Elucidation of escitalopram oxalate and related antidepressants as putative inhibitors of PTP4A3/PRL-3 protein in hepatocellular carcinoma: A multi-computational investigation

Hepatocellular carcinoma (HCC) persists to be one of the most devastating and deadliest malignancies globally. Recent research into the molecular signaling networks entailed in many malignancies has given some prominent insights that can be leveraged to create molecular therapeutics for combating HCC. Therefore, in the current communication, an in-silico drug repurposing approach has been employed to target the function of PTP4A3/PRL-3 protein in HCC using antidepressants: Fluoxetine hydrochloride, Citalopram, Amitriptyline, Imipramine, and Escitalopram oxalate as the desired ligands. The density function theory (DFT) and chemical absorption, distribution, metabolism, excretion, and toxicity (ADMET) parameters for the chosen ligands were evaluated to comprehend the pharmacokinetics, drug-likeness properties, and bioreactivity of the ligands. The precise interaction mechanism was explored using computational methods such as molecular docking and molecular dynamics (MD) simulation studies to assess the inhibitory effect and the stability of the interactions against the protein of interest. Escitalopram oxalate exhibited a comparatively significant docking score (-7.4 kcal/mol) compared to the control JMS-053 (-6.8 kcal/mol) against the PRL-3 protein. The 2D interaction plots exhibited an array of hydrophobic and hydrogen bond interactions. The findings of the ADMET forecast confirmed that it adheres to Lipinski's rule of five with no violations, and DFT analysis revealed a HOMO-LUMO energy gap of -0.26778 ev, demonstrating better reactivity than the control molecule. The docked complexes were subjected to MD studies (100 ns) showing stable interactions. Considering all the findings, it can be concluded that Escitalopram oxalate and related therapeutics can act as potential pharmacological candidates for targeting the activity of PTP4A3/PRL-3 in HCC.

Ligand-based drug design against Herpes Simplex Virus-1 capsid protein by modification of limonene through in silico approaches

The pharmacological effects of limonene, especially their derivatives, are currently at the forefront of research for drug development and discovery as well and structure-based drug design using huge chemical libraries are already widespread in the early stages of therapeutic and drug development. Here, various limonene derivatives are studied computationally for their potential utilization against the capsid protein of Herpes Simplex Virus-1. Firstly, limonene derivatives were designed by structural modification followed by conducting a molecular docking experiment against the capsid protein of Herpes Simplex Virus-1. In this research, the obtained molecular docking score exhibited better efficiency against the capsid protein of Herpes Simplex Virus-1 and hence we conducted further in silico investigation including molecular dynamic simulation, quantum calculation, and ADMET analysis. Molecular docking experiment has documented that Ligands 02 and 03 had much better binding affinities (- 7.4 kcal/mol and - 7.1 kcal/mol) to capsid protein of Herpes Simplex Virus-1 than Standard Acyclovir (- 6.5 kcal/mol). Upon further investigation, the binding affinities of primary limonene were observed to be slightly poor. But including the various functional groups also increases the affinities and capacity to prevent viral infection of the capsid protein of Herpes Simplex Virus-1. Then, the molecular dynamic simulation confirmed that the mentioned ligands might be stable during the formation of drug-protein complexes. Finally, the analysis of ADMET was essential in establishing them as safe and human-useable prospective chemicals. According to the present findings, limonene derivatives might be a promising candidate against the capsid protein of Herpes Simplex Virus-1 which ultimately inhibits Herpes Simplex Virus-induced encephalitis that causes interventions in brain inflammation. Our findings suggested further experimental screening to determine their practical value and utility.

The role and potential of computer-aided drug discovery strategies in the discovery of novel antimicrobials

Antimicrobial resistance (AMR) has become more of a concern in recent decades, particularly in infections associated with global public health threats. The development of new antibiotics is crucial to ensuring infection control and eradicating AMR. Although drug discovery and development are essential processes in the transformation of a drug candidate from the laboratory to the bedside, they are often very complicated, expensive, and time-consuming. The pharmaceutical sector is continuously innovating strategies to reduce research costs and accelerate the development of new drug candidates. Computer-aided drug discovery (CADD) has emerged as a powerful and promising technology that renews the hope of researchers for the faster identification, design, and development of cheaper, less resource-intensive, and more efficient drug candidates. In this review, we discuss an overview of AMR, the potential, and limitations of CADD in AMR drug discovery, and case studies of the successful application of this technique in the rapid identification of various drug candidates. This review will aid in achieving a better understanding of available CADD techniques in the discovery of novel drug candidates against resistant pathogens and other infectious agents.

Effects of L-ascorbic acid (C6H8O6: Vit-C) on collagen amino acids: DFT study

Vitamin C plays a very important role in the repair of connective tissue, especially for sports whose training causes the most damage to this tissue. Therefore, many people believe that L-ascorbic acid (C6H8O6: vitamin C) reduces the recovery time between sports exercises. The most abundant form of structural protein in the body is collagen. Collagen is characterized by a high concentration of the three amino acids glycine (Gly), proline (Pro), and hydroxyproline (Hyp), which creates its characteristic triple helix structure. Therefore, in this study, the effect of vitamin C presence on the sequence, interaction, and orientation of amino acids for collagen formation is investigated using computational simulation. This study aimed to investigate the mechanism of action of vitamin C in terms of thermodynamics and structure of the reaction. The calculations are performed using density function theory (DFT) by the base set of B3LYP/6-311++G (p,d). The results show that the presence of vitamin C is effective in the formation of collagen protein for this interaction and the mechanism of amino acid sequence (Gly-Hyp-Pro) is better in the formation of collagen protein in the presence of vitamin C. The presence of Vit-C in the formation and direction of hydroxyproline (Hyp) causes its separation from the prolyl 5-hydroxylase enzyme. In the absence of vitamin C, the reaction stops at this stage and proline cannot be converted into hydroxyproline. The computational data shows vitamin C prevents unwanted interactions and directs amino acid reactions to repair connective tissue (collagen). Therefore, vitamin C acts as a cofactor in the Prolyl 5-Hydroxylase enzyme and causes it to convert proline to hydroxyl.

DFT, ADMET and Molecular Docking Investigations for the Antimicrobial Activity of 6,6'-Diamino-1,1',3,3'-tetramethyl-5,5'-(4-chlorobenzylidene)bis[pyrimidine-2,4(1H,3H)-dione]

Heterocyclic compounds, including pyrimidine derivatives, exhibit a broad variety of biological and pharmacological activities. In this paper, a previously synthesized novel pyrimidine molecule is proposed, and its pharmaceutical properties are investigated. Computational techniques such as the density functional theory, ADMET evaluation, and molecular docking were applied to elucidate the chemical nature, drug likeness and antibacterial function of molecule. The viewpoint of quantum chemical computations revealed that the molecule was relatively stable and has a high electrophilic nature. The contour maps of HOMO-LUMO and molecular electrostatic potential were analyzed to illustrate the charge density distributions that could be associated with the biological activity. Natural bond orbital (NBO) analysis revealed details about the interaction between donor and acceptor within the bond. Drug likeness and ADMET analysis showed that the molecule possesses the agents of safety and the effective combination therapy as pharmaceutical drug. The antimicrobial activity was investigated using molecular docking. The investigated molecule demonstrated a high affinity for binding within the active sites of antibacterial and antimalarial proteins. The high affinity of the antibacterial protein was proved by its low binding energy (-7.97 kcal/mol) and a low inhibition constant value (1.43 µM). The formation of four conventional hydrogen bonds in ligand-protein interactions confirmed the high stability of the resulting complexes. When compared to known standard drugs, the studied molecule displayed a remarkable antimalarial activity, as indicated by higher binding affinity (B.E. -5.86 kcal/mol & Ki = 50.23 M). The pre-selected molecule could be presented as a promising drug candidate for the development of novel antimicrobial agents.