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.

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.

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.

The domain interface method in non-conforming domain decomposition multifield problems

The Domain Interface Method (DIM) is extended in this contribution for the case of mixed fields as encountered in multiphysics problems. The essence of the non-conforming domain decomposition technique consists in a discretization of a fictitious zero-thickness interface as in the original methodology and continuity of the solution fields across the domains is satisfied by incorporating the corresponding Lagrange Multipliers. The multifield DIM inherits the advantages of its irreducible version in the sense that the connections between non-matching meshes, with possible geometrically non-conforming interfaces, is accounted by the automatic Delaunay interface discretization without considering master and slave surfaces or intermediate surface projections as done in many established techniques, e.g. mortar methods. The multifield enhancement identifies the Lagrange multiplier field and incorporates its contribution in the weak variational form accounting for the corresponding consistent stabilization term based on a Nitsche method. This type of constraint enforcement circumvents the appearance of instabilities when the Ladyzhenskaya-Babuška-Brezzi (LBB) condition is not fulfilled by the chosen discretization. The domain decomposition framework is assessed in a large deformation setting for mixed displacement/pressure formulations and coupled thermomechanical problems. The continuity of the mixed field is studied in well selected benchmark problems for both mixed formulations and the objectivity of the response is compared to reference monolithic solutions. Results suggest that the presented strategy shows sufficient potential to be a valuable tool in situations where the evolving physics at particular domains require the use of different spatial discretizations or field interpolations.

The domain interface method: a general-purpose non-intrusive technique for non-conforming domain decomposition problems

A domain decomposition technique is proposed which is capable of properly connecting arbitrary non-conforming interfaces. The strategy essentially consists in considering a fictitious zero-width interface between the non-matching meshes which is discretized using a Delaunay triangulation. Continuity is satisfied across domains through normal and tangential stresses provided by the discretized interface and inserted in the formulation in the form of Lagrange multipliers. The final structure of the global system of equations resembles the dual assembly of substructures where the Lagrange multipliers are employed to nullify the gap between domains. A new approach to handle floating subdomains is outlined which can be implemented without significantly altering the structure of standard industrial finite element codes. The effectiveness of the developed algorithm is demonstrated through a patch test example and a number of tests that highlight the accuracy of the methodology and independence of the results with respect to the framework parameters. Considering its high degree of flexibility and non-intrusive character, the proposed domain decomposition framework is regarded as an attractive alternative to other established techniques such as the mortar approach.

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.

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.

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.

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.

Implementing an incontinence program in long-term care settings. A multidisciplinary approach

Urinary incontinence is a prevalent and costly problem in long-term care settings. Impaired bladder function can cause many physical and social problems, such as impaired skin integrity, falls, and altered psychological well-being. Fortunately, there are several low-risk interventions that can cure or improve continence status in many individuals, regardless of cognitive status. Basic assessment of medical and environmental status, as outlined in this article, can assist staff in determining transient conditions which often alter bladder control. Because many interventions are dependent on mobility, dexterity, and diet, an interdisciplinary approach is ideal.

Breast feeding and acute lower respiratory infection

The association between breast feeding and acute lower respiratory infection (ALRI) was studied in a case-control study in southern Italy. Two groups of children were studied: the first group comprised 73 infants, aged 0-6 months, whose diagnosis was pneumonia or bronchiolitis; the second group included 88 infants less than 12 months of age with a diagnosis of pertussis-like illness. Control infants were two groups of infants admitted to the same ward. Compared with controls, infants in the first group were less likely to have been breast fed (odds ratio 0.42, 95% CI 0.19-0.90). The protection conferred by breast feeding was stronger among infants who were receiving human milk at the time of admission (odds ratio 0.22, 95% CI 0.09-0.55) and was absent among those infants who had stopped breast feeding for two or more weeks before admission. Among infants who were severely ill, breast feeding was less likely than among those with milder illnesses. There was evidence in the stratified analysis of effect modification by the presence of other children in the family. Among the infants with pertussis-like illness, the incidence and duration of breast feeding were not different compared with controls. The results suggest that breast feeding has a strong protective effect against ALRI in industrialized countries also. No protection seems to be conferred by human milk against pertussis-like illness.

[The efficacy of creatine phosphate in the treatment of patients with heart failure. Its echographic evaluation after acute and protracted treatment]

The hemodynamic effects of acute and long-term administration of creatine phosphate were studied in 23 patients with heart failure (NYHA classes II and III) under stabilized treatment. Acute creatine phosphate (5 g i.v.) induced a significant increase of the ejection fraction (FE) and of other parameters of cardiac contractility. Once these improvements of cardiac contractility were obtained by acute treatment, further significant increases in cardiac function were observed if treatment was continued for six days, i.e. telesystolic diameter and volume, as well as parietal stress were significantly reduced, and ejection fraction and shortening fraction were significantly increased. Creatine phosphate treatment has a favourable influence on the hemodynamics of patients with an obvious contractility deficit and chronic ischemia of the myocardium.

[Role of magnesium in cardiovascular pathology]

In the first part of the paper the Authors give an up-to-date analysis of our current knowledge of magnesium metabolism, its relation with other electrolytes (namely sodium, potassium, calcium) and clinical symptoms due to its deficiency. The Authors then focus their attention on the relations between magnesium and cardiovascular pathologies and underline the role which magnesium deficiency may play in the onset of various forms of coronary artery disease: preinfarction angina, myocardial infarction, threatening ventricular arrhythmia and sudden death.

Antenatal and perinatal care in southern Italy. I. The mothers' reports

A population-based cross-sectional study of antenatal and perinatal care was performed in Campania, a region of southern Italy. One thousand three hundred women who had given birth in 1982 were interviewed. The number of antenatal visits was very low, less than 1% of the mothers having attended more than three times during pregnancy. The women at high obstetric risk did not attend more than those at low risk and certain aspects of their antenatal care were unsatisfactory. The place of birth was similar for high risk and low risk mothers, with 40% delivering in small private facilities (with few neonatal resuscitation facilities and often with inadequate infant transport services). The labour was induced or accelerated in 60% of the mothers. The organisation of perinatal care did not take into account many of the needs of the mothers such as presence of a relative at delivery, ambulation during labour, early relationship with the newborn, rooming-in, or encouragement to breastfeed.

Antenatal and perinatal care in southern Italy. II. The clinicians' reactions

One hundred obstetricians and 50 paediatricians engaged in public antenatal and perinatal care in southern Italy were interviewed about the provision of care in their facilities: 93% of the obstetricians judged the coverage of the target population to be insufficient and 53% of them considered the use of the risk approach to be unsatisfactory in public clinics. For example, no initiative was taken by 60% of public clinics when a woman at high risk failed to attend a booked antenatal visit. Bed rest during labour was prescribed by 72% of the obstetricians, a supporting relative was admitted to only 18% of the births and routine episiotomy was performed in 77% of primigravidae. Only 56% of the paediatricians interviewed allowed early contact between mother and baby. In public hospitals, 80% of paediatricians were present in the delivery room for the births. Screening for congenital hypothyroidism and phenylketonuria was executed in only 37% of the public hospitals. Newborn transport system adequate to national standards was available in only 33% of the hospitals. Antenatal and perinatal care need to be rapidly improved to meet population needs in southern Italy.

Organization of human class I homeobox genes

We report the genomic organization of 20 human class I homeoboxes and the predicted primary sequence of the encoded homeodomains. These homeoboxes are clustered in four complex HOX loci on chromosomes 2, 7, 12, and 17. The homeoboxes of one HOX locus can be aligned to the homeoboxes of the other HOX loci so that corresponding homeodomains in all loci can share the maximal peptide sequence identity. This correspondence of individual homeoboxes in different chromosomal loci suggests the hypothesis of large-scale duplications of a single complex locus. The existence of an ancestral complex locus might have predated the divergence of vertebrates and invertebrates.

The proposal of the Italian Committee on Occupational Cardiology

This paper describes a protocol of assessing specific working fitness of post-myocardial infarction patients proposed by the Italian Committee on Occupational Cardiology. After cardiovascular (cross-sectional echocardiography, Holter monitoring and maximal symptom-limited ergometric test) and psychological evaluation (CBA-2.0), two ambulatory ECGs were used during work to confirm the first judgement of specific work fitness expressed by occupational specialists. The preliminary results obtained in 106 uncomplicated male patients (mean age 49 +/- 8 years) show that: (i) return to work (89.6%) at 117 +/- 51 days after the acute event is mainly related to socio-occupational variables rather than to cardiovascular status; (ii) the results of the ambulatory monitoring usually confirm the first judgment of specific work fitness; (iii) heart rate responses recorded during work are unrelated to the judgment of fitness; and (iv) the repeatability of the results observed during the two ambulatory ECGs at work is good.

[Psychometric evaluation of the psychoemotional stability in patients considered suitable for heart transplant]

The main purpose of this study was to make an objective assessment of emotional stability as a selection criterion in 14 heart transplant candidates (13 M, 1 F, 45.5 +/- 6.6 years). A psychometric study was conducted using Cognitive Behavioral Assessment (CBA 2.0 Primary-Scale Battery) and the Beck Depression Inventory. The main results of this study were the identification of: a) emotionally unstable patients (42%) who did not respond to the above mentioned selection criterion; b) stable psychological traits such as hostility, aloofness, extroversion as described in type A Behavior Pattern and c) the presence of secondary alexitimic responses suggesting a protective denial of the meaning of the disease. The psychometric method used seems useful in the selection of heart transplant candidates, however, a follow-up can better define the range of emotional stability.

[Dynamic electrocardiographic evaluation of the circadian rhythms of the ectopic ventricular beats in healthy and cardiopathic subjects]

The 24 hour study was carried out on 34 subjects, 17 cardiopathy 13 male and 4 female, mean age 56 +/- 14) and 17 normal (10 male and 7 female, mean age 41 +/- 18) with, on average, over 30 PVC/h in the dynamic ECG: no statistically significant difference in mean PVC/h was recorded between the two groups. Single cosinor analysis demonstrated a statistically significant circadian rhythm (p less than 0.05) in 11 cardiopathic (64.7%) and 13 normal subjects (76.4%). Population mean cosinor failed to demonstrate a significant rhythm in either of the two groups. Results suggest that personal circadian rhythms should be studied to identify the most appropriate antiarrhythmic treatment.

[Long-term clinical study of a new molecule (nifedipine) in ischemic cardiopathy]

Results with a new anti-angina molecule (nifedipine: Adalat) in the long-term management of 28 patients with ischaemic heart disease are presented. The effectiveness of the drug was judged outstanding on the strength of its reduction of angina outstanding on the strength of its reduction of angina crises and consumption of NTG beads. Non side-effects were noted.