Uracil Mustard Research Articles

Comprehensive quantum chemical calculations and molecular docking analysis of uracil mustard by first principle

Uracil mustard belongs to the nitrogen mustard family and is primarily used in anticancer drugs. The research that follows, investigates many quantum chemical features such as the computation of global minimum energies with no negative wavenumber values using the Density Functional Theory (DFT) with Becke three functional and 6-311G (d, p)/6–311++G (d, p) basis sets. All the vibrational modes have been calibrated and justified in comparison to their experimental counterparts. Mustard's polarizability and hyperpolarizability components, Natural Bond Analysis (NBO), electronic properties, Fukui function analysis, various global parameters, Quantum Theory of Atoms In Molecule (QTAIM) analysis, ADMET analysis, and docking analysis have all been investigated using the same theory and basis sets, indicating its biochemical significance. The biological activity of the molecule is reported by using PASS software. The Full fitness score and binding affinity parameters are utilized to determine the binding strength with 6cq3 protein. The acidity of the title molecule is calculated in water solvent by polarizable continuum model (PCM) solvent effects (estimated in water). The HOMO, LUMO, and MESP plots are used to explore the nature of binding and surfaces. The Fukui functions are computed using Mulliken atomic charges for neutral atoms, cations, and anions. The Ultraviolet–visible (UV–vis) of the molecule is computed employing the TD-DFT method.

Molecular Docking and Dynamics Investigations for Identifying Potential Inhibitors of the 3-Chymotrypsin-like Protease of SARS-CoV-2: Repurposing of Approved Pyrimidonic Pharmaceuticals for COVID-19 Treatment.

This study demonstrates the inhibitory effect of 42 pyrimidonic pharmaceuticals (PPs) on the 3-chymotrypsin-like protease of SARS-CoV-2 (3CLpro) through molecular docking, molecular dynamics simulations, and free binding energies by means of molecular mechanics–Poisson Boltzmann surface area (MM-PBSA) and molecular mechanics–generalized Born surface area (MM-GBSA). Of these tested PPs, 11 drugs approved by the US Food and Drug Administration showed an excellent binding affinity to the catalytic residues of 3CLpro of His41 and Cys145: uracil mustard, cytarabine, floxuridine, trifluridine, stavudine, lamivudine, zalcitabine, telbivudine, tipiracil, citicoline, and uridine triacetate. Their percentage of residues involved in binding at the active sites ranged from 56 to 100, and their binding affinities were in the range from −4.6 ± 0.14 to −7.0 ± 0.19 kcal/mol. The molecular dynamics as determined by a 200 ns simulation run of solvated docked complexes confirmed the stability of PP conformations that bound to the catalytic dyad and the active sites of 3CLpro. The free energy of binding also demonstrates the stability of the PP–3CLpro complexes. Citicoline and uridine triacetate showed free binding energies of −25.53 and −7.07 kcal/mol, respectively. Therefore, I recommend that they be repurposed for the fight against COVID-19, following proper experimental and clinical validation.

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 Original Research Article Bartzatt; JCTI, 2(2): 50-58, 2015; Article no.JCTI.2015.007 51 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 Angstroms 2 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.

Alkylation of DNA by nitrogen mustards: A DFT study

Reactivity of aziridinium ion and mono- as well as cross-linked adducts formed during alkylation of DNA (GC base pair) by nitrogen mustards were analysed, using density functional theory (DFT). DFT based global- and local reactivity descriptors were used to compare reactivity of the aziridinium ion intermediates and mono-adducts. Our results witnessed the inability of global reactivity parameters to explain higher reactivity of mustine. Out of the chosen set of seven drug molecules, propensity of cross-linked adduct formation by uracil mustard was observed to be highest compared to other family members. Electrophilic Fukui function was found to be useful in explaining the local reactivity pattern. Gibbs free energy of solvation for the second aziridinium ions were observed to be higher compared to that of the first aziridinium ions.

Design, synthesis, and biological activity of hybrid compounds between uramustine and DNA minor groove binder distamycin A.

The design, synthesis, characterization, DNA binding properties, and cytotoxic activity of a novel series of hybrids, namely, a molecular combination of the natural antibiotic distamycin A and the antineoplastic agent uramustine, are reported, and the structure-activity relationships are discussed. This homologous series 29-34 consisted of the minor groove binder distamycin A joined to uramustine (uracil mustard) by suitable aliphatic carboxylic acid moieties containing a flexible polymethylene chain that is variable in length [(CH(2))(n)(), where n = 1-6). All the hybrid compounds in this series exhibit enhanced activity compared to both distamycin A and uramustine derivatives 22-27 used for conjugation, giving IC(50) values in the range 7.26-0.07 microM following a 1 h exposure of human leukemic K562 cells, with maximal activity shown when n = 6. The distance between the uramustine and distamycin frame is crucial for the cytotoxicity, with compounds having linker lengths of four to six being at least 20-fold more cytotoxic than linker lengths one to three. Taq polymerase stop experiments demonstrated selective covalent binding of uramustine-distamycin hybrids to A/T rich DNA sequences, which was again more efficient with compounds 32-34 with a longer linker length. Two consequences can be derived from our study: (a) the distamycin moiety directs binding to the minor groove of A/T rich DNA sequences and, consequently, is responsible for the alkylation regioselectivity found in footprinting studies; (b) the higher flexibility due to a longer linker between the distamycin and uracil moieties allows the formation of complexes with the mustard moiety situated more deeply in the minor groove and, hence, with better alkylating properties.

Uracil mustard revisited

A patient with diffuse large cell lymphoma who had a complete response lasting 35 years following a 3-day course of uracil mustard stimulated a recall review of patients treated with this oral alkylating agent. Records of patients treated with uracil mustard between 1958 and 1970 were reviewed. A current histologic review according to the International Formulation was performed when possible. Total doses of uracil mustard were similar to those of mechlorethamine, although there were variations in the dose schedule. Employing criteria used over 25 years ago to evaluate patients' responses, the overall regression rate for 94 non-Hodgkin lymphoma patients was 69.2% (complete response [CR] 23.4%). Of 62 patients with Hodgkin disease, 69.4% responded (CR 9.7%). For 39 patients with chronic lymphatic leukemia, the combined complete and partial response rate was 74% (CR 7.7%). Thrombocytopenia was the primary toxicity. Uracil mustard is an unmarketed, inexpensive oral alkylating agent that has been effective in the treatment of patients with lymphoma, chronic lymphatic leukemia, and thrombocythemia. Perhaps it should be reevaluated.

Excision of DNA adducts of nitrogen mustards by bacterial and mammalian 3-methyladenine-DNA glycosylases.

Nitrogen mustards are among the DNA alkylating agents most widely used in chemotherapy. The homogeneous Escherichia coli AlkA protein (3-methyladenine-DNA glycosylase II) is shown to excise damaged guanine and adenine bases from DNA modified by mechlorethamine, uracil mustard, phenylalanine mustard and chlorambucil, and less efficiently acridine mustard adducts. Homogeneous recombinant human and rat 3-methyladenine-DNA glycosylases excise adducts formed by nitrogen mustards less efficiently than the AlkA protein. In addition to the in vitro excision of adducts, the AlkA protein eliminates cytotoxic mechlorethamine adducts from DNA in vivo.

The effects of a benzoic acid mustard derivative of distamycin a (FCE 24517) and related minor groove-binding distamycin analogues on the activity of major groove-binding alkylating agents

The distamycin derivative FCE 24517 is a potent antitumour agent. Efforts have been made towards elucidating the mechanism of action of this compound which, to date, have highlighted a high level of DNA sequence specificity for covalent adduct formation. Compared to classical alkylating agents, FCE 24517 forms very few covalent adducts with double-stranded DNA, and thus appears to be a weak alkylating agent. Examination of the effects of this minor groove-binding agent on the major groove of DNA have been facilitated by use of the alkylating agents mustine, melphalan, dabis maleate, quinacrine mustard and uracil mustard. Pretreatment of plasmid DNA with FCE 24517 followed by reaction with any one of these mustards gave rise to a marked abolition of N-7 guanine adduct formation, as assayed by Maxam and Gilbert sequencing gels. The smallest effect was seen for quinacrine mustard, whereas total abolition of N-7 guanine alkylation was seen with uracil mustard. Using related structural analogues of FCE 24517 in the same experiments, it was not possible to reproduce this effect, with very few exceptions. Some effects were seen when using distamycin A itself in these experiments, although these were marginal compared to those seen for FCE 24517. We were able to extrapolate our findings to a whole cell system using murine L-1210 leukaemia cells. Alkaline elution experiments showed that treatment of cultured cells with FCE 24517 followed by either mustine or uracil mustard caused a marked inhibition of DNA interstrand crosslink formation, compared to treatment with mustine or uracil mustard alone. The present study has demonstrated the marked effect that FCE 24517 has upon the reactivity of double-stranded DNA, an effect possibly separate from that of its alkylating function. This study has highlighted the complex nature of the DNA interactive compound FCE 24517 which possesses potent and broad spectrum antitumour activity.

An application of 3D-QSAR to the analysis of the sequence specificity of DNA alkylation by uracil mustard.

The sequence specificity of DNA alkylation by uracil mustard was examined using a novel three-dimensional QSAR method known as HASL, or the hypothetical active site lattice. The structures of a variety of 4-mer sequences obtained from pBR322 and SV40 were related to their degree of guanine-N7 alkylation by uracil mustard. The resulting correlations were found to point to a significant contribution from bases on the 3' side of the target guanine nucleotide. The HASL models derived from the analysis of 52 guanine-containing 4-mer sequences were used to highlight those atomic features in the favored TGCC sequence that were found most important in determining specificity. It was found that the NH2-O systems present in the two GC base pairs on the 3' side of the target guanine were significantly correlated to the degree of alkylation by uracil mustard. This finding is consistent with a prealkylation binding event occurring between these sites along the major groove and the uracil mustard O2/O4 system.

DNA sequence selectivity of guanine-N7 alkylation by nitrogen mustards is preserved in intact cells.

Nitrogen mustard alkylating agents react with isolated DNA in a sequence selective manner, and the substituent attached to the drug reactive group can impose a distinct sequence preference. It is not clear however to what extent the observed DNA sequence preferences are preserved in intact cells. The highly reiterated sequence of human alpha DNA has been used to determine the sites of guanine-N7 alkylation following treatment of cells with three nitrogen mustards, mechlorethamine, uracil mustard and quinacrine mustard, known to react in isolated DNA with distinctly different sequence preferences. Alpha DNA from drug treated cells was extracted, purified, end-labeled, and a 296 base pair, singly end-labelled, fragment isolated. Following the quantitative conversion of alkylation sites to strand breaks the fragments were separated on DNA sequencing gels. Clear differences were observed between the alkylation patterns of the three compounds, and the selectivities were qualitatively similar to those predicted and observed in the same sequence alkylated in vitro. In particular the unique preferences of uracil and quinacrine mustards for 5'-PyGC-3' and 5'-GT/GPu-3' sequences, respectively, were preserved in intact cells suggesting that the pattern of sequence dependent reactivity is not grossly affected by the nuclear milieu.

Comparative Pharmacokinetics of DNA Lesion Formation and Removal Following Treatment of L1210 Cells with Nitrogen Mustards

The kinetics of formation and removal of DNA interstrand crosslinks (ISC), DNA-protein crosslinks (DPC), and single strand breaks (SSB) by several nitrogen mustards were compared in order to determine the degree to which lesion selectivity may vary. The kinetic measurements using DNA alkaline elution methodology were obtained in mouse L1210 cells treated with mechlorethamine (HN2), phenylalanine mustard (L-PAM), uracil mustard (UM), 6-methyl-UM, and quinacrine mustard (QM). The ISC or DPC challenge delivered to cells was gauged on the basis of the kinetics as either total ISC or DPC produced, or as the area under the lesions versus time curve (AUC). By either measure (excepting QM), ISC correlated well with loss of colony survival, whereas DPC did not. The ISC/DPC ratio may therefore be a useful index of lesion selectivity. This ratio was significantly greater for 6-methyl-UM than for HN2. The ratio was also greater for L-PAM than for HN2 but only when gauged by AUC; this was attributable to an unusually slow rate for ISC removal in the case of L-PAM. The preferential reaction of UM at some 5'-GC-3' sites in purified DNA had suggested that UM might produce ISC with increased efficacy. UM, however, was somewhat less efficacious in ISC production than was 6-methyl-UM, which lacked selectivity for alkylation at 5'-GC-3'. QM was the only compound that produced detectable SSB, and the SSB were so numerous that ISC could not be quantitated.(ABSTRACT TRUNCATED AT 250 WORDS)

Synthesis and Murzne P388 Antitumor Activity of Uridine Mustard: A Preliminary Report

Abstract 5′-[Bis (2—chloroethyl) amino]—5′-deoxy uridine (uri-dine mustard), compound 5, was synthesized and characterized by its 1H, 13 C, and two-dimensional homonuclear shift correlated (COSY) and two—dimensional heteronuclear correlated NMR spectra. In comparative murine studies, uridine mustard was substantially less leukopenic than the equitherapeutic dose of uracil mustard.

Effect of ionic strength and cationic DNA affinity binders on the DNA sequence selective alkylation of guanine N7-positions by nitrogen mustards

Large variations in alkylation intensities exist among guanines in a DNA sequence following treatment with chemotherapeutic alkylating agents such as nitrogen mustards, and the substituent attached to the reactive group can impose a distinct sequence preference for reaction. In order to understand further the structural and electrostatic factors which determine the sequence selectivity of alkylation reactions, the effect of increased ionic strength, the intercalator ethidium bromide, AT-specific minor groove binders distamycin A and netropsin, and the polyamine spermine on guanine N7-alkylation by L-phenylalanine mustard (L-Pam), uracil mustard (UM), and quinacrine mustard (QM) was investigated with a modification of the guanine-specific chemical cleavage technique for DNA sequencing. For L-Pam and UM, increased ionic strength and the cationic DNA affinity binders dose dependently inhibited the alkylation. QM alkylation was less inhibited by salt (100 mM NaCl), ethidium (10 microM), and spermine (10 microM). Distamycin A and netropsin (100 microM) gave an enhancement of overall QM alkylation. More interestingly, the pattern of guanine N7-alkylation was qualitatively altered by ethidium bromide, distamycin A, and netropsin. The result differed with both the nitrogen mustard (L-Pam less than UM less than QM) and the cationic agent used. The effect, which resulted in both enhancement and suppression of alkylation sites, was most striking in the case of netropsin and distamycin A, which differed from each other. DNA footprinting indicated that selective binding to AT sequences in the minor groove of DNA can have long-range effects on the alkylation pattern of DNA in the major groove.

Molecular aspects of carcinogenesis. Part B

Nitrogen mustards represent a major group of alkylating agents that are used in the chemotherapy of cancer. It is commonly accepted that they exert their cytotoxic effects by their ability to produce interstrand crosslinks in DNA. The main target site of the two identical alkylating moieties is the N-7 position of guanine. By a Maxam-Gilbert-type reaction it is possible to identify "hot spots" for alkylation by nitrogen mustards. Analysis of data obtained reveal the importance of the DNA context for efficient alkylation. For most of~ the compounds the highest reactivity is observed ila regions of G clusters, while in the neighbourhood of cytosine residues alkylation is reduced. As a consequence intrastrand rather than interstrand crosslinks would be the major DNA lesions resulting from exposure to those agents. In contrast, uracil mustard and quinacrine mustard differ from the other nitrogen mustards with respect to their alkylaltion specificity. Although both of them, like the other compounds, preferentially react with the N-7 of D-guanosine, their efficiency is determined by specific interactions with the DNA. In the case of uracil mustard this causes a sequence preference for 5'-Y-G-C-3', and it should thus be superior at producing interstrand crosslinks. Since the substituent attached to the alkylating group of the drug can alter the DNA sequence preference for the reaction it may be possible to design new agents to optimise the selectivity of reaction with critical DNA sequences.

Degradation and Disposal of some Antineoplastic Drugs

Bulk quantities and pharmaceutical preparations of the antineoplastic drugs carmustine (BCNU), lomustine (CCNU), chlorozotocin, N-[2-chloroethyl]-N′-[2,6-dioxo-3-piperidinyl]-N-nitrosourea (PCNU), methyl CCNU, mechlorethamine, melphalan, chlorambucil, cyclophosphamide, ifosfamide, uracil mustard, and spiromustine may be degraded using nickel-aluminum alloy in KOH solution. The drugs are completely destroyed and only nonmutagenic reaction mixtures are produced. Destruction of cyclophosphamide in tablets requires refluxing in HCI before the nickel-aluminum alloy reduction. Streptozotocin, chlorambucil, and mechlorethamine may be degraded using an excess of saturated sodium bicarbonate solution. The nitrosourea drugs BCNU, CCNU, chlorozotocin, PCNU, methyl CCNU, and Streptozotocin were also degraded using hydrogen bromide in glacial acetic acid. The drugs were completely destroyed but some of the reaction mixtures were mutagenic and the products were found to be, in some instances, the corresponding mutagenic, denitrosated compounds.

DNA sequence selectivity of guanine-N7 alkylation by nitrogen mustards.

Nitrogen mustards alkylate DNA primarily at the N7 position of guanine. Using an approach analogous to that of the Maxam-Gilbert procedure for DNA sequence analysis, we have examined the relative frequencies of alkylation for a number of nitrogen mustards at different guanine-N7 sites on a DNA fragment of known sequence. Most nitrogen mustards were found to have similar patterns of alkylation, with the sites of greatest alkylation being runs of contiguous guanines, and relatively weak alkylation at isolated guanines. Uracil mustard and quinacrine mustard, however, were found to have uniquely enhanced reaction with at least some 5'-PyGCC-3' and 5'-GT-3' sequences, respectively. In addition, quinacrine mustard showed a greater reaction at runs of contiguous guanines than did other nitrogen mustards, whereas uracil mustard showed little preference for these sequences. A comparison of the sequence-dependent variations of molecular electrostatic potential at the N7-position of guanine with the sequence dependent variations of alkylation intensity for mechlorethamine and L-phenylalanine mustard showed a good correlation in some regions of the DNA, but not others. It is concluded that electrostatic interactions may contribute strongly to the reaction rates of cationic compounds such as the reactive aziridinium species of nitrogen mustards, but that other sequence selectivities can be introduced in different nitrogen mustard derivatives.

Inhibitory effects of 5-(2-pyrazinyl)-4-methyl-1,2-dithiol-3-thione (Oltipraz) on carcinogenesis induced by benzo[a]pyrene, diethylnitrosamine and uracil mustard.

5-(2-Pyrazinyl)-4-methyl-1,2-dithiol-3-thione (Oltipraz) was studied for its capacity to inhibit carcinogen-induced neoplasia in female ICR/Ha mice. When administered by oral intubation 48 h prior to benzo[a]pyrene (BP), also given by oral intubation, Oltipraz inhibited the occurrence of pulmonary adenomas and tumors of the forestomach. The ratio of the number of tumors occurring in the mice receiving Oltipraz to that of the corresponding controls was: lung, 0.36 and forestomach 0.38. Inhibition also occurred when Oltipraz was given p.o. 24 h prior to BP. In other experiments, oral administration of Oltipraz 48 h prior to p.o. administration of diethylnitrosamine or uracil mustard inhibited pulmonary adenoma formation but to a lesser extent than with BP as the carcinogen. The low toxicity of Oltipraz found previously, coupled with evidence of protective effects against chemically diverse carcinogens, suggests that this compound should be studied further for its possible use as an agent for the chemoprevention of neoplasia.

Qualitative and quantitative analysis of uracil anticancer drugs

Two uracil anticancer drugs can be selectively identified and estimated by means of two colour reactions. 5-Fluorouracil is treated with bromine water in borax medium, and then with 2,4-dinitrophenylhydrazine in acidic medium to give an orange-red precipitate which produces a distinctly violet solution when treated with potassium hydroxide solution. Uracil mustard, containing alkylating groups, is heated with α-picoline in aqueous solution. The quaternary salt thus produced is condensed in alkaline medium with sodium 1,2-naphthoquinone-4-sulphonate, giving a pink colour. The possibility of using these colour tests for the determinations of these anticancer drugs in pure and dosage forms has been studied.

Uracil Mustard in the Treatment of Thrombocytosis

Uracil mustard was used for the treatment of thrombocytosis in 14 patients, eight who had polycythemia vera and six who had essential thrombocytosis. Intermittent treatment with 1 to 2 mg/day for 14 days was used for most patients, and continuous treatment was used for three patients. The nadir of the platelet count occurred during a mean period of five to seven weeks, and the mean duration between courses was seven months. The drug selectively depressed the platelet count, with a minimal effect on leukocytes and erythrocytes. Uracil mustard is an effective drug for the control of thrombocytosis.

Uracil mustard in the treatment of thrombocytosis

Uracil mustard in the treatment of thrombocytosis