Computational Screening of T-Muurolol for an Alternative Antibacterial Solution against Infections: An In Silico Approach for Phytochemical-Based Drug Discovery.

infections present a significant threat to the global healthcare system. The increasing resistance to existing antibiotics and their limited efficacy underscores the urgent need to identify new antibacterial agents with low toxicity to effectively combat various infections. Hence, in this study, we have screened T-muurolol for possible interactions with several -specific bacterial proteins to establish its potential as an alternative antibacterial agent.

Structural, Biochemical, and Computational Characterization of Sulfamides as Bimetallic Peptidase Inhibitors.

The sulfonamide function is used extensively as a general building block in various inhibitory scaffolds and, more specifically, as a zinc-binding group (ZBG) of metalloenzyme inhibitors. Here, we provide biochemical, structural, and computational characterization of a metallopeptidase in complex with inhibitors, where the mono- and bisubstituted sulfamide functions are designed to directly engage zinc ions of a bimetallic enzyme site. Structural data showed that while monosubstituted sulfamides coordinate active-site zinc ions via the free negatively charged amino group in a canonical manner, their bisubstituted counterparts adopt an atypical binding pattern divergent from expected positioning of corresponding tetrahedral reaction intermediates.

Molecular dynamics simulations provide structural insight into binding of cyclic dinucleotides to human STING protein.

Human stimulator of interferon genes (STING) is a signaling adaptor protein that triggers innate immune system by response to cytosolic DNA and second messenger cyclic dinucleotides (CDNs). Natural CDNs contain purine nucleobase with different phosphodiester linkage types (3'-3', 2'-2' or mixed 2'-3'-linkages) and exhibit different binding affinity towards STING, ranging from micromolar to nanomolar. High-affinity CDNs are considered as suitable candidates for treatment of chronic hepatitis B and cancer.

Conformational energies and equilibria of cyclic dinucleotides in vacuo and in solution: computational chemistry vs. NMR experiments.

Performance of computational methods in modelling cyclic dinucleotides - an important and challenging class of compounds - has been evaluated by two different benchmarks: (1) gas-phase conformational energies and (2) qualitative agreement with NMR observations of the orientation of the χ-dihedral angle in solvent. In gas-phase benchmarks, where CCSD(T) and DLPNO-CCSD(T) methods have been used as the reference, most of the (dispersion corrected) density functional approximations are accurate enough to justify prioritizing computational cost and compatibility with other modelling options as the criterion of choice. NMR experiments of 3'3'-c-di-AMP, 3'3'-c-GAMP, and 3'3'-c-di-GMP show the overall prevalence of the anti-conformation of purine bases, but some population of syn-conformations is observed for guanines.

Ligand Strain and Its Conformational Complexity Is a Major Factor in the Binding of Cyclic Dinucleotides to STING Protein.

STING (stimulator of interferon genes) is a key regulator of innate immunity that has recently been recognized as a promising drug target. STING is activated by cyclic dinucleotides (CDNs) which eventually leads to expression of type I interferons and other cytokines. Factors underlying the affinity of various CDN analogues are poorly understood.

Protein-Ligand Interactions in the STING Binding Site Probed by Rationally Designed Single-Point Mutations: Experiment and Theory.

STING protein (stimulator of interferon genes) plays an important role in the innate immune system. A number of potent compounds regulating its activity have been reported, mostly derivatives of cyclic dinucleotides (CDNs), natural STING agonists. Here, we aim to provide complementary information to large-scale "ligand-profiling" studies by probing the importance of STING-CDN protein-ligand interactions on the protein side.

Enzymatic Preparation of 2'-5',3'-5'-Cyclic Dinucleotides, Their Binding Properties to Stimulator of Interferon Genes Adaptor Protein, and Structure/Activity Correlations.

Cyclic dinucleotides are second messengers in the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway, which plays an important role in recognizing tumor cells and viral or bacterial infections. They bind to the STING adaptor protein and trigger expression of cytokines via TANK binding kinase 1 (TBK1)/interferon regulatory factor 3 (IRF3) and inhibitor of nuclear factor-κB (IκB) kinase (IKK)/nuclear factor-κB (NFκB) signaling cascades. In this work, we describe an enzymatic preparation of 2'-5',3'-5'-cyclic dinucleotides (2'3'CDNs) with use of cyclic GMP-AMP synthases (cGAS) from human, mouse, and chicken.

Structure-mechanism-based engineering of chemical regulators targeting distinct pathological factors in Alzheimer's disease.

The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-β (Aβ), metal-Aβ, reactive oxygen species, and free organic radicals.

Halides with Fifteen Aliphatic C-H···Anion Interaction Sites.

Since the aliphatic C-H···anion interaction is relatively weak, anion binding using hydrophobic aliphatic C-H (Cali-H) groups has generally been considered not possible without the presence of additional binding sites that contain stronger interactions to the anion. Herein, we report X-ray structures of organic crystals that feature a chloride anion bound exclusively by hydrophobic Cali-H groups. An X-ray structure of imidazolium-based scaffolds using Cali-H···A(-) interactions (A(-) = anion) shows that a halide anion is directly interacting with fifteen Cali-H groups (involving eleven hydrogen bonds, two bidentate hydrogen-bond-type binding interactions and two weakly hydrogen-bonding-like binding interactions).

Intriguing Electrostatic Potential of CO: Negative Bond-ends and Positive Bond-cylindrical-surface.

The strong electronegativity of O dictates that the ground state of singlet CO has positively charged C and negatively charged O, in agreement with ab initio charge analysis, but in disagreement with the dipole direction. Though this unusual phenomenon has been fairly studied, the study of electrostatic potential (EP) for noncovalent interactions of CO is essential for better understanding. Here we illustrate that both C and O atom-ends show negative EP (where the C end gives more negative EP), favoring positively charged species, whereas the cylindrical surface of the CO bond shows positive EP, favoring negatively charged ones.

Interactions of small gold clusters, Aun (n=1-3), with graphyne: theoretical investigation.

The interactions of gold atom and clusters (Au2 and Au3) with the active sites of graphyne (GY) have been investigated using density functional theory (PBE, PBE-D3, and B3LYP-D3). In order to compare performance of DFT functional (BP86, PBE, TPSSh, B3LYP, PBE-D3, TPSSh-D3, and B3LYP-D3), the interactions of Au2 with various functional groups such as -sp, -sp(2) and aromatic sp(2) carbon atoms, -sp, -sp(2) and aromatic sp(2)-bonds have been investigated and also compared with the ab initio MP2 results. Additionally, the nature of interactions for graphyne-Au2 complexes are interpreted by means of the natural bond orbital (NBO), the quantum theory of atoms in molecules (QTAIM) and energy decomposition analysis (EDA) and compared with those of related graphene-Au2.

Do coinage metal anions interact with substituted benzene derivatives?

The nature of the anion-π interaction has been investigated by carrying out ab initio calculations of the complexes of coinage metal anions (Au(-), Ag(-), and Cu(-)) with different kinds of π-systems. The binding energies indicate that gold anion has the highest and copper anion has the lowest affinity for interactions with π-systems. Different aspects of the anion-π interaction in these systems have been investigated, including charge-transfer effects (using the Merz-Kollman method), "atoms-in-molecules" (AIM) topological parameters, and interaction energies (using energy decomposition analysis, EDA).

Comparison of gas phase intrinsic properties of cytosine and thymine nucleobases with their O-alkyl adducts: different hydrogen bonding preferences for thymine versus O-alkyl thymine.

In recent years, there has been increasing interest in damaged DNA and RNA nucleobases. These damaged nucleobases can cause DNA mutation, resulting in various diseases such as cancer. Alkylating agents are mutagenic and carcinogenic in a variety of prokaryotic and eukaryotic organisms.

Theoretical investigation on antioxidant activity of bromophenols from the marine red alga Rhodomela confervoides: H-atom vs electron transfer mechanism.

Bromophenols are known as antioxidant radical scavengers for some biomolecules such as those in marine red alga. Full understanding of the role played by bromophenols requires detailed knowledge of the radical scavenging activities in probable pathways, a focus of ongoing research. To gain detailed insight into two suggested pathways, H-atom transfer and electron transfer, theoretical studies employing first principle quantum mechanical calculations have been carried out on selected bromophenols.

Interactions of coinage metal clusters with histidine and their effects on histidine acidity; theoretical investigation.

Understanding the nature of interaction between metal nanoparticles and biomolecules such as amino acids is important in the development and design of biosensors. In this paper, binding of M(3) clusters (M = Au, Ag and Cu) with neutral and anionic forms of histidine amino acid was studied using density functional theory (DFT-B3LYP). It was found that the interaction of histidine with M(3) clusters is governed by two major bonding factors: (a) the anchoring N-M and O-M bonds and (b) the nonconventional N-H···M and O-H···M hydrogen bonds.

Interactions of glutathione tripeptide with gold cluster: influence of intramolecular hydrogen bond on complexation behavior.

Understanding the nature of the interaction between metal nanoparticles and biomolecules has been important in the development and design of sensors. In this paper, structural, electronic, and bonding properties of the neutral and anionic forms of glutathione tripeptide (GSH) complexes with a Au(3) cluster were studied using the DFT-B3LYP with 6-31+G**-LANL2DZ mixed basis set. Binding of glutathione with the gold cluster is governed by two different kinds of interactions: Au-X (X = N, O, and S) anchoring bond and Au···H-X nonconventional hydrogen bonding.

DFT study of the interaction of cytidine and 2'-deoxycytidine with Li+, Na+, and K+: effects of metal cationization on sugar puckering and stability of the N-glycosidic bond.

Density functional theory (DFT) calculations were performed at the B3LYP level with a 6-311++G(d,p) basis set to systematically explore the geometrical multiplicity and binding strength for complexes formed by Li(+), Na(+), and K(+) with cytidine and 2'-deoxycytidine. All computational studies indicate that the metal ion affinity (MIA) decreases from Li(+) to Na(+) and K(+) for cytosine nucleosides. For example, for cytidine the affinity for the above metal ions are 79.