Like-Charge Guanidinium Pairing between Ligand and Receptor: An Unusual Interaction for Drug Discovery and Design?

Molecular docking-based interaction studies on imidazo[1,2-a] pyridine ethers and squaramides as anti-tubercular agents

Development of new anti-tubercular agents is required in the wake of resistance to the existing and newly approved drugs through novel-validated targets like ATP synthase, etc. The major limitation of poor correlation between docking scores and biological activity by SBDD was overcome by a novel approach of quantitatively correlating the interactions of different amino acid residues present in the target protein structure with the activity. This approach well predicted the ATP synthase inhibitory activity of imidazo[1,2-a] pyridine ethers and squaramides (r = 0.84) in terms of Glu65b interactions. Hence, the models were developed on combined (r = 0.78), and training (r = 0.82) sets of 52, and 27 molecules, respectively. The training set model well predicted the diverse dataset (r = 0.84), test set (r = 0.755), and, external dataset (r_ext = 0.76). This model predicted three compounds from a focused library generated by incorporating the essential features of the ATP synthase inhibition with the pIC₅₀ values in the range of 0.0508-0.1494 µM. Molecular dynamics simulation studies ascertain the stability of the protein structure and the docked poses of the ligands. The developed model(s) may be useful in the identification and optimization of novel compounds against TB.

Anion⋯anion interaction within Ch(CH3)X4- (Ch = S, Se, Te; X = Cl, Br, I) dimers stabilized by chalcogen bonds

In a crystal, a pair of homoanions (Te(C₆H₅)Cl₄^-) are arranged in a parallel manner, close enough to interact with each other. Quantum chemical analysis indicates the existence of two strong noncovalent chalcogen bonds engaging the σ-hole of the chalcogen atoms from one unit and electron density accumulated on the Cl atom of the neighboring unit. In a solid, chalcogen bonds are supported by a multitude of HBs between interacting (Te(C₆H₅)Cl₄^-) anions and the C₅H₅NBr⁺ counterions. These studies are extended to the model homodimers [(Ch(CH₃)X₄)^-]₂, where Ch represents an atom of group 16 (S, Se, and Te) while X = Cl, Br, and I. In these model systems, the aromatic ring was replaced by a methyl group and the counterions were not included. The consequence of this is a different noncovalent bond network in comparison to the system in a solid (the absence of intermolecular HBs and the presence of dihalogen bonds). The tendency for more exoenergetic complexation increases in the Cl < Br < I series. The chalcogen size effect is much smaller. However, critical to the stability of this system is overcoming the Coulomb repulsion between the two monoanions. This is possible because of the polarizable environment that exists in the crystal due to the presence of counter ions.

Molecular docking-based interactions in QSAR studies on Mycobacterium tuberculosis ATP synthase inhibitors

Tuberculosis (TB) is a global threat with a large burden across the continents in terms of mortality, morbidity, and financial losses. The disease has evolved into multi-drug-resistant (MDR-TB) and extensively drug-resistant (XDR-TB) tuberculosis owing to numerous factors ranging from patients' non-compliance to demographical implications. There have been very few new drugs for resistant TB. Resistance has already been reported even for the newly introduced drug bedaquiline. An attempt has been made to integrate both structure-based and QSAR drug design techniques (QSAR-SBDD) for the identification of novel leads. The docking scores normally do not correlate with the activity. Hence, the docking results have been analysed in terms of the number of interactions rather than docking scores. The parameters derived from interactions have been used in developing the QSAR models. The best model shows a good correlation (r = 0.908) between the activity and interaction parameter 'C' describing the sum of all the interactions with each amino acid residue. This model also predicts external dataset with a good correlation (r_ext = 0.851) and can be used for the identification of novel chemical entities (NCEs) and repurposed drugs for TB therapeutics.

The combined action of cations and anions of ionic liquids modulates the formation and stability of G-quadruplex DNA

G-Quadruplex (Gq) formation and stabilization by any molecule is an essential requirement for its application in therapy, especially in oncology. Metal cations have shown higher propensity of the formation of the Gq structure and its stabilization. In this study, the role of both cations and anions of ionic liquids (ILs) on the Gq formation of human telomere (hTeloG) and its stability was investigated using spectroscopic and molecular dynamics simulation techniques. Irrespective of the nature of anions of ILs, tetramethylguanidinium (TMG) cations associated with different anions can form an antiparallel Gq structure in hTeloG. However, the propensity of the formation of an antiparallel Gq structure and its stability depend on the chain length of anions of ILs. Gq is significantly less stable in ILs having longer hydrocarbon chain anions compared to the short chain anions suggesting that the hydrophobicity of the anion plays a critical role in the stability and formation of the Gq structure by ILs. The data indicate that longer hydrocarbon chain anions of ILs preferably interact in the loop region of Gq through hydrophobic interaction which enhances the overall binding of the cation of ILs with Gq causing a decrease in the stacking energy between the G-quartets as well as Hoogsteen hydrogen bonds between the guanine bases leading to the destabilization of the antiparallel Gq structure.

Structure-Activity Relationship Studies on Oxazolo[3,4-a]pyrazine Derivatives Leading to the Discovery of a Novel Neuropeptide S Receptor Antagonist with Potent In Vivo Activity

Neuropeptide S modulates important neurobiological functions including locomotion, anxiety, and drug abuse through interaction with its G protein-coupled receptor known as neuropeptide S receptor (NPSR). NPSR antagonists are potentially useful for the treatment of substance abuse disorders against which there is an urgent need for new effective therapeutic approaches. Potent NPSR antagonists in vitro have been discovered which, however, require further optimization of their in vivo pharmacological profile. This work describes a new series of NPSR antagonists of the oxazolo[3,4-a]pyrazine class. The guanidine derivative 16 exhibited nanomolar activity in vitro and 5-fold improved potency in vivo compared to SHA-68, a reference pharmacological tool in this field. Compound 16 can be considered a new tool for research studies on the translational potential of the NPSergic system. An in-depth molecular modeling investigation was also performed to gain new insights into the observed structure-activity relationships and provide an updated model of ligand/NPSR interactions.

Construction of thermally robust and porous shrimp ferritin crystalline for molecular encapsulation through intermolecular arginine-arginine attractions

Protein colloid crystals are considered as high porous soft materials, presenting great potentials in nutrients and drug encapsulation, but protein crystal fabrication usually needs precipitant and high protein concentration. Herein, an easy implemented approach was reported for the construction of protein colloid crystals in diluted solution with shimp ferritin as building blocks by taking advantage of the strength of multiple intermolecular arginine-arginine interactions. The X-ray single-crystal structure reveals that a group of exquisite arginine-arginine interactions between two neighboring ferritin enable them self-assembly into long-range ordered protein soft materials. The arginine-arginine interactions mediate crystal generation favored at pH 9.5 with 200 mM NaCl, and the resulting colloid crystals exhibit high thermal stability (90 °C for 30 min). Importantly, the interglobular cavity in colloid crystals is three times larger in volume than that of intrinsic ferritin cavity in each unit cell, which can be used for molecular encapsulation.

Anion-anion and anion-neutral triel bonds

The ability of a TrCl4- anion (Tr = Al, Ga, In, Tl) to engage in a triel bond with both a neutral NH3 and CN- anion is assessed by ab initio quantum calculations in both the gas phase and in aqueous medium. Despite the absence of a positive σ or π-hole on the Lewis acid, strong triel bonds can be formed with either base. The complexation involves an internal restructuring of the tetrahedral TrCl4- monomer into a trigonal bipyramid shape, where the base can occupy either an axial or equatorial position. Although this rearrangement requires a substantial investment of energy, it aids the complexation by imparting a much more positive MEP to the site that is to be occupied by the base. Complexation with the neutral base is exothermic in the gas phase and even more so in water where interaction energies can exceed 30 kcal mol-1. Despite the long-range coulombic repulsion between any pair of anions, CN- can also engage in a strong triel bond with TrCl4-. In the gas phase, complexation is endothermic, but dissociation of the metastable dimer is obstructed by an energy barrier. The situation is entirely different in solution, with large negative interaction energies of as much as -50 kcal mol-1. The complexation remains an exothermic process even after the large monomer deformation energy is factored in.

Design, synthesis biological activity, and docking of novel fluopyram derivatives containing guanidine group

Succinate dehydrogenase (SDH), a crucial bridge enzyme between the respiratory electron transfer chain and tricarboxylic acid (or Krebs) cycle, has been identified as an ideal target for the development of effective fungicide. In this study, a series of 24 novel SDH inhibitors (SDHIs) were designed, synthesized, and characterized by ¹H NMR, ¹³C NMR, and HRMS. In vitro fungicidal activity experiments, most of the compounds exhibited broad-spectrum antifungal activities against five plant pathogenic fungi. Compounds 9j and 9k showed excellent activities against Pythium aphanidermatum with EC₅₀ values of 9.93 mg/L and 10.50 mg/L, respectively, which were superior to the lead compound Fluopyram with an EC₅₀ value of 19.10 mg/L. Furthermore, the toxicity of these compounds was also tested against Meloidogyne incognita J2 nematodes. The results indicated that compound 9x exhibited moderate nematicidal activity (LC₅₀/48 h = 71.02 mg/L). Molecular docking showed that novel guanidine amide of 9j formed hydrogen bonds with crucial residues, which was crucial to the binding of an inhibitor and SDH. This present work indicates that these derivatives may serve as novel potential fungicides targeting SDH.

Understanding noncovalent bonds and their controlling forces

The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.

On the capability of metal–halogen groups to participate in halogen bonds

Halogens in a M–X bond are inhibited from forming a halogen bond but can do so in certain circumstances, with or without a σ-hole.

Arginine "Magic": Guanidinium Like-Charge Ion Pairing from Aqueous Salts to Cell Penetrating Peptides

It is a textbook knowledge that charges of the same polarity repel each other. For two monovalent ions in the gas phase at a close contact this repulsive interaction amounts to hundreds of kilojoules per mole. In aqueous solutions, however, this Coulomb repulsion is strongly attenuated by a factor equal to the dielectric constant of the medium. The residual repulsion, which now amounts only to units of kilojoules per mole, may be in principle offset by attractive interactions. Probably the smallest cationic pair, where a combination of dispersion and cavitation forces overwhelms the Coulomb repulsion, consists of two guanidinium ions in water. Indeed, by a combination of molecular dynamics with electronic structure calculations and electrophoretic, as well as spectroscopic, experiments, we have demonstrated that aqueous guanidinium cations form (weakly) thermodynamically stable like-charge ion pairs. The importance of pairing of guanidinium cations in aqueous solutions goes beyond a mere physical curiosity, since it has significant biochemical implications. Guanidinium chloride is known to be an efficient and flexible protein denaturant. This is due to the ability of the orientationally amphiphilic guanidinium cations to disrupt various secondary structural motifs of proteins by pairing promiscuously with both hydrophobic and hydrophilic groups, including guanidinium-containing side chains of arginines. The fact that the cationic guanidinium moiety forms the dominant part of the arginine side chain implies that the like-charge ion pairing may also play a role for interactions between peptides and proteins. Indeed, arginine-arginine pairing has been frequently found in structural protein databases. In particular, when strengthened by a presence of negatively charged glutamate, aspartate, or C-terminal carboxylic groups, this binding motif helps to stabilize peptide or protein dimers and is also found in or near active sites of several enzymes. The like-charge pairing of the guanidinium side-chain groups may also hold the key to the understanding of the arginine "magic", that is, the extraordinary ability of arginine-rich polypeptides to passively penetrate across cellular membranes. Unlike polylysines, which are also highly cationic but lack the ease in crossing membranes, polyarginines do not exhibit mutual repulsion. Instead, they accumulate at the membrane, weaken it, and might eventually cross in a concerted, "train-like" manner. This behavior of arginine-rich cell penetrating peptides can be exploited when devising smart strategies how to deliver in a targeted way molecular cargos into the cell.

Assessment of the Presence and Strength of H-Bonds by Means of Corrected NMR

The downfield shift of the NMR signal of the bridging proton in a H-bond (HB) is composed of two elements. The formation of the HB causes charge transfer and polarization that lead to a deshielding. A second factor is the mere presence of the proton-accepting group, whose electron density and response to an external magnetic field induce effects at the position of the bridging proton, exclusive of any H-bonding phenomenon. This second positional shielding must be subtracted from the full observed shift in order to assess the deshielding of the proton caused purely by HB formation. This concept is applied to a number of H-bonded systems, both intramolecular and intermolecular. When the positional shielding is removed, the remaining chemical shift is in much better coincidence with other measures of HB strength.

A new method to access triazole-fused spiro-guanidines from the reaction of isothiocyanates tethered N-sulfonyl-1,2,3-triazoles and amines

The reaction of isothiocyanate tethered N-sulfonyl-1,2,3-triazoles and amines afforded asymmetrical guanidines in fair to excellent yields through a two-component tandem reaction process.