated good therapeutic potency against all the tested cell lines with GI50 value of <10 μM.

Dual Noncovalent Binding Modes Enabled via Single Thiourea Motif: An Emerging Arsenal for Supramolecular Polymeric Nanomedicine

AbstractThe structural rigidity of thiourea (TU) motifs has made them useful in supramolecular (bio)materials. However, the role of the TU motif in a single system endowing dual noncovalent interactions, i.e., Hydrogen‐bonding (H‐bonding) association and metal‐coordination interaction, to afford nanomedicine is still unexplored. Herein a smart supramolecular polymeric nanomedicine constructed via TU motifs privileged dual noncovalent interactions, toward synergistic chemo/chemodynamic (CT/CDT) cancer therapy is reported. The study first synthesized a six‐arm star‐shaped amphiphilic polymer vehicle containing pendant TU motifs, poly(acylthiourea‐co‐oligo(ethylene glycol) ethyl acrylate)6 (P(TU‐co‐OEGEA)6), followed by addressing both H‐bonding association and metal‐coordination to fabricate supramolecular nanomedicine (e.g., Dox/Cu@P(TU‐co‐OEGEA)6). Structural privilege and functional diversity of TU motifs constitute an outstanding scaffold, not only offering an H‐bonding site to associate doxorubicin (Dox) but also acting as a ligand to coordinate copper (Cu). Thereby, one TU motif can enable dual noncovalent binding modes, triggering multiple curative outcomes. TU/Dox and TU/Cu noncovalent interactions can induce intermolecular configuration, yielding prompted cargo loading and in vivo stability. Moreover, benefiting from pH‐responsive Dox release and Fenton‐like copper redox chemistry, accompanied by Dox‐induced intratumoral H2O2 elevation and prompted •OH generation, synergistic CT/CDT with extraordinary anti‐tumor efficacy is indeed accomplished. This work provides a new paradigm using TU motifs regulated dual supramolecular forces to meet therapeutic goals.

Targeting the Main Protease (Mpro, nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies.

The main protease Mpro, nsp5, of SARS-CoV-2 (SCoV2) is one of its most attractive drug targets. Here, we report primary screening data using nuclear magnetic resonance spectroscopy (NMR) of four different libraries and detailed follow-up synthesis on the promising uracil-containing fragment Z604 derived from these libraries. Z604 shows time-dependent binding. Its inhibitory effect is sensitive to reducing conditions. Starting with Z604, we synthesized and characterized 13 compounds designed by fragment growth strategies. Each compound was characterized by NMR and/or activity assays to investigate their interaction with Mpro. These investigations resulted in the four-armed compound 35b that binds directly to Mpro. 35b could be cocrystallized with Mpro revealing its noncovalent binding mode, which fills all four active site subpockets. Herein, we describe the NMR-derived fragment-to-hit pipeline and its application for the development of promising starting points for inhibitors of the main protease of SCoV2.

Synthesis, characterization, DNA interaction, molecular docking, and α-amylase and α-glucosidase inhibition studies of a water soluble Zn(II) phthalocyanine.

In this study, 2(3),9(10),16(17),23(24)-tetrakis-[(N-methyl-(1-benzylpiperidin-4-yl)oxy)phthalocyaninato]zinc(II) iodide (ZnPc-2) was synthesized and characterized using spectral methods (FT-IR, 1H-NMR, UV-Vis and mass spectroscopy). The interaction of ZnPc-2 with DNA was investigated by using the UV/Vis titrimetric method, thermal denaturation profile, agarose gel electrophoresis and molecular docking studies. Additionally, the antidiabetic activity of ZnPc-2 was revealed spectroscopically by studying α-amylase and α-glucosidase inhibition activities. The spectroscopic results indicated that ZnPc-2 effectively binds to calf thymus-DNA (CT-DNA) with a Kb value of 7.5 × 104 M-1 and interacts with CT-DNA via noncovalent binding mode. Gel electrophoresis results also show that ZnPc-2 binds strongly to DNA molecules and exhibits effective nuclease activity even at low concentrations. Furthermore, docking studies suggest that ZnPc-2 exhibits a stronger binding tendency with DNA than the control compounds ethidium bromide and cisplatin. Consequently, due to its strong DNA binding and nuclease activity, ZnPc-2 may be suitable for antimicrobial and anticancer applications after further toxicological tests. Additionally, antidiabetic studies showed that ZnPc-2 had both α-amylase and α-glucosidase inhibition activity. Moreover, the α-glucosidase inhibitory effect of ZnPc-2 was approximately 3500 times higher than that of the standard inhibitor, acarbose. Considering these results, it can be said that ZnPc-2 is a moderate α-amylase and a highly effective α-glucosidase inhibitor. This suggests that ZnPc-2 may have the potential to be used as a therapeutic agent for the treatment of type 2 diabetes.

Synthesis, structure elucidation, SC-XRD/DFT, molecular modelling simulations and DNA binding studies of 3,5-diphenyl-4,5-dihydro-1H-pyrazole chalcones

Deoxyribonucleic acid (DNA) acts as the most important intracellular target for various drugs. Exploring the DNA binding interactions of small bioactive molecules offers a structural guideline for designing new drugs with higher clinical efficacy and enhanced selectivity. This study presents the facile synthesis of pyrazoline-derived compounds (4a)-(4f) by reacting substituted chalcones with hydrazine hydrate using formic acid. The structure elucidation of substituted pyrazoline compounds was carried out using 1H-NMR, FT-IR and elemental analyses. While the crystal structures of two compounds (4a) and (4b) have been resolved by single-crystal X-ray diffraction (SC-XRD) analysis. Hirshfeld surface analysis also endorsed their greater molecular stability. Computational calculations at DFT/B3LYP/6-311++G(d,p) were executed to compare the structural properties (bond angle and bond length) and explore reactivity descriptors, frontier molecular orbitals (FMO), Mulliken atomic charges (MAC), molecular electrostatic potential (MEP) and electronic properties. All the compounds were evaluated for DNA binding interactions by UV-Vis spectrophotometric analysis. The results revealed that compounds (4a)-(4f) bind to DNA via non-covalent binding mode having binding constant values ranging from 1.22 × 103 to 6.81 × 104 M−1. The negative values of Gibbs free energy also proved the interaction of studied compounds with DNA as a spontaneous process. The findings of molecular docking simulations depicted that these studied compounds showed significant binding interactions with DNA and these results were consistent with experimental findings. Compound (4b) was concluded as the most potent compound of the series with the highest binding constant (4.95 × 104) and strongest binding affinity (-8.48 kcal/mol). Communicated by Ramaswamy H. Sarma

N’-Ferrocenylmethyl-N’-phenylbenzohydrazide as a potential DNA binding compound: a combined experimental and computational study

Due to increased lipophilicity, stability, and decreased cytotoxicity in biological systems, ferrocene derivatives are promising building blocks for therapeutic agents. This manuscript reports the binding of N’-ferrocenylmethyl-N’-phenylbenzohydrazide (FhD) with deoxyribonucleic acid (DNA) studied by absorption spectroscopy and cyclic voltammetry. Binding constants and binding free energies for the FhD-DNA complex were measured using these two methods as 5100 M−1, 6109 M−1 and −21.2 kJ/mol, −21.6 kJ/mol, respectively. DFT calculations were also performed and revealed important physical characteristics of the FhD compound. Subsequently, the system was explored by computational molecular docking, confirming a non-covalent mode of binding via minor groove with a binding energy of −25.5 kJ/mol. Furthermore, molecular dynamics of the docked complex of FhD with DNA were carried out for 100 ns followed by MM-GBSA to have a deep understanding of the complex’s dynamic behavior in physiological systems, and to determine the Gibbs free energy which was −14.31 Kcal/mol over a 100 ns window. The results show important antitumor potential of FhD due to its spontaneous non-covalent interaction with DNA and the efficient binding stability of the FhD-DNA complex in a physiological system.

A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1.

Coenzyme A (CoA) is a key cellular metabolite which participates in diverse metabolic pathways, regulation of gene expression and the antioxidant defense mechanism. Human NME1 (hNME1), which is a moonlighting protein, was identified as a major CoA-binding protein. Biochemical studies showed that hNME1 is regulated by CoA through both covalent and non-covalent binding, which leads to a decrease in the hNME1 nucleoside diphosphate kinase (NDPK) activity. In this study, we expanded the knowledge on previous findings by focusing on the non-covalent mode of CoA binding to the hNME1. With X-ray crystallography, we solved the CoA bound structure of hNME1 (hNME1-CoA) and determined the stabilization interactions CoA forms within the nucleotide-binding site of hNME1. A hydrophobic patch stabilizing the CoA adenine ring, while salt bridges and hydrogen bonds stabilizing the phosphate groups of CoA were observed. With molecular dynamics studies, we extended our structural analysis by characterizing the hNME1-CoA structure and elucidating possible orientations of the pantetheine tail, which is absent in the X-ray structure due to its flexibility. Crystallographic studies suggested the involvement of arginine 58 and threonine 94 in mediating specific interactions with CoA. Site-directed mutagenesis and CoA-based affinity purifications showed that arginine 58 mutation to glutamate (R58E) and threonine 94 mutation to aspartate (T94D) prevent hNME1 from binding to CoA. Overall, our results reveal a unique mode by which hNME1 binds CoA, which differs significantly from that of ADP binding: the α- and β-phosphates of CoA are oriented away from the nucleotide-binding site, while 3'-phosphate faces catalytic histidine 118 (H118). The interactions formed by the CoA adenine ring and phosphate groups contribute to the specific mode of CoA binding to hNME1.

MD-Based Assessment of Covalent Inhibitors in Noncovalent Association Complexes: Learning from Cathepsin K as a Test Case.

A sufficiently stable noncovalent association complex between a covalent inhibitor and its protein target is regarded as a prerequisite for the formation of a covalent complex. As this transient form can hardly be assessed experimentally, computational modeling is required to probe the suitability of a given ligand at this particular stage. To investigate which criteria should be fulfilled by suitable candidates in a molecular dynamics (MD) assessment, a systematic study was conducted with 20 complexes of cathepsin K, a papain-like cysteine protease of pharmaceutical relevance. The covalent inhibitors in these complexes were converted to their pre-reaction states, and the resulting noncovalent complexes were subjected to MD simulations. The critical distance between the electrophilic and nucleophilic reaction partners was monitored as a potential parameter to assess the suitability for covalent bond formation. Across various warhead types, a distance between 3.6 and 4.0 Å, comparable to the sum of the generalized Born radii of carbon and sulfur, was found to be stably maintained under appropriate conditions. The protonation state of the catalytic dyad and the resulting solvation pattern dramatically affected the noncovalent binding mode and the distance of the warhead to the active site. For several complexes, fluctuations in the orientation of the warhead were observed due to torsional rotations in adjacent bonds. This observation helped to explain the gradual transitions from noncovalent to covalent complexes observed in the crystal structures of three closely related nitrile-based inhibitors. According to comparative simulations conducted for a set of 13 cathepsin S complexes, the overall findings of the study appear to be transferable to related cysteine proteases as targets of covalent inhibitors.

Investigating the Impact of Covalent and Non-covalent Binding Modes of Inhibitors on Bruton's Tyrosine Kinase in the Treatment of B Cell Malignancies - Computational Insights.

Bruton tyrosine kinase plays a key role in the survival, proliferation, activation, and differentiation of B-lineage cells and the signaling of other receptors. It is overexpressed and constitutively active in the pathogenesis of B cell malignancies and has therefore become a target for therapeutic intervention. Some success has been achieved in the discovery of small molecules, especially in the development of irreversible inhibitors. However, these inhibitors are punctuated by off target effects and have also become less effective in patients with mutations at Cys481. This motivated the search for inhibitors with improved efficacy and different binding modes. In this study, we employed two new second generation inhibitors with different binding modes, Zanubrutinib and AS-1763, which are at various levels of clinical trials, to highlight the molecular determinants in the therapeutic inhibition of BTK through computational studies. This study revealed that Zanubrutinib and AS-1763 exhibited free total binding energies of -98.76 ± 4.63 kcal/mol and -51.81 ± 9.94 kcal/mol, respectively, with Zanubrutinib engaging in peculiar hydrogen bond interactions with the hinge residues Glu475 and Met477 including Asn484 and Tyr485 while AS-1763 engaged Lys430, Asp539, and Arg525. These residues contributed the most towards the free total binding energy with energies above -1.0 kcal/mol. The compounds further interacted differentially with other binding site residues through pi-alkyl, pi-cation, pianion, pi-pi-T-shaped, pi-sigma, pi-sulfur and pi-donor hydrogen bonds, and Van der Waals interactions. These interactions resulted in differential fluctuations of the residues with the consequential unfolding of the protein. Insights herein would be useful in guiding the discovery of more selective and potent small molecules.

Abstract CT126: An open-label, first-in-human study of BAY2927088 in patients with advanced non-small cell lung cancer (NSCLC) harboring an EGFR and/or HER2 mutation

Abstract Background: Despite targeted agents recently approved for treating patients with advanced NSCLC harboring EGFR exon 20 insertion (ex20ins) mutations, there is still a high unmet need for more effective agents with good tolerability. BAY2927088 is an oral, reversible, highly potent TKI targeting EGFR and HER2 driver mutations with high selectivity for ex20ins vs wild-type EGFR. In addition, BAY2927088 retains potent antiproliferative activity in the presence of EGFR C797S acquired resistance (AR) mutation due to its non-covalent binding mode. In preclinical studies, BAY2927088 demonstrated strong dose-dependent in vivo tumor growth inhibition in NSCLC EGFR ex20ins mutant patient-derived xenograft models and models carrying the AR mutation C797S (Siegel et al, ENA 2022). The strong potency and high selectivity of BAY2927088 for mutant vs wild-type EGFR offers the prospect of an improved therapeutic window in the clinical setting vs available EGFR TKIs. Methods: 21607 is an open-label, multicenter, first-in-human Phase I study of BAY2927088 in patients with advanced NSCLC harboring EGFR or HER2 mutations. The study comprises dose escalation, backfill, and dose expansion. The dose escalation is enrolling patients with EGFR or HER2 driver mutations and follows a modified continual reassessment method, allowing for concurrent backfill to previously cleared dose levels that demonstrated therapeutically relevant exposures or direct evidence of clinical activity in patients harboring ex20ins or EGFR C797S mutations. Dose-limiting toxicities are evaluated for 21 days. The primary objective of dose escalation is to determine BAY2927088 safety, tolerability, PK, and maximum tolerated dose. Dose expansion will enroll patients based on specific EGFR/HER2 mutations and previous treatment, including those with ex20ins mutation either naïve or pretreated with ex20ins-targeted agents and those with AR EGFR C797S mutation. Key objectives of dose expansion are to further characterize BAY2927088 safety, tolerability, and to characterize PK of the optimal dose(s) selected during dose escalation and backfill. Key secondary objectives include determining antitumor activity based on overall response rate per RECIST v1.1 and the recommended Phase II dose of BAY2927088. Eligible patients must have measurable disease per RECIST v1.1, have a documented EGFR or HER2 mutation in tumor tissue or plasma, have disease progression after treatment with ≥1 systemic therapy for advanced disease, be appropriate candidates for experimental therapy, be aged ≥18 years, have ECOG PS of 0 or 1, and have adequate organ function. Key exclusion criteria include presence of serious cardiac conditions, interstitial lung disease, active CNS metastasis, or leptomeningeal disease. The trial is currently enrolling patients in dose-escalation and backfill parts (NCT05099172). Citation Format: Daniel Tan, Koichi Goto, Herbert HF Loong, Tsung-Ying Yang, Shirish Gadgeel, Erminia Massarelli, Gennaro Daniele, Xiuning Le, Yuki Shinno, Haruyasu Murakami, Tomohiro Sakamoto, Jose C. Ruffinelli, Shun Lu, Yiping Zhang, Tae Min Kim, Barbara J. Brennan, Chunlin Chen, Miranda Joosten, Zebin Wang, Su-Fen Pu, Weichao Bao, Martin Kornacker, Roberta Ferraldeschi, Paolo Grassi, Boon Cher Goh. An open-label, first-in-human study of BAY2927088 in patients with advanced non-small cell lung cancer (NSCLC) harboring an EGFR and/or HER2 mutation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr CT126.

Novel Class of Proteasome Inhibitors: In Silico and In Vitro Evaluation of Diverse Chloro(trifluoromethyl)aziridines.

The ubiquitin-proteasome pathway (UPP) is the major proteolytic system in the cytosol and nucleus of all eukaryotic cells. The role of proteasome inhibitors (PIs) as critical agents for regulating cancer cell death has been established. Aziridine derivatives are well-known alkylating agents employed against cancer. However, to the best of our knowledge, aziridine derivatives showing inhibitory activity towards proteasome have never been described before. Herein we report a new class of selective and nonPIs bearing an aziridine ring as a core structure. In vitro cell-based assays (two leukemia cell lines) also displayed anti-proliferative activity for some compounds. In silico studies indicated non-covalent binding mode and drug-likeness for these derivatives. Taken together, these results are promising for developing more potent PIs.

Design and Synthesis of Carbothioamide/Carboxamide-Based Pyrazoline Analogs as Potential Anticancer Agents: Apoptosis, Molecular Docking, ADME Assay, and DNA Binding Studies.

To discover anticancer drugs with novel structures and expand our research scope, pyrazoline derivatives (3a–3l) were designed and synthesized through cyclization of chalcones with thiosemicarbazide/semicarbazide in CH3COOH as a solvent. All newly synthesized pyrazoline derivatives were fully characterized using several spectroscopic experiments such as 1H, 13C NMR, FT-IR spectroscopy, and mass analysis. By HPLC, the purity of all analogs was found above 95% and both lead compounds (3a and 3h) were also validated by HRMS. Anticancer activity of synthesized pyrazoline derivatives (3a–3l) was investigated by the MTT assay against the human lung cancer cell (A549), human cervical cancer cell (HeLa), and human primary normal lung cells (HFL-1). Staurosporine (STS) was used as a standard drug. The anticancer results showed that two potent analogs 3a and 3h exhibit excellent activity against A549 (IC50 = 13.49 ± 0.17 and 22.54 ± 0.25 μM) and HeLa cells (IC50 = 17.52 ± 0.09 and 24.14 ± 0.86 μM) and low toxicity against the HFL-1 (IC50 = 114.50 ± 0.01 and 173.20 ± 10 μM). The flow cytometry was further used to confirm the anticancer activity of potent derivatives against the A549 cancer cell line. DNA binding interaction of anticancer agents 3a and 3h with Ct-DNA has been carried out by absorption, fluorescence, EtBr (dye displacement assay), circular dichroism, cyclic voltammetry and time-resolved fluorescence, which showed noncovalent binding mode of interaction. Anticancer activity of both lead compounds (3a and 3h) may be attributed to DNA binding. The evaluation of the antioxidant potential of pyrazoline analogs 3a and 3h by 2,2-diphenyl-1-picrylhydrazyl free radical showed promising antioxidant activity with IC50 values of 0.132 ± 0.012 and 0.215 ± 0.025 μg/mL, respectively. In silico molecular docking of pyrazoline derivatives was also performed using autodock vina software against the DNA hexamer with PDB ID: 1Z3F and ADMET properties to explore their best hits.

Serum albumin as a primary non-covalent binding protein for nitro-oleic acid

This work explores the interaction of 9/10-nitro-oleic acid (NO2-OA) with human serum albumin (HSA). The molecular mechanism of the biological action of NO2-OA is to our knowledge based on a reversible covalent reaction–Michael addition of nucleophilic amino acid residues of proteins. Since HSA is an important fatty acid transporter, a key question is whether NO2-OA can bind covalently or non-covalently to HSA, similarly to oleic acid (OA), which can interact with the FA1-FA7 binding sites of the HSA molecule. 1H NMR studies and competition analysis with OA and the drugs ibuprofen and warfarin were used to investigate a potential non-covalent binding mode. NO2-OA/HSA binding was confirmed to compete with warfarin for FA-7 with significantly higher affinity. NO2-OA competes with ibuprofen for FA-3 and FA-6, however, in contrast to the situation with warfarin, the binding affinities are not significantly different. The described interactions are based exclusively on non-covalent binding. No covalent binding of NO2-OA to HSA was detected by MS/MS. More detailed studies based on MALDI-TOF-MS and Ellman's assay indicated that HSA can be covalently modified in the presence of NO2-OA to a very limited extent. It was also shown that NO2-OA has a higher affinity to HSA than that of OA.

2-Imidazole as a Substitute for the Electrophilic Group Gives Highly Potent Prolyl Oligopeptidase Inhibitors.

Different five-membered nitrogen-containing heteroaromatics in the position of the typical electrophilic group in prolyl oligopeptidase (PREP) inhibitors were investigated and compared to tetrazole. The 2-imidazoles were highly potent inhibitors of the proteolytic activity. The binding mode for the basic imidazole was studied by molecular docking as it was expected to differ from the acidic tetrazole. A new putative noncovalent binding mode with an interaction to His680 was found for the 2-imidazoles. Inhibition of the proteolytic activity did not correlate with the modulating effect on protein–protein-interaction-derived functions of PREP (i.e., dimerization of alpha-synuclein and autophagy). Among the highly potent PREP inhibiting 2-imidazoles, only one was also a potent modulator of PREP-catalyzed alpha-synuclein dimerization, indicating that the linker length on the opposite side of the molecule from the five-membered heteroaromatic is critical for the disconnected structure–activity relationships.

Zirconium and Aluminum MOFs for Low-Pressure SO2 Adsorption and Potential Separation: Elucidating the Effect of Small Pores and NH2 Groups.

Finding new adsorbents for the desulfurization of flue gases is a challenging task but is of current interest, as even low SO2 emissions impair the environment and health. Four Zr- and eight Al-MOFs (Zr-Fum, DUT-67(Zr), NU-1000, MOF-808, Al-Fum, MIL-53(Al), NH2-MIL-53(Al), MIL-53(tdc)(Al), CAU-10-H, MIL-96(Al), MIL-100(Al), NH2-MIL-101(Al)) were examined toward their SO2 sorption capability. Pore sizes in the range of about 4-8 Å are optimal for SO2 uptake in the low-pressure range (up to 0.1 bar). Pore widths that are only slightly larger than the kinetic diameter of 4.1 Å of the SO2 molecules allow for multi-side-dispersive interactions, which translate into high affinity at low pressure. Frameworks NH2-MIL-53(Al) and NH2-MIL-101(Al) with an NH2-group at the linker tend to show enhanced SO2 affinity. Moreover, from single-gas adsorption isotherms, ideal adsorbed solution theory (IAST) selectivities toward binary SO2/CO2 gas mixtures were determined with selectivity values between 35 and 53 at a molar fraction of 0.01 SO2 (10.000 ppm) and 1 bar for the frameworks Zr-Fum, MOF-808, NH2-MIL-53(Al), and Al-Fum. Stability tests with exposure to dry SO2 during ≤10 h and humid SO2 during 5 h showed full retention of crystallinity and porosity for Zr-Fum and DUT-67(Zr). However, NU-1000, MOF-808, Al-Fum, MIL-53(tdc), CAU-10-H, and MIL-100(Al) exhibited ≥50-90% retained Brunauer-Emmett-Teller (BET)-surface area and pore volume; while NH2-MIL-100(Al) and MIL-96(Al) demonstrated a major loss of porosity under dry SO2 and MIL-53(Al) and NH2-MIL-53(Al) under humid SO2. SO2 binding sites were revealed by density functional theory (DFT) simulation calculations with adsorption energies of -40 to -50 kJ·mol-1 for Zr-Fum and Al-Fum and even above -50 kJ·mol-1 for NH2-MIL-53(Al), in agreement with the isosteric heat of adsorption near zero coverage (ΔHads0). The predominant, highest binding energy noncovalent binding modes in both Zr-Fum and Al-Fum feature μ-OHδ+···δ-OSO hydrogen bonding interactions. The small pores of Al-Fum allow the interaction of two μ-OH bridges from opposite pore walls with the same SO2 molecule via OHδ+···δ-OSOδ-···δ+HO hydrogen bonds. For NH2-MIL-53(Al), the DFT high-energy binding sites involve NHδ+···δ-OS together with the also present Al-μ-OHδ+···δ-OS hydrogen bonding interactions and C6-πδ-···δ+SO2, Nδ-···δ+SO2 interactions.

Toward an Understanding of Pan-Assay Interference Compounds and Promiscuity: A Structural Perspective on Binding Modes.

Pan-assay interference compounds (PAINS) are promiscuous compound classes that produce false positive hits in high-throughput screenings. Yet, the mechanisms of PAINS activity are poorly understood. Although PAINS are often associated with protein reactivity, several recent studies have shown that they also mediate noncovalent interactions. Aiming at a deep understanding of PAINS promiscuity, we performed an analysis of the Protein Data Bank to characterize the binding modes of PAINS. We explored the binding mode conservation of 34 PAINS classes present in 871 ligands and among 517 protein targets. The two major findings of this work are the following: First, different PAINS classes exhibit different levels of binding mode conservation. Our novel classification of PAINS based on binding mode similarity enables a rational assessment of PAINS from a structural perspective. Second, PAINS classes with variable binding modes can bind with high affinity. The evaluation of noncovalent binding modes of PAINS-like compounds sheds light on the mechanisms of promiscuous binding. Our findings could facilitate the decisions on how to deal with PAINS and help scientists to understand why PAINS produce hits in their screenings.

Thermodynamic Evaluation of the Interactions between Anticancer Pt(II) Complexes and Model Proteins.

In this work, we have analysed the binding of the Pt(II) complexes ([PtCl(4′-phenyl-2,2′:6′,2″-terpyridine)](CF3SO3) (1), [PtI(4′-phenyl-2,2′:6′,2″-terpyridine)](CF3SO3) (2) and [PtCl(1,3-di(2-pyridyl)benzene) (3)] with selected model proteins (hen egg-white lysozyme, HEWL, and ribonuclease A, RNase A). Platinum coordination compounds are intensively studied to develop improved anticancer agents. In this regard, a critical issue is the possible role of Pt-protein interactions in their mechanisms of action. Multiple techniques such as differential scanning calorimetry (DSC), electrospray ionization mass spectrometry (ESI-MS) and UV-Vis absorbance titrations were used to enlighten the details of the binding to the different biosubstrates. On the one hand, it may be concluded that the affinity of 3 for the proteins is low. On the other hand, 1 and 2 strongly bind them, but with major binding mode differences when switching from HEWL to RNase A. Both 1 and 2 bind to HEWL with a non-specific (DSC) and non-covalent (ESI-MS) binding mode, dominated by a 1:1 binding stoichiometry (UV-Vis). ESI-MS data indicate a protein-driven chloride loss that does not convert into a covalent bond, likely due to the unfavourable complexes’ geometries and steric hindrance. This result, together with the significant changes of the absorbance profiles of the complex upon interaction, suggest an electrostatic binding mode supported by some stacking interaction of the aromatic ligand. Very differently, in the case of RNase A, slow formation of covalent adducts occurs (DSC, ESI-MS). The reactivity is higher for the iodo-compound 2, in agreement with iodine lability higher than chlorine.