Glucosamine is a component of many cellular glycoproteins that constitutes the cartilage, and it has several biological activities, such as anti-inflammatory, antioxidant, antifibrotic, and anticancer, and has been used in arthritis and dermatological treatments. Considering that the biological activities of glucosamine occur mainly in an aqueous environment, it is essential to understand the effects of an aqueous solvent on its geometric and electronic parameters using ab initio molecular dynamics. The Car–Parrinello molecular dynamics results show that the hydroxyl groups form stable hydrogen bonds with the water molecules with intensities ranging from weak (closed-shell interaction) to intermediate (partially covalent interactions). The H bonds formed between the amino group and the water molecule range from weak (closed-shell) to strong (covalent), and it shows an infinity residence time. The natural bonding orbital (NBO) approach was applied to analyze the effects of charge-transfer interactions on the behavior of the hydrogen bonds. The main contribution to stabilizing energies comes from n → σ* hyperconjugation and explains the stability of the H bonds. The energy barrier for the proton transfer from water to the amino group is 0.88 kcal/mol, and the van der Waals complex energy is 0.3 kcal/mol. The low protonation energy barrier shows that glucosamine can be protonated in an aqueous environment at room temperature, which helps to explain many of its biological activities.

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A dihydropyrimidine (DHPM) derivative was synthesized, characterized by X-ray diffraction and searched in silico for its inhibitory activities against AccD5 enzyme, the CT domain of a Mycobacterium tuberculosis ACCase. Its molecular structure was compared to another DHPM derivative (DHPM II). The results have shown that the (±)2,6-methano-4-thioxo-3,4,5,6-tetrahydro-2H-[1,3,5] benzoxadiazocines (DHPM I) and (±)2,6-methano-4-oxo-3,4,5,6-tetrahydro-2H-[1,3,5] benzoxadiazocines (DHPM II) belong to the monoclinic and triclinic systems, respectively, and their crystal structures are stabilized by N–H⋯O, O–H⋯O and N–H⋯S interactions. The DHPM derivatives established hydrogen bond interactions with the oxyanion-stabilizing residues (Gly-434/Ala-435) beyond the Thr-217, Phe-394 and Ile-216 in the biotin pocket. The predicted MoB of the DHPM derivatives (21R, 24S, 22R) configuration showed that its phenyl moiety was positioned on the interface between the biotin and propionyl-CoA pockets, suggesting a possible blockade of both subsites. Additionally, the hydrogen bonds involving the O-bridged phenyl ring of the DHPM derivatives (21S, 24R, 22S) configuration with Gly434 in the oxyanion-stabilizing region placed its phenyl moiety in the bottom of the biotin pocket establishing hydrophobic interactions with Leu164, Tyr167, Val459 and Ala155. These results indicate the DHPM derivatives as potential AccD5 inhibitors and promising starting points for future optimizations. Although the overlap of DHPM I and DHPM II did not present significant differences, the exchange of a sulfur atom for an oxygen atom increased the predicted biological potential.

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Dopamine is an important neurotransmitter belonging to the catecholamine family, which acts on the central nervous system. This catecholamine plays a key role in regulating a variety of functions, such as motor and cognitive functions. This class of neurotransmitters is important for normal neurophysiology and is also the target of a broad spectrum of therapeutic and illicit agents. Evaluating the interaction of these neurotransmitters, in particular, dopamine with water molecules, is crucial for a better understanding of the conformational preferences of dopamine in solution, which consequently assists in the design of new drugs for the treatment of diseases associated with a malfunction of the system, and direct measurement, which is particularly essential for early warning of certain diseases. In this sense, the objective of this work is to examine the effects of aqueous solvation on the geometric and electronic parameters of dopamine using Car-Parrinelo Molecular Dynamics. The Car-Parrinello Molecular Dynamics simulation was performed using the CPMD program package (Version 4.1). The results indicate that dopamine interact swith several water molecules, with the formation of hydrogen bonds. In particular, there are two hydrogen bonds (H5···Owf and N3···Hwd) with an infinite residence time that strongly suggests the protonation of these groups.