Measuring the Alkylation Kinetics and Drug Likeness of Four Candidate Antineoplastic Compounds

Aims: To synthesize small molecule alkylating compounds and analyze the kinetics of the alkylation in aqueous solution. Determine molecular properties and the drug likeness of these four compounds as potential antineoplastic agents and apply statistical analysis to identify interrelationships of properties. Study Design: Four compounds were synthesized, characterized, and studied for alkylation capability. The alkylation kinetics were elucidated, as well as drug likeness properties. The interrelationships of properties were examined by statistical methodology. Place and Duration of Study: Department of Chemistry, Durham Science Center, University of Nebraska at Omaha, Omaha NE, from May 2015 to June 2015. Methodology: Four compounds were modified by the covalent bonding of an alkyl halide substituent or nitrogen mustard group. The four compounds were placed in aqueous solution at pH 7.4 and 37°C to monitor alkylation efficiency that targeted p-chloroaniline. Alkylation was monitored utilizing fluorescamine and measurement at 400 nm. Time and absorbance plots determined whether alkylation step is first-order or second-order. Molecular properties Log P, formula weight, polar surface area, etc., were determined. Statistical analysis and path analysis revealed which molecular property was most responsible for rate constant values. Results: Compounds A, B, C, and D showed ranges of Log P, formula weight, and polar surface area of 0.010 to 4.21, 177.59 to 714.77, and 29.64 to 88.63, respectively. All compounds showed a favorable drug likeness, with only compound C showing a violation of the Rule of 5. The Log P values and number of alkylation reactive sites were most responsible for rate constant value. Conclusion: Small molecule alkylating agents are synthesized, the efficiency of alkylation measured in aqueous solution utilizing fluorescamine at pH 7.4 and 37°C. Rate-order of reactions is determined utilizing fluorescamine assay for surviving primary amine groups. The four compounds showed a favorable drug likeness based on molecular properties

Potential Antineoplastic Structural Variations of Uracil Mustard (Uramustine) Retaining Cytotoxic Activity and Drug-likeness Suitable for Oral Administration

Aims: To present 12 new variants of uracil mustard having drug-like properties and cytotoxic functional group, by utilizing uracil mustard (uramustine) as a lead compound. Utilize rigorous substructure and similarity of a molecular scaffold to determine drug like variants. Physicochemical properties determined indicate the variants have favorable drug-likeness. Study Design: Conduct molecular database search utilizing features of substructure and similarity based upon uracil mustard. Place and Duration of Study: Department of Chemistry, Medicinal Chemistry Study Section, University of Nebraska at Omaha, Omaha Nebraska between January 2015 to March 2015. Methodology: Uracil mustard consists of the pyrimidine derivative uracil, having the bifunctional nitrogen mustard cytotoxic moiety covalently bonded onto the ring. A systematic search, utilizing substructure component and similarity, within an in-silico database search successfully determined 12 variants. Rigorous criteria for drug-likeness was implemented to screen potential candidates that included the application of the Rule of 5. In addition, maintaining the cytotoxic moiety of nitrogen mustard was crucial. Results: A total of 12 variants of uracil mustard was identified after an extensive molecular database search using rigorous criteria. All 12 variants, and including uracil mustard, showed zero violations of the Rule of 5, thereby indicating favorable drug-likeness. Values of polar surface area for all compounds at less than 80 Angstroms2 are suitable for central nervous system penetration. Polar surface area, number of atoms, and Log P for all compounds increased as the molecular weight increases. Structure substituents include nitrogen mustard groups, hydroxyl, alkyl and carbonyl moieties. Cluster analysis discerned greatest similarity among members of this group. Conclusion: Applying rigorous search criteria within a molecular data base, for comparison and reject, successfully identified 12 variants of uracil mustard that show favorable drug-likeness in addition to cytotoxic capability. The design of new antitumor agents is important for increasing efficacy of the clinical treatment of cancer

Evaluation of a Simple Carrier Molecule to Enhance Drug Penetration of Dermal Layers by Utilizing Multivariate Methods, Structure Property Correlations, and Continuous System Modeling

Nicotinic acid is shown to be comparable to dihydropyridine in its capacity to facilitate penetration of an attached antibacterial drug through dermal layers. Antibacterial drugs examined with nicotinic acid or dihydropyridine carriers were b-lactam antibiotics: methicillin, oxacillin, benzylpenicillin, penicillin F, penicillin dihydro F, propicillin, carbenicillin, penicillin K, penicillin X, and ampicillin. An oxymethyl (-O-CH2-) group is inserted as the linker between the antibiotic and the carrier group. Structure Property Correlations and multivariate methods such as regression analysis, cluster analysis, principal component analysis, discriminate analysis, self-organizing tree algorithm, and factor analysis clearly showed that nicotinic acid performs as an effective carrier drug and is comparable to dihydropyridine. The skin penetration constant Kp was calculated for all 10 antibiotics having either dihydropyridine or nicotinic acid as carrier, and was found to have a mean of 5.13E-05 cm/hour and 1.83E-05 cm/hour, respectively. The standard deviation for each group showed the numerical values overlap as did the 90% confidence interval for each group. A hierarchical tree organization of skin shows the overlapped dermal layers as they exist in normal skin and for the model utilized in this work. A Deming-Regression analysis also shows the nicotinic acid and dihydropyridine structures to have similar and correlated water solubility. Plotting Kp of the dihydropyridine structures as independent variable versus Kp of the nicotinic acid structures show good correlation (Pearson correlation r = 0.6606) and no significant departure from linearity. Connected box plots showed the majority of Kp values for each group of modified antibiotics to exist in a tight cluster. Polar graph of the Log Kow values showed the two groups of modified anti- biotics to be correlated and numerically adjacent in trend. ChemSketch property calculations and modeling demonstrates the affects of structural oxygens, nitrogens, carbonyl groups, amide groups, and aromatic rings that are important in understanding the pervasiveness through dermal layers. Continuous model analysis by acslXtreme is utilized and demonstrates three models of the dispersion of drugs through dermal layers based on diffusivity constant (D), Log Kp from Log Kow and formula weight, and Kp as a function of time

Relative Properties and Relative Potency of Various Hydrazide Compounds That Inhibit Growth of Mycobacterium tuberculosis

The molecular properties of compounds expressing growth inhibition of Mycobacterium tuberculosis are determined and examined for underlying relationships by pattern recognition methods. Pattern recognition methods such as hierarchical cluster analysis will show relationships between compounds. Descriptive statistical analysis of molecular properties reveal commonality among bacteriostatic compounds. Outliers within any category of descriptor is identified by Grubb’s test. Potency of growth inhibition measured as MIC (minimum inhibitory concentration) after in vitro evaluation will be compared and analyzed. Structure moieties and their effect on activity is identified. All compounds analyzed showed substantial growth inhibition of Mycobacterium tuberculosis, having MIC values ranging from 16.7 μgrams/milliliter to 65.9 μgrams/milliliter (isoniazid MIC at 14.7 μgrams/milliliter). Ranges in values of Log P, number of atoms, and molecular weight were, respectively: -1.89 to 1.10, 11 to 25 (isoniazid at 10), and 150.18 grams/mole to 345.38 grams/mole (isoniazid at 137.14). All eight compounds and isoniazid showed favorable bioactivity within six categories of measureable bioactivity scores. The molecular properties of eight compounds and isoniazid varied, however, remained favorable in drug-likeness with zero violations of the Rule of 5. Interrelationships of the descriptors were revealed by statistical analysis

Determination of barbituric acid, utilizing a rapid and simple colorimetric assay

Barbituric acid is widely used in the manufacturing of plastics, textiles, polymers, and pharmaceuticals. Three assay methods are presented, which can utilize either aqueous or solid samples. The detection of as little as 10 μg of barbituric acid can be accomplished, either as an aqueous or solid sample, when using micro reaction tubes. The red–violet endpoint is easily discerned and results upon the formation of a violuric acid derivative. A Spot Test protocol is described which allows for a positive/negative indication of barbituric acid presence. The Spot Test is sensitive to as little as 18.75 μg/ml of barbituric acid. The construction of a Standard Curve for assaying multiple samples and over longer time periods is demonstrated, and is shown to be linear from 18.75 μg/ml to 2.25 mg/ml of barbituric acid. Spectrophotometer readings are made from an absorption peak appearing at 530 nm. The molar absorptivity of the violuric acid derivative is calculated to be 31.4 per mol/l per cm. The micro reaction tube assay will quantitate as little as 10 μg of barbituric acid through interpolation with controls containing a known amount of analyte. Inorganic salts such as NaCl, NaN3, LiBr, and CaCO3 do not interfere with endpoint determination. Many organic compounds (also pharmaceuticals) do not inhibit the reaction

Pyrimethamine Based Anti-protozoan Agents from Isostere and Heuristic Structure-similarity Search

Aims: To generate new medicaments for control and treatment of the parasitic protozoan Toxoplasma gondii. Study Design: Structure similarity search and isostere search was conducted over a broad range of structure categories. Correlation and highest similarity scores were implemented to select the best drug candidates. Place and Duration of Study: University of Nebraska, Department of Chemistry, Durham Science Center, 6001 Dodge Street, Omaha Nebraska 68182, from June 2016 to February 2017. Methodology: Utilizing pyrimethamine as the parent compound, a broad range of similar structures and isosteres were found by applying search methods. The compounds having the highest correlation and similarity scores were selected for the study of molecular properties. The molecular properties were determined and examined for underlying relationships by pattern recognition hierarchical cluster analysis and K-means cluster analysis. Results: Thirty compounds were identified to have a very high level of structure similarity or isosteric relationship to pyrimethamine. The molecular structures and molecular properties are presented for all compounds, inclusive of pyrimethamine. Hierarchical cluster analysis and K-means cluster analysis indicated compounds with highest underlying similarity to pyrimethamine. Box plots showed the over-all distribution of important pharmaceutical properties, such as molecular weight, Log P, polar surface area, number of rotatable bonds, molecular volume, and number of hydrogen bond donors. Structure components are compared to elucidate potential clinical activity. Multiple regression is applied on all compounds to generate a numerical relationship for prediction of similar compounds. Save for only one isostere, all compounds showed zero violations of the Rule of 5, indicating favorable drug-likeness and bioavailability. Conclusion: Thirty compounds highly analogous to pyrimethamine were identified following heuristic search course. The molecular properties were determined for all compounds and indicated genuine potential for treatment of toxoplasmosis. Correlation of structure and pattern recognition methods indicated 30 compounds of clinical potential and property analogy to pyrimethamine

Neurological Impact of Zinc Excess and Deficiency In vivo

Zinc is an essential mineral that can cause pathological effects whether in excess or deficiency. Zinc is a component for over 250 enzymes and is required for cell growth, cell division, and cell function. Zinc is found in muscle and bones, with the prostrate, liver, skin, and kidney having detectable levels of zinc. However, zinc present in excess or deficiency can cause significant pathology in patients that include deleterious effects neurologically. Zinc in excess in vivo can cause focal neuronal pathology, while zinc deficiency can bring about mental lethargy, neuropsychiatric disorders, and reduced nerve conduction. Zinc is assimilated within the body by oral ingestion, dermal exposure, and pulmonary inhalation. Although not generally viewed as a cause of cancer, studies suggest that zinc is associated with progression of prostate malignancy. Toxic levels of zinc have been shown to induce lethargy, neurotoxicity, and gliotoxicity. High levels of zinc causes neuronal death in cortical cell tissue culture. Zinc is known to accumulate following the death of neurons in global ischemia. Therefore, zinc deficiency or excess is of significant clinical concern

Potency and Properties of Hydrazide Compounds That Inhibit the Growth of Mycobacterium tuberculosis

Aims: To examine the properties of hydrazide compounds shown to inhibit Mycobacterium tuberculosis. To identify properties that affect efficiency of bacterial inhibition. Study Design: Utilizing data from previous studies of compounds that inhibit Mycobacterium tuberculosis, then statistical and pattern recognition methods are applied to identify interrelationships. Place and Duration of Study: Department of Chemistry, Durham Science Center, University of Nebraska at Omaha, from January 2016 to July 2016. Methodology: Interrelationships of pharmacological properties were identified by use of various pattern recognition techniques, such as hierarchical cluster analysis and path analysis. Molecular properties and descriptors for all compounds were determined, with additional characteristics such as structure scaffolding and functional group position was accomplished. Statistical analysis, including Pearson r correlation, Mann-Whitney test, one-way ANOVA, Kruskal-Wallis, and descriptive statistics were determined. Multiple regression analysis of molecular property values allows prediction of similar compounds. Determination of any numerical outliers was accomplished by applying Grubb’s test. Results: Mycobacterium tuberculosis inhibiting compounds contained either an aromatic ring or were non-aromatic structures (no ring). There was weak negative correlation of MIC to formula weight. The average formula weight, polar surface area, and Log P, is 183.55 grams/mole, 63.70 A2, and 0.768, respectively. Values of MIC ranged from 14.7 µg/mL to 100 µg/mL. Extent of bacterial inhibition was similar between aromatics to non-aromatics. No outliers were identified by Grubb’s test for all values of MIC taken together. Path analysis showed polar surface area to have most effect on MIC. Conclusion: The measured level of growth inhibition MIC, showed strong positive relationship to polar surface area, number of hydroxyl and amine groups, oxygen and nitrogen atoms. Two aromatic compounds having a pyridine ring were found to be most similar to isoniazid. Aromatic and non-aromatic compounds showed similar levels of bacterial inhibition overall

Spectrophotometric and colorimetic methodology to detect and quantify hydrazide based chemotherapeutic drugs

Pharmaceuticals having the hydrazide functional group are an important division within anti-tuberculosis, anti-parasitic, anti-cancer, and anti-radiation chemotherapeutics. This work presents a colorimetric methodology to detect and quantify hydrazide based pharmaceuticals. Processes for rapid spot test, qualitative colorimetric assay, and spectrophotometric quantitative assay are presented. The reagent 2,6-dichloroquinon-4-chloroimine (Gibb\u27s reagent) is utilized to accomplish the various analytical objectives. The rapid spot test and qualitative colorimetric assay enables a detection of hydrazide drugs to a level of 0.0037 grams per milliliter. Quantitative spectrophotometric detection of hydrazide drugs is sensitive to a level of 128.2 micrograms permilliliter. The molar absorptivity () is calculated to be 25.32 Liters/(molexcm) at 970nm. Inorganic salts and organic compounds were found not to interfere with colorimetric detection of hydrazide drugs, and this includes NaBr, NaCl, MgSO4, 2-naphthol, benzoin, p-aminobenzoic acid various other compounds. Reagents necessary for this methodological approach are readily available. The colorimetric response of these tests is readily identified by visual inspection. These methods then are highly sensitive and provide a manner to determine this important type of drugs from environmental as well as biological origins

Prediction of Novel Anti-Ebola Virus Compounds Utilizing Artificial Neural Network (ANN)

Artificial Neural Network (ANN) analysis is shown to predict the molecular properties of new anti-EBOLA compounds following training/learning by use of 60 previously known and studied drugs. Following training/learning by applying properties of 60 known drugs the TIBERIUS ANN system can efficiently predict the molecular properties of comparable new drugs. Molecular weight (MW) is an important and dominant property of perspective drugs considered for clinical trials. TIBERIUS ANN was able to predict comparable values of MW for drugs following training cycles. One-way ANOVA, F and T tests indicate that actual and predicted MW have the same means (P=.99). Passing-Bablok regression showed that ANN predicted MW are comparable to actual MW. The coefficient of variation indicated actually less variation in predicted MW as opposed to actual MW. A plot of actual MW values versus ANN predicted MW values, produced a line having no departure from linearity (P=.82), and a 95% ellipses having 55 drugs therein. TIBERIUS ANN allows investigators to input separate property values to predict suitable outcome based on the 60 known drugs. ANN prediction of pharmaceutical properties of new drugs is shown to be efficient and accurate when based on a known set of drugs for training/learning cycle