Synthesis and analysis of novel catecholic ligands as inhibitors of catechol-O-methyltransferase.

l-DOPA, a dopamine precursor, is commonly used as a treatment for patients with conditions such as Parkinson's disease. This therapeutic l-DOPA, as well as the dopamine derived from l-DOPA, can be deactivated via metabolism by catechol-O-methyltransferase (COMT). Targeted inhibition of COMT prolongs the effectiveness of l-DOPA and dopamine, resulting in a net increase in pharmacological efficiency of the treatment strategy. Following the completion of a previous ab initio computational analysis of 6-substituted dopamine derivatives, several novel catecholic ligands with a previously unexplored neutral tail functionality were synthesized in good yields and their structures were confirmed. The ability of the catecholic nitriles and 6-substituted dopamine analogues to inhibit COMT was tested. The nitrile derivatives inhibited COMT most effectively, in agreement with our previous computational work. pKa values were used to further examine the factors involved with the inhibition and molecular docking studies were performed to support the ab initio and experimental work. The nitrile derivatives with a nitro substituent show the most promise as inhibitors, confirming that both the neutral tail and the electron withdrawing group are essential on this class of inhibitors.

Propargylglycine-based antimicrobial compounds are targets of TolC-dependent efflux systems in Escherichia coli.

A library of novel l-propargylglycine-based compounds were designed and synthesized with the goal of inhibiting the growth of Gram-negative bacteria by targeting LpxC, a highly conserved Gram-negative enzyme which performs an essential step in the lipid A biosynthetic pathway. These compounds were designed with and without a nucleoside and had varying tail structures, which modulate their lipophilicity. The synthetic scheme was improved compared to previous methods: a methyl ester intermediate was converted to a hydroxamic acid, which obviated the need for a THP protecting group and improved the yields and purity of the final compounds. Antimicrobial activity was observed for non-nucleoside compounds containing a phenyl propargyl ether tail (5) or a biphenyl tail (6). An MIC of 16 µg/mL was achieved for 6 in Escherichia coli, but inhibition was only possible in the absence of TolC-mediated efflux. Compound 5 had an initial MIC >160 µg/mL in E. coli. Enhancing outer membrane permeability or eliminating efflux reduced the MIC modestly to 100 µg/mL and 80 µg/mL, respectively. These results highlight the importance of hydrophobicity of this class of compounds in developing LpxC inhibitors, as well as the design challenge of avoiding multidrug efflux activity.

Design, Modeling and Synthesis of 1,2,3-Triazole-Linked Nucleoside-Amino Acid Conjugates as Potential Antibacterial Agents.

Copper-catalyzed azide-alkyne cycloadditions (CuAAC or click chemistry) are convenient methods to easily couple various pharmacophores or bioactive molecules. A new series of 1,2,3-triazole-linked nucleoside-amino acid conjugates have been designed and synthesized in 57-76% yields using CuAAC. The azido group was introduced on the 5'-position of uridine or the acyclic analogue using the tosyl-azide exchange method and alkylated serine or proparylglycine was the alkyne. Modeling studies of the conjugates in the active site of LpxC indicate they have promise as antibacterial agents.

Pairwise Additivity and Three-Body Contributions for Density Functional Theory-Based Protein-Ligand Interaction Energies.

The prediction of protein-ligand binding energies is crucial in computer-assisted drug design. This property can be calculated in a straightforward fashion as the difference in the energies between a binding site-ligand complex and the separated binding site and ligand. Often, though, there is value in knowing how different amino acid residues in the protein binding site interact with the ligand. In this case, the interaction energy can be calculated as the sum of pairwise energies between each amino acid residue in the binding site and the ligand, and the sum of these energies is often equated with the total interaction energy. The validity of this pairwise additivity approximation can be assessed by experimental evidence, such as double-mutant cycles. In this work, we test the pairwise additivity approximation on the sulfotransferase-l-DOPA complex for 16 density functional theory (DFT) methods with varying degrees of exact (Hartree-Fock) exchange. Several "families" of functionals are studied, including BLYP, B3LYP, and CAM-B3LYP, as well as M06L, M06, and M062X. We also calculate the three-body contributions to interaction energy for the same DFT methods and assess when they are significant. We find that the amount of exact exchange or other nonlocal contributions has a direct influence on how closely the sum of pairwise energies approximates the total interaction energy. We also find that three-body interactions can be significant and that their significance can be predicted with good accuracy.

Investigating Paracetamol's Role as a Potential Treatment for Parkinson's Disease: Ab Initio Analysis of Dopamine, l-DOPA, Paracetamol, and NAPQI Interactions with Enzymes Involved in Dopamine Metabolism.

Recently, it was found that paracetamol can extend the therapeutic window of l-DOPA treatment for Parkinson's disease [Golding (2019) BJPharm, 4(2), Article 619]. It has been posited that the effect could be due to paracetamol and its metabolite, NAPQI, inhibiting pain signals in the spinal column. In this work, we examine the possibility that the therapeutic effect of the paracetamol for the Parkinson's disease patient may be due to an inhibition of the enzymes that metabolize dopamine and/or l-DOPA, thus effectively extending the lifetime of the l-DOPA treatment. In this work, we use the M062X/6-311+G* level of theory to calculate the electronic binding energies (including explicit desolvation) of several ligands (paracetamol, NAPQI, dopamine, and l-DOPA) with a series of enzymes important to the production and metabolism of dopamine and compare them to calculated binding energy values for the natural substrates for those enzymes in order to predict possible inhibition. Benchmark interaction energies for a subset of the systems studied are calculated using the more accurate second-order Møller-Plesset perturbation (MP2) method in order to calibrate the accuracy of the M062X method. If we assume that the interaction energies calculated here can serve as a proxy for in vivo inhibition, then we can predict that paracetamol and NAPQI should not inhibit the natural production of dopamine and may in fact inhibit the metabolism of l-DOPA and dopamine, thus extending the length of l-DOPA treatments.

The importance of aromatic-type interactions in serotonin synthesis: protein-ligand interactions in tryptophan hydroxylase and aromatic amino acid decarboxylase.

The biosynthesis of serotonin requires aromatic substrates to be bound in the active sites of the enzymes tryptophan hydroxylase and aromatic amino acid decarboxylase. These aromatic substrates are held in place partially by dispersion and induction interactions with the enzymes' aromatic amino acid residues. Mutations that decrease substrate binding can result in a decrease in serotonin production and thus can lead to depression and related disorders. We use optimized crystal structures of these two enzymes to examine pair-wise electronic interaction energies between aromatic residues in the active sites and the aromatic ligands. We also perform in silico mutations on the aromatic residues to determine the change in interaction energies as mutations occur. Our second-order Moller-Plessett perturbation theory calculations show that drastic changes in interaction energy can occur and, in light of our previous work, we are able to use these data to offer predictions on the loss of protein function and on the possibility of disease upon mutation. We also examine local and gradient corrected density functional theory methods to evaluate their ability to predict these induction/dispersion-dominated interaction energies. We find that the hybrid B3LYP cannot model these interactions well, whereas the GGA HCTH407 offers largely qualitatively correct results, and the local functional SVWN quantitatively mimics the MP2 results rather well.

Interaction energies between tetrahydrobiopterin analogues and aromatic residues in tyrosine hydroxylase and phenylalanine hydroxylase.

The phenylalanine residues 300 and 309 in the enzyme tyrosine hydroxylase are known to aid in the positioning and binding of tetrahydrobiopterin (BH4) to the enzyme active site. The residues phenylalanine 254 and tyrosine 325 similarly aid in binding BH4 in phenylalanine hydroxylase. BH4 is a cofactor necessary for enzyme function, and mutations in these residues have been shown to cause a decrease in enzyme function. We examine the pairwise interactions between each aromatic residue and BH4 using second-order Moller Plesset theory and density functional theory to determine the amount of binding due to these aromatic residues. Further, we perform in silico point mutations of these residues to determine if several likely mutations can cause a decrease in protein function. Our results show that dispersion dominates these interactions, and electrostatics alone is not enough to bind the BH4.

Examination of tyrosine/adenine stacking interactions in protein complexes.

The π-stacking interactions between tyrosine amino acid side chains and adenine-bearing ligands are examined. Crystalline protein structures from the protein data bank (PDB) exhibiting face-to-face tyrosine/adenine arrangements were used to construct 20 unique 4-methylphenol/N9-methyladenine (p-cresol/9MeA) model systems. Full geometry optimization of the 20 crystal structures with the M06-2X density functional theory method identified 11 unique low-energy conformations. CCSD(T) complete basis set (CBS) limit interaction energies were estimated for all of the structures to determine the magnitude of the interaction between the two ring systems. CCSD(T) computations with double-ζ basis sets (e.g., 6-31G*(0.25) and aug-cc-pVDZ) indicate that the MP2 method overbinds by as much as 3.07 kcal mol(-1) for the crystal structures and 3.90 kcal mol(-1) for the optimized structures. In the 20 crystal structures, the estimated CCSD(T) CBS limit interaction energy ranges from -4.00 to -6.83 kcal mol(-1), with an average interaction energy of -5.47 kcal mol(-1), values remarkably similar to the corresponding data for phenylalanine/adenine stacking interactions. Geometry optimization significantly increases the interaction energies of the p-cresol/9MeA model systems. The average estimated CCSD(T) CBS limit interaction energy of the 11 optimized structures is 3.23 kcal mol(-1) larger than that for the 20 crystal structures.

Aromatic interactions in the binding of ligands to HMGCoA reductase.

3-Hydroxy-3-methyglutaryl-coenzyme A (HMGCoA) reductase is the enzyme that catalyzes the rate-determining step in cholesterol synthesis; it is also the target for statin drugs, which are competitive inhibitors of the enzyme. We examine potentially important enzyme-ligand interactions currently not incorporated into statin drug design: weak, induction/dispersion interactions between ligands and residue tyrosine 479 in the HMGCoA reductase active site. HMGCoA is a large molecule with a long coenzyme A "tail", and in order to study the interactions of interest, it was necessary to find the smallest possible portion of the HMGCoA molecule that would serve as a reasonable model for the entire molecule. Using this minimal model, we calculated BSSE-corrected electronic interaction energies between the residue and the ligand molecule using several DFT methods (local, hybrid, and gradient-corrected DFT methods) as well as MP2. We also performed several in silico mutations of the tyrosine 479 residue to determine the potential effects of these changes on protein-ligand interaction energies. Our work shows that this previously unexploited protein-ligand interaction between tyrosine residue 479 and HMGCoA can be important in the design of future statin drugs. Per our previous work, our results show that local DFT methods more closely match MP2 energy values for aromatic binding than do hybrid or gradient-corrected DFT methods.

Non-Born-Oppenheimer molecular structure and one-particle densities for H2D+.

We show that the nonadiabatic (non-Born-Oppenheimer) ground state of a three-nuclei system can be effectively calculated with the use of an explicitly correlated Gaussian basis set with floating centers. Sample calculations performed for the H2D+ system with various basis set sizes show good convergence with respect to both the total energy and the expectation values of the internuclear distances (molecular geometry), the distances between the nuclei and the electrons, and between the electrons. We also provide a derivation of the formulas for one-particle density calculations and some density plots showing the spatial distribution of the H2D+ nuclear and electronic densities.

Nonadiabatic Calculations of the Dipole Moments of LiH and LiD.

We present very high-accuracy fully nonadiabatic calculated values for the dipole moments for the ground states of LiH and LiD. These results were calculated via numerical differentiation of the energy obtained at different electric field strengths. The values for the energy were obtained from variational optimization with analytical gradients of the wave function expanded in a basis of explicitly correlated floating s-type Gaussian functions. The values obtained for LiH and LiD, 2.3140 and 2.3088 a.u., are nearly identical to those obtained by experiment.

Non-Born-Oppenheimer isotope effects on the polarizabilities of H2.

We present non-Born-Oppenheimer quantum-mechanical calculations of the behavior of isolated molecules of the H2 isotopomer series in static electric fields. Some conceptual aspects of such calculations are discussed. The values for polarizabilities and hyperpolarizabilities of the H2 isotopomers which we present are the first ever fully nonadiabatic calculated values of these properties.