Quantum Mechanical Assessment of Protein-Ligand Hydrogen Bond Strength Patterns: Insights from Semiempirical Tight-Binding and Local Vibrational Mode Theory.

Hydrogen bonds (HB)s are the most abundant motifs in biological systems. They play a key role in determining protein-ligand binding affinity and selectivity. We designed two pharmaceutically beneficial HB databases, database A including ca. 12,000 protein-ligand complexes with ca. 22,000 HBs and their geometries, and database B including ca. 400 protein-ligand complexes with ca. 2200 HBs, their geometries, and bond strengths determined via our local vibrational mode analysis. We identified seven major HB patterns, which can be utilized as a de novo QSAR model to predict the binding affinity for a specific protein-ligand complex. Glycine was reported as the most abundant amino acid residue in both donor and acceptor profiles, and N-H⋯O was the most frequent HB type found in database A. HBs were preferred to be in the linear range, and linear HBs were identified as the strongest. HBs with HB angles in the range of 100-110°, typically forming intramolecular five-membered ring structures, showed good hydrophobic properties and membrane permeability. Utilizing database B, we found a generalized Badger's relationship for more than 2200 protein-ligand HBs. In addition, the strength and occurrence maps between each amino acid residue and ligand functional groups open an attractive possibility for a novel drug-design approach and for determining drug selectivity and affinity, and they can also serve as an important tool for the hit-to-lead process.

Papaya Leaf Extracts as Potential Dengue Treatment: An In-Silico Study.

Dengue fever (DF), dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS) cause serious public health problems, with nearly 390 million people affected and 20,000 deaths per year in tropical and subtropical countries. Despite numerous attempts, no antiviral drug or vaccine is currently available to combat the manifestation. The challenge of discovering an efficient vaccine is enhanced by the surplus presence of efficient vectors and drug resistance from the virus. For centuries, papaya (Carica papaya) extracts have been traditionally used to treat DF, DHF, and DSS. In the present study, we systematically investigated seven compounds isolated from papaya leaf extract with regard to their potential as inhibitors for non-structural (NS) proteins, NS3 and NS5, which play a crucial role in viral RNA replication. The computational tools applied stretched across classical molecular docking, molecular dynamics (MD) simulations and SwissADME used to calculate binding affinities; binding free energies; Absorption, Distribution, Metabolism, and Excretion (ADME); and drug-likeness properties, thus, identifying Kaempferol, Chlorogenic acid, and Quercetin as potential candidates, with Kaempferol and Quercetin scoring best. Therefore, for the Kaempferol and Quercetin complexes, hybrid quantum mechanical/molecular mechanical (QM/MM) geometry and frequency calculations were performed, followed by the local mode analysis developed in our group to quantify Kaempferol-NS and Quercetin-NS hydrogen bonding. Given the non-toxic nature and the wide availability of the Kaempferol and Quercetin papaya extract in almost all of the susceptible regions, and our results showing high NS3 and NS5 binding affinities and energies, strong hydrogen bonding with both NS3 and NS5, and excellent ADME properties, we suggest Kaempferol and Quercetin as a strong NS3 and NS5 inhibitor to be further investigated in vitro.