[Clinical analysis of corneal interface infection]

Objective: To analyze the clinical features of corneal interface infection. Methods: A retrospective case series study was conducted to explore the clinical features of interstitial corneal infection. The data of eight patients (eight eyes) who were diagnosed with interstitial corneal infection after undergoing corneal transplant or corneal refractive surgery and visited Beijing Tongren Eye Center from January to December 2018 were collected, including two male and six female patients aged between 18 and 55 years (median age, 27 years). The patients' general information, surgical type, onset time, and clinical manifestations were recorded. The lesions were examined by in vivo corneal laser confocal microscopy (IVCM), and microbial cultures and drug sensitivity tests were performed. Results: Among the 8 patients, 4 had undergone small-incision lenticule extraction (SMILE), 2 had undergone lamellar keratoplasty, and 2 had undergone endothelial keratoplasty. The onset of infection occurred between 2 and 30 days after surgery, with a mean of 9.8 days. Among the 3 patients who had undergone SMILE, the treatment outcome was corneal haze or opacity, while the remaining 5 cases required corneal transplantation for interstitial infections. The pathogens of the 4 cases of interstitial infection after corneal transplantation were all Candida species. Under the IVCM, patients with corneal interstitial bacterial infections showed a large amount of necrotic tissue with no normal tissue structure in the corneal stroma, with infiltration of inflammatory cells and local aggregation of inflammatory cells, but no typical pathogen was observed. Patients with fungal infections showed fungal hyphae under the corneal cap (filamentous fungal infection) or dense, punctate, high-reflection structures in the corneal interstitial space (yeast-like fungal infection). Conclusions: Corneal interlayer infection is difficult to diagnose early and has a poor prognosis. IVCM can assist in early diagnosis. The pathogen spectrum of corneal interlayer infection may differ from that of corneal infection caused by trauma.

[Analysis of clinical manifestations and imaging characteristics of in vivo confocal microscopy for Nocardia keratitis]

Objective: To analyze the clinical manifestations and imaging characteristics of in vivo confocal microscopy (IVCM) for Nocardia keratitis. Methods: It was a retrospective case series study. Medical records of 16 consecutive patients (16 eyes) with Nocardia keratitis were collected from the Department of Ophthalmology at Beijing Tongren Hospital, Capital Medical University between 2018 and 2022. The group consisted of 11 males and 5 females. The inclusion criteria for the study were the presence of typical clinical manifestations of Nocardia keratitis and at least one positive pathogenic test (corneal scraping or microbial culture) indicating Nocardia infection. The medical history, clinical and microbiological examination data of the patients were analyzed, including risk factors, diagnosis time, clinical manifestations, diagnostic methods, strain isolation, cure time, and best corrected visual acuity before and after treatment. This study utilized techniques such as slit lamp microscopy, in vivo confocal microscopy (IVCM), scraping cytology, microbial culture, and mass spectrometry identification. Results: The main risk factors for Nocardia keratitis included plant or foreign body injuries (5 out of 16 cases), contact lens use (4 out of 16 cases), and surgery (2 out of 16 cases). The average time to diagnosis was (20.8±11.8) days, with the shortest time being 8 days and the longest being 60 days. The best corrected visual acuity was less than 0.05 in 7 patients, between 0.05 to 0.3 in 7 patients, and greater than or equal to 0.3 in 2 patients. The typical symptoms included superficial gray-white infiltration in a wreath-like pattern on the cornea, corneal ulcers with dry and gray-white necrotic tissue coverage, and in severe cases, corneal ulcer perforation. Nocardia corneal infection was identified in 12 out of 16 cases by scraping cytology, 9 out of 16 cases by mass spectrometry, and 8 out of 16 cases by both methods. IVCM showed the presence of fine and moderately reflective filamentous hyphae in the subepithelial and superficial stromal layer of the cornea, arranged in elongated, beaded, and branched structures. Infiltration of many hyper-reflective round inflammatory cells was also seen around the hyphae. Fourteen cases were treated with medication and 2 cases were treated with corneal transplantation. The average cure time was (37.5±25.2) days and there were no cases of recurrence during the follow-up period (all greater than 6 months). Conclusions: Nocardia keratitis is primarily characterized by dense, round, or wreath-like infiltration in the early stage, and by gray-white dry necrotic secretion and hypopyon on the surface of corneal ulcers in the middle and late stages. Fine, branched or beaded, and moderately reflective filamentous structures are the hallmark of the corneal lesion on the IVCM images.

[Mechanism of combined treatment of rhein and emodin in Rhubarb for ulcerative colitis]

This study aimed to explore the efficacy and mechanism of combined rhein and emodin in the treatment of ulcerative colitis(UC) from the aspects of network pharmacology, animal inflammation improvement and molecular mechanism. Network pharmacology predicted that combined rhein and emodin acted on 52 potential targets, mainly participating in signaling pathways such as cancer, PI3 K/AKT, microRNAs in cancer and apoptosis. PI3 K/AKT signaling pathway has been reported to be closely related to UC, and the optimal candidate pathway for combined therapy. The UC mice model was established by dextran sodium sulfate, and then the modeled mice were randomly divided into control group, model group, rhein group, emodin group, rhein+emodin group and sulfasalazine group. After administration, compared with the conditions in model group, body weight, disease activity index(DAI) score, colon length, TNF-α, IL-6, IL-1β and myeloperoxidase(MPO) of mice in rhein+emodin group were improved(P<0.01); colonic mucosal injury was significantly reduced; the expression of p-PI3 K/PI3 K and p-AKT/AKT proteins were down-regulated(P<0.01). All the above indices were better than those in the rhein/emodin group alone. The Jin's Q-values of the effect of combined rhein and emodin on colon length, TNF-α, IL-6, IL-1β, MPO, p-PI3 K/PI3 K and p-AKT/AKT were all greater than 1.15, which indicated that there was obvious synergistic effect between rhein and emodin. In all, rhein and emodin have synergistic effect in the treatment of UC, and the mechanism may be related to the inhibition of PI3 K/AKT signaling pathway and the down-regulation of proinflammatory factors. They are the new components in the treatment of UC, which is worthy of attention.

Characterization of nitrilases from Variovorax boronicumulans that functions in insecticide flonicamid degradation and β-cyano-L-alanine detoxification

AIMS

To characterize the functions of nitrilases of Variovorax boronicumulans CGMCC 4969 and evaluate flonicamid (FLO) degradation and β-cyano-L-alanine (Ala(CN)) detoxification by this bacterium.

METHODS AND RESULTS

V. boronicumulans CGMCC 4969 nitrilases (NitA and NitB) were purified and substrate specificity assay indicated that both of them degraded insecticide FLO to N-(4-trifluoromethylnicotinoyl)glycinamide (TFNG-AM) and 4-(trifluoromethyl)nicotinol glycine (TFNG). Ala(CN), a plant detoxification intermediate, was hydrolyzed by NitB. Escherichia coli overexpressing NitA and NitB degraded 41.2 and 93.8% of FLO (0.87 mmol·L^-1 ) within 1 h, with half-lives of 1.30 and 0.25 h, respectively. NitB exhibited the highest nitrilase activity toward FLO. FLO was used as a substrate to compare their enzymatic properties. NitB was more tolerant to acidic conditions and organic solvents than NitA. Conversely, NitA was more tolerant to metal ions than NitB. CGMCC 4969 facilitated FLO degradation in soil and surface water and utilized Ala(CN) as a sole nitrogen source for growth.

CONCLUSIONS

CGMCC 4969 efficiently degraded FLO mediated by NitA and NitB; NitB was involved in Ala(CN) detoxification.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study promotes our understanding of versatile functions of nitrilases from CGMCC 4969 that is promising for environmental remediation.

[Potential pleiotropism of cancer-related single nucleotide polymorphisms among Chinese population]

Objective: To investigate the potential pleiotropism of cancer-related single nucleotide polymorphisms (SNPs) among Chinese population. Methods: Based on the catalogue of GWAS jointly constructed by the National Human Genome Research Institute and the European Institute of Bioinformatics, according to population origin (Chinese population and non-Chinese population) and disease traits (cancer and non-cancer traits). All SNPs found by GWAS before August 2020 were divided into four categories: cancer in Chinese population, non-cancer in Chinese population, cancer in non-Chinese population and non-cancer in non-Chinese population. The number, correlation and linkage of the four categories of SNPs were described. Results: By August 2020, a total of 196 813 SNPs from 4 096 GWAS were included in the GWAS directory. The information that SNPs refer to unknown or were not related to the disease was excluded, and 117 441 independent SNPs were finally included. There were 619 SNPs related to cancer and 9 569 SNPs related to non-cancer disease in Chinese population, respectively. There were 4 624 SNPs related to cancer and 106 448 SNPs related to non-cancer disease (trait) in non-Chinese population, respectively. Three SNPs, rs2736100, rs6983267 and rs401681, were associated with two or more types of cancer in both Chinese and non-Chinese populations. Seven SNPs, rs7705526, rs2736100, rs10993994, rs2735839, rs4430796, rs174537 and rs9271588, were associated with cancer and non-cancer diseases in both Chinese and non-Chinese populations, respectively. Conclusion: There is a potential pleiotropism of cancer-related SNPs in Chinese population.

[Effect analysis of sequential laser application in treating the hypertrophic scars of burn children at early stage]

Objective: To explore the effects of sequential application of intensive pulsed light and carbon dioxide laser in treating the hypertrophic scars of burn children at early stage. Methods: A retrospective cohort before-after control study in the same patients was conducted. From January 2016 to December 2018, 145 burn children with hypertrophic scar at the early stage who met the inclusion criteria were admitted to the First Hospital of Jilin University, including 82 males and 63 females, aged 1 to 12 (3 (2, 6)) years. All the children were firstly treated with intense pulsed light therapy (no anesthesia or intravenous-inhalation combined anesthesia) at an interval of once per month, and then changed to carbon dioxide laser therapy (topical anesthesia or intravenous-inhalation combined anesthesia) when the degree of scar hyperemia was reduced, at an interval of once every 3 months, for a total of 3 times. Before the first intense pulsed light treatment (hereinafter referred to as before the first treatment) and 3 months after the last carbon dioxide laser treatment (hereinafter referred to as after the last treatment), scar scoring was evaluated by Vancouver Scar Scale (VSS), and scar hyperemia (denoted as hemoglobin level) was measured with Antera 3D^® camera. The times of intense pulsed light, the time of single treatment, the anesthesia method, and the time of intravenous-inhalation combined anesthesia of intense pulsed light and carbon dioxide laser treatment were analyzed. After the last treatment, Likert Scale was used to evaluate the efficacy satisfaction of both doctors and patients. Adverse reactions were recorded during the treatment. Data were statistically analyzed with Wilcoxon signed rank sum test, and paired sample t test. Results: The color, vascular distribution, thickness, and softness scores, and total score in VSS scoring of scars of children after the last treatment were significantly lower than those before the first treatment (Z=-6.05, -10.34, -9.84, -9.28, -10.43, P<0.01). The hemoglobin level of scar of children after the last treatment was 1.86±0.24, significantly lower than 2.27±0.32 before the first treatment (t=17.65, P<0.01). A total of 411 times of intense pulsed light therapy were performed, (2.8±0.6) times per person, and the single treatment time was 35 (20, 45) s. There were 392 times (95.38%) without anesthesia, and 19 times (4.62%) with intravenous-inhalation combined anesthesia with time of 6 (5, 8) min. The single treatment time of carbon dioxide laser therapy was 5 (3, 10) min. There were 364 times (83.68%) of topical anesthesia and 71 times (16.32%) of intravenous-inhalation combined anesthesia with time of 10 (8, 15) min. After the last treatment, the efficacy satisfaction scores of doctors and patients were (4.3±0.7) and (3.8±1.0) points, respectively. Blisters occurred in 5 cases after intense pulsed light treatment, which were healed naturally after drainage. One child developed local skin infection, skin redness and swelling accompanied by purulent exudate after carbon dioxide laser treatment, which was improved after skin disinfection and external use of mupirocin ointment. No inflammatory pigmentation, worsening of hyperplasia of scar, erythema, or other skin adverse reactions or anesthetics-related adverse reactions occurred in any child. Conclusions: Sequential application of intense pulsed light and carbon dioxide laser to treat the hypertrophic scars of burn children at early stage can obviously improve the appearance and texture of scar, with higher satisfaction of doctors and patients and fewer adverse reactions.

A mutational signature associated with alcohol consumption and prognostically significantly mutated driver genes in esophageal squamous cell carcinoma

Background

Esophageal squamous cell carcinoma (ESCC) is often diagnosed at an advanced and incurable stage. Information on driver genes and prognosticators in ESCC remains incomplete. The objective was to elucidate significantly mutated genes (SMGs), mutational signatures, and prognosticators in ESCC.

Patients and methods

Three MutSig algorithms (i.e. MutSigCV, MutSigCL and MutSigFN) and '20/20+' ratio-metric were employed to identify SMGs. Nonnegative matrix factorization was used to decipher mutational signatures. Kaplan-Meier survival analysis, multivariate Cox and logistic regression models were applied to analyze association between mutational features and clinical parameters.

Results

We identified 26 SMGs, including 8 novel (NAV3, TENM3, PTCH1, TGFBR2, RIPK4, PBRM1, USP8 and BAP1) and 18 that have been previously reported. Three mutational signatures were identified to be prevalent in ESCC including clocklike C>T at CpG, APOBEC overactive C>T at TpCp[A/T], and a signature featured by T>C substitution. The T>C mutational signature was significantly correlated with alcohol consumption (OR: 3.59; 95% CI: 2.30-5.67; P < 0.001). This alcohol consumption signature was also observed in liver cancer and head and neck squamous cell carcinoma, and its mutational activity was substantially higher in samples with mutations in TP53. Survival analysis revealed that TENM3 mutations (HR: 5.54; CI: 2.68-11.45; P < 0.001) and TP53 hotspot mutation p.R213* (HR: 3.37; CI: 1.73-8.06; P < 0.001) were significantly associated with shortened survival outcome. The association remained statistically significant after controlling for age, gender, TNM stage and tumor grade.

Conclusions

We have uncovered several new SMGs in ESCC and defined an alcohol consumption related mutational signature. TENM3 mutations and the TP53 hotspot mutation p.R213* are independent prognosticators for poor survival in ESCC.

SOX2 gene expression and its role in triple negative breast cancer tissues

The aim of this work was to study the expression of SOX2 gene in triple negative breast cancer and its role. One hundred and twenty specimens of paraffin-embedded triple negative breast cancer (TNBC) tissues were collected from Harbin Medical University Cancer Hospital, Heilongjiang, China between January 2014 and March 2018. The expression of SOX2 was detected using immunohistochemistry, and the relationship between the expression of SOX2 and clinical features was analyzed. Breast cancer cell lines (normal group, SOX2 interference group, SOX2 overexpression group) were cultured in vitro to detect the proliferation and cloning ability of the cell lines. The expression of SOX2 was related to lymph node metastasis and stage of breast cancer (P less than 0.05), but was not related to age, menopause or tumor size (P > 0.05); the expression of SOX2 in the overexpression group was significantly greater than that in the normal group after 72 hours, and no significant difference between the overexpression group and the interference group was observed. The number of clone cells with a diameter of 0.5 mm in the interference group was lower compared to the normal group, and that of the overexpression group was higher, but not significant. SOX2 is associated with the high invasiveness of breast cancer and can be used as a therapeutic target to inhibit the metastasis of cancer cells. SOX2 can promote the proliferation of breast cancer cells and affect the size of clone cells in its involvement in clone.

Near-Term Decrease in Brain Volume following Mild Traumatic Injury Is Detectible in the Context of Preinjury Volumetric Stability: Neurobiologic Insights from Analysis of Historical Imaging Examinations

BACKGROUND AND PURPOSE

Neurodegeneration after mild traumatic brain injury may manifest as decreasing regional brain volume that evolves from months to years following mild traumatic brain injury and is associated with worse clinical outcomes. We hypothesized that quantitative brain volume derived from CT of the head, performed for clinical indications during routine care, would change with time and provide insights into the putative neuroinflammatory response to mild traumatic brain injury.

MATERIALS AND METHODS

We searched the electronic medical record of our institution for NCCTs of the head performed in patients with mild traumatic brain injury and included those who also underwent NCCTs of the head 1 month to 1 year before and after mild traumatic brain injury for an indication unrelated to trauma. Controls underwent 3 sequential NCCTs of the head with indications unrelated to trauma. The whole-brain and intracranial volume groups were computed using ITK-SNAP. Brain volumes normalized to intracranial volumes were compared across time points using the Wilcoxon signed-rank test.

RESULTS

We identified 48 patients from 2005 to 2015 who underwent NCCTs of the head in the emergency department for mild traumatic brain injury and had NCCTs of the head performed both before and after mild traumatic brain injury. Median normalized brain volumes significantly decreased on the follow-up study post-mild traumatic brain injury (0.86 versus 0.84, P < .001) and were similar compared with pre-mild traumatic brain injury studies (0.87 versus 0.86, P = .927). There was no significant difference between normalized brain volumes in the 48 controls.

CONCLUSIONS

A decrease in brain volume following mild traumatic brain injury is detectable on CT and is not seen in similar patients with non-mild traumatic brain injury during a similar timeframe. Given the stability of brain volume before mild traumatic brain injury, CT volume loss may represent the subtle effects of neurodegeneration.

Twenty-year trends of primary liver cancer incidence rates in an urban Chinese population

The objective of this study was to describe trends in the incidence rates of primary liver cancer in a geographically defined Chinese population. Primary liver cancer cases (N=13 685) were diagnosed between 1981 and 2000 and identified by the Tianjin Cancer Registry. Age-adjusted and age-specific incidence rates were examined in both males and females. Poisson regression was employed to assess the incidence rate trends. Crude and age-adjusted incidence rates in the study period were: 27.4/100 000 and 16.4/100 000 in males and 11.5/100 000 and 6.4/100 000 in females, respectively. While the results from Poisson regression analyses suggest statistically significant trends of declining incidence rates of primary liver cancer overall, trends were not consistent across age and sex groups. The decline in incidence was observed, for the most part, in the 40-69 age group, with a greater decrease in males. Our findings provide a new evidence of a downward trend in incidence rates of this disease in China for a period of 20 years. As the observed decline is relatively small and inconsistent across sex and age groups, a continued epidemiological observation on this condition is required.

A 3D structural model of memapsin 2 protease generated from theoretical study

AIM

To build a 3D structural model of memapsin 2 (M2) protease for theoretical study and drug design.

METHODS

Structural alignment was performed based on multiple and pairwise sequence alignment of three templates. After the initial model was generated, energy minimization was completed by applying molecular mechanics method. Molecular dynamics (MD) technique was used to do further structural optimization.

RESULTS

The 3D structural model of memapsin 2 was constructed. The model is reasonable according to several validation criteria. The active-site motifs of M2 are structurally supported by a beta-sheet rich domain and linked together with this domain through alpha helices. Tyr132 contained in beta-hairpin is a general characteristic of aspartic protease. The Calpha atom superimposing result is a direct verification that M2 is structurally unique but still belongs to the aspartic protease superfamily.

CONCLUSION

The 3D-structure model from our study is informative to guide future molecular biology study about M2 and drug design based on database searching.

Building 3D-structural model of kappa opioid receptor and studying its interaction mechanism with dynorphin A(1-8)

AIM

To construct the 3D-structural model of human kappa opioid receptor (HKOR) and study its interacting mechanism with dynorphin A(1-8) (Dyn8).

METHODS

Comparative molecular modeling was applied to build the 7 transmembrane (TM) helical domain of HKOR using the bovine rhodopsin (OPSD) model as a template. Molecular dynamics was performed to minimize the HKOR model and to simulate the 3D-structure of Dyn8 based on the NMR results of dynorphin A(1-14). The extracellular loops (EL) were built by self-constructed database searching. DOCK4.0 program was performed to construct Dyn8 complex with HKOR.

RESULTS

(1) The model of HKOR was obtained and validated by theoretical and experimental data. (2) The Dyn8-HKOR interacting mechanism is reasonably explained: Side chain of residue Asp138 interacts with protonated nitrogen atom at the N-terminal residues of Dyn8 through electrostatic and hydrogen bonding, which play an important role in ligand binding with receptor. (3) Negatively charged amino acids in the second extracellular loop (EL2) as Asp223 and Glu209 interact with the C-terminal positively charged residues in Dyn8, and Glu209 is a likely determinant of peptide ligand specificity.

CONCLUSION

Some amino acid residues positioned in EL2, TM3, TM4, and TM5 form the binding site and therefore determine the selectivity of kappa peptide agonist.

Building three-dimensional structures of HIV-1 coreceptor CCR5 and its interaction with antagonist TAK779 by comparative molecular modeling

AIM

To study the mechanism of interaction of CCR5 receptor with its antagonist TAK779.

METHODS

Comparative molecular modeling has been used to develop the 3D-structural models of CCR5 receptor and its complex with TAK779. Molecular mechanics has been applied to optimize the above molecular models. Quantum mechanics has been utilized to calculate the structural information of TAK779. DOCK4.0 program is employed to dock the TAK779 molecular into the binding site of CCR5 receptor.

RESULTS

The 3D-structural model of CCR5 receptor is constructed using the 3D-model of frog rhodopsin as a template. The binding pocket is situated in the transmembrane helices 3, 5, 6, and 7, and it is composed of conserved residues of Tyr108, Gly111, Ser114, Glu283, Gly286, and Cys290, and conservatively varied residues including Thr105, Leu107, Phe112, Gly115, Lys197, and Met287. O1, N7, N17, and O19 of TAK779 are the active center of TAK779. The pyran cycle and the aminium group of TAK779 interact with residues in the binding pocket of CCR5 receptor, the other part of TAK779 interacts with residues from the extracellular loops of CCR5. The binding energy of TAK779 with CCR5 is -51.606 kcal/mol.

CONCLUSION

The model constructed and the interaction mode reported in the present study are useful in further understanding the molecular mechanism of receptor-virus recognition and designing new inhibitors of HIV-1 infection.

Comparative molecular modeling on 3D-structure of opioid receptor-like 1 receptor

AIM

To build the three-dimensional structure of opioid receptor-like 1 (ORL1) receptor.

METHODS

Structural elements of ORL1 receptor were predicted from sequence alignments of opioid and related receptors of G protein-coupled receptor (GPCR) based on (i) the consensus, biophysical interpretations of alignment-derived properties, and (ii) tertiary structural homology to frog rhodopsin; The extracellular loops of ORL1 were built by self-constructed database searching based on geometrical constraints; initial model was refined computationally with energy minimization by molecular mechanics method.

RESULTS

The calculated structure of ORL1 receptor has clusters of hydrogen bonds existing in interhelices and extracellular loops; the ORL1 receptor has a possible ligand-binding "crevice" situated on the extraside of the transmembrane domains between helices 3, 5, 6, and 7, which is partially covered by the extracellular loop 2 (EL-2); The binding cavity may consist of a "highly conserved region" involving the residues of Asp130, Tyr131, and an outer "conservatively variable region" containing the residues near the interface of transmembrane (TM) helices-EL loops; The molecular model obtained is qualitatively consistent with ligand affinities, hybrid peptide studies, and other experimental data.

CONCLUSION

The structural model of ORL1 receptor from this study is helpful for clarifying experimental observations of ligands interacting with opioid receptors, and for designing new biological investigations.

Study on mechanism of interaction of nociceptin and opioids binding with opioid receptor-like 1 receptor

AIM

To study the mechanism of interaction of nociceptin and opioids with ORL1 receptor.

METHODS

Molecular dynamics study was carried out before nociceptin was manually docked into the binding site of ORL1 receptor; DOCK4.0 program was applied to dock four stereoisomers of lofentanyl and etorphine into the binding pocket of ORL1 receptor; Binding energies were calculated, the relationship between binding energy and binding affinity was studied.

RESULTS

Nociceptin fits well into the binding pocket, the N-terminal FGGF tetrapeptide is located in the inner region of the binding cavity, the nociceptin (5-7) interacts with the conservatively variable residues near the other end of binding pocket, and maybe determines selectivity of ORL1 receptor over dynorphin A, the positively charged core of nociceptin (8-13) binds predominantly with negatively charged EL-2 loop, which is thought to be able to mediate receptor activation. The shortest fully active analogue of nociceptin (1-13) is also discussed. The main difference between these two opioids and nociceptin exists in the kinds and the number of conserved and variable residues in the binding pocket and thereafter in the strength of their interaction. Prediction for binding affinities of four stereoisomers of lofentanyl has been performed based on their binding energies, the similar pharmacophore of lofentanyl and other fentanyl analogs, and the good correlation between binding energies and their experimental binding affinities (-log Ki values).

CONCLUSION

Ligand docking results from this study are helpful in clarifying experimental observations of ligands interaction with opioid receptors, thus furthering biological investigations.

Molecular modeling on solvent effect and interaction mechanism of fentanyl analogs to mu-opioid receptor

AIM

To do theoretical study about solvation effect and interaction mechanism of fentanyl analogs (FA) to mu opioid receptor (microOR).

METHODS

Flexible docking (FlexiDock) was performed by using the possible active conformations of FA and optimized 3D structure of mu opioid receptor. Binding energies were calculated. Comparative molecular force field analysis (CoMFA) and quantitative structure activity relationship (QSAR) studies were carried out based on results of flexible docking. Solvation effects were considered by studying interaction of FA with water molecules. Partial least square (PLS) analysis was used to calculate regression equation for analgesic activities using binding energies as descriptive factor.

RESULTS

1) Binding conformations of these analogs derived by flexible docking were reasonable. 2) It was most possible for the FA to exist in water solution in the form of binding conformations. 3) Energetic calculation and QSAR analysis showed a good correlation between the calculated binding energies of FA and their analgesic activities. 4) Based on the 3D-model, the possible interaction mechanism of FA with mu opioid receptor can be illustrated reasonably.

CONCLUSION

The nature of the correlation between the binding affinities and analgesic activities of FA was explained by our modeling result.

Antimycoplasmal activities of (S)-(-)-9-fluoro-2,3-dihydro-3-methyl-10 -[4-(2-pyridyl)-1-piperazinyl]-7-oxo-7H-pyrido[1,2,3-de][1,4]benzoxazine -6-carboxylic acid (YH-6) in comparison with other antibiotics in vitro

AIM

To determine the susceptibilities of Mycoplasma and Ureaplasma to (S)-(-)-9-fluoro-2,3-dihydro-3-methyl-10 -[4-(2-pyridyl)-1-piperazinyl]-7-oxo-7H-pyrido[1,2,3-de][1,4]benzoxazine -6-carboxylic acid (YH-6) and to compare it with those referential quinolones, macrolides, and tetracyclines.

METHODS

The minimum inhibitory concentration (MIC) were determined by microdilution method in vitro.

RESULTS

The MIC of YH-6 for Ureaplasma urealyticum (Uu: 250 micrograms.L-1), Mycoplasma hominis (Mh: 500 micrograms.L-1), M orale (Mo: 125 micrograms.L-1) and M salivarium (Ms: 125 micrograms.L-1) were closely similar to those of macrolides (erythromycin and leucomycin) and were 2-8 folds greater than those of ofloxacin (Ofl). Uu and Mh easily induced resistance to erythromycin and tetracycline. They did not easily form resistance to quinolone (YH-6, Ofl), josamycin and tylosin. Tetracycline-resistance (Tcr) or erythromycin-resistance (EMr) strains of Uu (or Mh) had cross-resistance to erythromycin or tetracycline. However, they had no cross-resistance to quinolone, josamycin and tylosin.

CONCLUSION

YH-6 was a highly active quinolone against Mycoplasma, but could hardly induce resistance to Uu. EMr- or Tcr- strains of Uu (or Mh) had no cross-resistance to YH-6.

An enantioselective total synthesis of (+)-geissoschizine

[formula: see text] A concise asymmetric synthesis of the indole alkaloid (+)-geissoschizine (1) has been completed. The synthesis features the highly diastereoselective vinylogous Mannich reaction of 3 with 4 to give 5, which is elaborated into the key tetracyclic intermediate 7 in two steps. Following the stereoselective introduction of the ethylidene moiety to give 9, reduction of the lactam and radical decarboxylation via an acyl selenide gave 12, which was converted into (+)-geissoschizine by formylation. The synthesis requires only 11 chemical operations and proceeds in an overall yield of 17%.

Opioid peptide receptor studies, 11: involvement of Tyr148, Trp318 and His319 of the rat mu-opioid receptor in binding of mu-selective ligands

Previous data obtained with the cloned rat mu opioid receptor demonstrated that the "super-potent" opiates, ohmefentanyl (RTI-4614-4) and its four enantiomers, differ in binding affinity, potency, efficacy, and intrinsic efficacy. Molecular modeling (Tang et al., 1996) of fentanyl derivatives binding to the mu receptor suggests that Asp147, Tyr148, Trp318, and His319 are important residues for binding. According to this model, Asp147 interacts with the positively charged opiate agonist to form potent electrostatic and hydrogen-bonding interactions. In this study, the role of weak electrostatic and hydrogen-bonding "pi-pi" interactions of the O atom of the carbonyl group and the phenyl ring structures of RTI-4614-4 and its four enantiomers with residues Tyr148, Trp318, and His319 were explored via site-directed mutagenesis. Tyr148 (in transmembrane helix 3 {TMH3}), Trp318 (TMH7), and His319 (TMH7) were individually replaced with phenylalanine or alanine. Receptors transiently expressed in COS-7 cells were labeled with [125I]IOXY according to published procedures. Mutation of Tyr148 to phenylalanine reduced the binding affinities of some mu-selective agonists (2-7 fold) but did not alter the affinities of DAMGO, naloxone, and the non-selective opiates etorphine and buprenorphine. In contrast, this mutation significantly increased the binding affinities (decreased the Kd values) of [D-Ala2,D-Leu5]enkephalin, IOXY, and dermorphin. Mutation of Trp318 decreased opioid receptor binding to almost undetectable levels. Substitution of alanine for His319 significantly reduced binding affinities for the opioid ligands tested (1.3- to 48-fold), but did not alter the affinities of naloxone and bremazocine. These results indicate the importance of Tyrl48 and His319 for the binding of fentanyl derivatives to the mu receptor. Functional studies using the mutant receptors will provide additional insight into the mechanism of action of RTI-4614-4 and its four enantiomers.

Molecular modeling on kappa opioid receptor and its interaction with nonpeptide kappa opioid agonists

AIM

To study the interaction between kappa-opioid receptor and its nonpeptide agonists.

METHODS

The "conservation patterns" for G-protein coupled receptors (GPCR) were used to determine 7 transmembrane (TM) regions. Taking the crystallographic coordinates of bacteriorhodopsin (BR) as the template, the 3D structural model was constructed for 7 TM of kappa-opioid subtype with molecular mechanics (MM) method. Five highly active nonpeptide kappa-opioid agonists were docked into the 7 helices of kappa-opioid receptor to study the ligand-receptor interaction.

RESULTS

Four important interactions between U-50488-like agonists and kappa-opioid receptors were drawn according to our modeling study: (1) the protonated pyrrolidine nitrogen of the ligands formed a hydrogen-bond with the carboxyl of Asp138; (2) the carbonyl oxygen of ligands forms a hydrogen bond to the hydroxyl of Ser187; (3) the aryl groups connected to acylamide of the agonists inserted into a hydrophobic cavity enclosed by residues Val239, Val236, Phe235, Val232, Leu186, and Trp183; (4) the pyrrolidine of the ligands in the complexes was surrounded by Ile290, Asp138, Ile194, Ile135, and Cys131.

CONCLUSION

The proposed interaction mechanism is helpful for further mutant experiments and designing novel potent kappa-opioid agonists.

Relationship between structure and anti-oxidation of tocopherol with molecular orbit theory

AIM

To explore the relationship between different structures of tocopherol (Toc) and some phenol compounds and their anti-oxidative activities.

METHODS

Use the ab initio calculation of molecular mechanics and quantum chemistry.

RESULTS

The anti-oxidation of Toc was related to the ability to release active hydrogen, i.e., related to the O-H electron populations, frontier orbital energy (au), and the decreased amount of energy at the reaction ending stage. The order of hydroxyl O-H electron populations in different Toc model molecules were alpha < gamma < or = beta < delta, which was consistent with their anti-oxidation reported.

CONCLUSION

The molecular orbit (MO) theory and the quantum chemical parameters can be used to analyze the anti-oxidation of phenol compounds with different structures.

Establishment of kappa opioid receptor agonists pharmacophore with molecular modeling method

AIM

To build up nonpeptide kappa-opioid receptor agonists pharmacophore.

METHODS

Five structurally diverse, highly active nonpeptide kappa-opioid agonists were retrieved from MDL MDDR database. Molecular mechanics method were used to seek out 50 lower energy conformations for each compound. Taking nitrogen atom of pyrrolidine and acyl acetamide as overlay points, 5 agonists were superimposed to each other with their most favorite conformation. From the overlay map, the structure specificity of nonpeptide kappa-opioid receptor agonists were elucidated.

RESULTS

According to this pharmacophore, the pyrrolidine ring, the carbonyl group of acyl acetamide, and the hydrophobic group attached to acyl acetamide were suggested to be the structure-specific moieties of kappa-opioid agonists. Moreover, by comparing kappa 1-opioid receptor sequence of mouse with other G-protein-coupled receptors, we determined those conserve residues existing on transmembrane regions which might interact with the suggested groups. The carboxyl of Asp138 might interact with N atom of pyrrolidine by forming a hydrogen bond. The hydroxyl of Ser187 and the carbonyl group of kappa-opioid agonists might form another hydrogen bond, which was critical for its kappa selective affinity. The hydrophobic group attached to acyl acetamide might have hydrophobic interaction with aromatic residues of kappa-opioid receptors.

CONCLUSION

These kappa agonists pharmacophore were helpful to select specific positions in the lead compounds to be occupied by hydrophobic moieties to limit their ability to across the blood-brain barrier.

Analysis of electronic structures of physostigmine analogs

AIM

To elucidate the action mechanism and structural prerequisites of 21 physostigmine analogs as acetylcholinesterase inhibitors at the molecular level, and help the rational design of these dihydroindoline inhibitors.

METHODS

Initial structures of these compounds were built and minimized by SYBYL 6.2 molecular modeling software. Conformations of those molecules with the highest predictive abilities in the Comparative Molecular Field Analysis model were chosen to the semiempirical quantum chemical calculations.

RESULTS

(1) The highest occupied molecular orbital (HOMO) consisted mainly of the orbitals in phenyl group and N1 atom; the lowest unoccupied molecular orbital (LUMO) of the molecules was contributed from phenyl group and C11 atom. While the HOMO energies did not show any recognizable relationship with activity, the LUMO energies showed a decreased tendency with increasing activity. The active compounds showed lower LUMO energies. (2) The carbon atom (C11) had the most positive net atom charge. The most active compound had the most positive charge on this carbon, but had the lower charges on the carbonyl oxygen (O12) which was the most negative charge atom. (3) The bond order of carbon-oxygen bond (C11-O10) was invariant across the series of the compounds. (4) Compounds with too high or too low total dipole moment had lower activities, while the most active one had a lower molecular polarizability.

CONCLUSION

A molecular model was suggested to explain the possible mode of action by which these compounds inhibit acetylcholinesterase.

A 3D-QSAR study on ginkgolides and their analogues with comparative molecular field analysis

Comparative molecular field analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) paradigm was used to study the correlation between the physicochemical properties and the in vitro bioactivities of ginkgolide analogues. The correlation derived from CoMFA analysis has a good predictive capability. Based on the result of CoMFA analysis, we designed some compounds. Pharmacological assay indicated that three of these new designed compounds are 2 and 4 times more potent than that of ginkgolides.

Interpreting the effect of methyl group at the three carbon bridge of (-)-huperzine A on its anticholinesterase activity by molecular dynamics method

Based on the recently resolved crystal structure of complex (-)-huperzine A-AChE, we simulated the interaction between (-)-huperzine A analogues and AChE using molecular dynamics method. It was revealed that the methyl group at the three carbon bridge of (-)-huperzine A can form a weak hydrogen bond with the phenol hydroxyl oxygen of Tyr121 and the main-chain oxygen of Gly118 of AChE, respectively.

Structure-activity relationship of channel binding affinity of quaternary ammonium ions

AIM

To explore the structure-activity relationship of quaternary ammonium (QA) ions at the external binding site of K+ channel.

METHODS

InsightII and MOPAC 6.0 molecular modeling package were used to calculate the free energy of hydration (delta Ghydration), the energy of the highest occupied orbital (EHOMO), and the energy of the lowest unoccupied orbital (ELUMO) for each QA ion, respectively. The partial least square method was used to analyze the relationship between the binding free energy and these descriptive parameters.

RESULTS

Generally, the higher the ELUMO of a QA ion was, the weaker its solvation was and accordingly the stronger binding affinity. For a QA ion larger than tetraethylammonium (TEA), its large size was unfavorable to its channel binding affinity.

CONCLUSION

The binding affinity of all QA ions correlated well with delta Ghydration and ELUMO.

Molecular modeling of voltage-gated potassium channel pore

AIM

To build a structure model for the pore of voltage-gated Shaker potassium channel and examine its validity.

METHODS

(1) Structural restraints were derived from experimental and theoretical studies; (2) An initial structural motif satisfying the derived restraints was first constructed, and further refined by restrained molecular mechanics; (3) The quality of the model was judged by the criterion that whether it could clarify molecular mechanisms of channel functions and explain the known experimental facts.

RESULTS

(1) A computer pore structure was proposed, in which the residues within signature sequence (corresponding to Shaker 439-446) dipped into the membrane and formed the narrow part of the pore in a non-periodic conformation, while the other residues in the P region constituted the outer mouth of the pore; (2) The ion selectivity was achieved through cation-pi orbital interaction mechanism at position 445 and oxygen cage mechanism at position 447; (3) Different binding modes led to different affinity of CTX and AgTx2 to channel; and (4) The inside of pore was dominated by negative electrostatic potential.

CONCLUSION

The model proposed was consistent with the derived restraints from the experimental results.

Molecular modeling of mu opioid receptor and receptor-ligand interaction

AIM

To construct the 3D structural model of mu opioid receptor (mu OR) and study the interaction between mu OR and fentanyl derivatives.

METHODS

The 3D structure of mu OR was modeled using the bacteriorhodopsin (bRh) as a template, in which the alignments of transmembrane (TM) of bRh and mu OR were achieved by scoring the alignment between the amino acid sequence of mu OR and the structure of bRh. The fentanyl derivatives were docked into the 7 helices of mu OR and the binding energies were calculated.

RESULTS

(1) The receptor-ligand interaction models were obtained for fentanyl derivatives. (2) In these models, the fundamental binding sites were possibly Asp147 and His297. The negatively charged oxygen of Asp147 and the positively charged ammonium group of ligand formed the potent electrostatic and hydrogen-binding interactions. Whereas the interactions between the positively charged nitrogen of His297 and the carbonyl oxygen of ligand were weak. In addition, there were some pi-pi interactions between the receptor and the ligand. (3) The binding energies of the receptor-ligand complexes had a good correlation with the analgesic activities (-lg ED50) of the fentanyl derivatives.

CONCLUSION

This model is helpful for understanding the receptor-ligand interaction and for designing novel mu OR selective ligands.

Molecular modeling of interaction between delta opioid receptor and 3-methylfentanylisothiocyanate

AIM

To construct a 3D structural model of delta opioid receptor (delta OR) and study its interaction with 3-methylfentanylisothiocyanate (SuperFIT).

METHODS

Using the bacteriohodopsin as a template, the 3D structure of delta OR was modeled; SuperFIT was docked into its inside.

RESULTS

The interaction model between delta OR and (3R, 4S)-SuperFIT was achieved, in which the important binding sites possibly were Asp128, Ser106, Phe104, Tyr308, and Pro315. Asp128 formed the electrostatic and hydrogen-binding interactions with the protonated nitrogen on piperidine of the ligand. Ser106 formed the electrostatic interaction with the N atom of isothiocyano group of the ligand; whereas Phe104, Tyr308, and Pro315 formed the hydrophobic interactions with the S atom of isothiocyano group. In addition, there were some other interactions between delta OR and the ligand.

CONCLUSION

The residues Phe104, Tyr308, Pro315, and Ser106 of delta OR are crucial to the delta selectivity of the ligand, which is beneficial for designing novel delta-selective ligand.

Interaction models of 3-methylfentanyl derivatives with mu opioid receptors

AIM

To study the interaction model of 3-methylfentanyl derivatives with mu opioid receptor.

METHODS

After a systematic conformational search, a three-dimensional quantitative structure-activity relationship study was carried out with comparative molecular field analysis (CoMFA).

RESULTS

1) The 6 CoMFA models had good predictive values and each model corresponded to the minimum-energy conformations of 13 compounds studied; 2) The important geometric parameters of mu pharmacophore d1 (A), d2 (A), d3 (A), d4 (A), d5 (A), and d6 (A) were 5.2, 5.4, 4.9, 10.6, 10.2, and 5.8 in Model A; 5.2, 6.5, 3.6, 10.6, 11.6, and 5.8 in Model B; 5.2, 4.6, 4.9, 11.6, 9.2, and 6.5 in Model C; 5.2, 5.4, 4.9, 10.5, 10.3, and 5.8 in Model D; 3.6, 5.4, 4.9, 5.7, 7.5, and 5.7 in Model E; 5.2, 4.7, 4.9, 11.2, 9.5, and 6.4 in Model F, respectively.

CONCLUSIONS

The several bioactive conformations of fentanyl analogs possibly existed and did not need to be the absolute minimum-energy conformation, each of which was involved in the interaction with mu opioid receptor.

Binding conformers searching method for ligands according to the structures of their receptors and its application to thrombin inhibitors

AIM

To develop a method of finding binding conformers for ligands according to the three-dimensional structures of their receptors.

METHODS

Combining the systematic search method of ligand with the molecular docking approach of ligand fitting into its receptor, we developed a binding conformer searching method for ligands.

RESULTS

The binding conformers of phosphonopeptidyl thrombin inhibitors were recognized. The binding (interaction) energies between these inhibitors and thrombin were calculated with molecular mechanical method.

CONCLUSION

Both of the total binding energies and steric binding energies have good correlations with the inhibitory activities of these thrombin inhibitors, demonstrating that our approach is reasonable. It can also be used to explain the inhibition mechanism of thrombin interacting with these inhibitors.

Molecular modeling of mu opioid receptor and its interaction with ohmefentanyl

AIM

To build up the structure model of mu opioid receptor, then combined with the receptor model, to investigate the action mechanism of ohmefentanyl on the receptor.

METHODS

Using the three-dimensional structure of bacteriorhodopsin as a template, we constructed mu opioid receptor model on computer. Ohmefentanyl was then docked into the supposed receptor binding sites.

RESULTS

A good ligand-receptor interaction model was achieved. The possible binding sites were found to be Asp147 and His319. The protonated N atom of ohmefentanyl form potent electrostatic and hydrogen-bonding interactions with residue Asp147 of the receptor, the O atom of the carbonyl group form weak electrostatic and hydrogen-bonding interactions with residue His319, and the two phenyl groups form pi-pi interactions with some aryl residues of the receptor around ligand.

CONCLUSION

The ligand-receptor interaction model should be helpful for rational design of novel analgesic.

Molecular modeling of interactions between tetrahydroprotoberberines and dopamine receptors

AIM

To build up the structure models of dopamine receptors, then combined with the receptor models, to investigate the action mechanism of tetrahydroprotoberberines (THPB) on dopamine receptors at the molecular level.

METHODS

Using the three-dimensional structure of bacteriorhodopsin as a template, we have constructed dopamine D1 and D2 receptor models on computer. l-Stepholidine was selected as the leading compound of THPB and docked into D1 and D2 receptor active sites.

RESULTS

After manual adjustment and energy minimization, the ligand-receptor interaction models were achieved. Based on these models, the possible action mechanism of THPB on dopamine receptors was suggested that the protonated N atom of THPB form electrostatic interaction and hydrogen-bonding interaction with residue Asp in TM3 of the receptor, the two substituents in D ring of THPB form hydrogen-bonding interactions with two Ser residues in TM5 of the receptor, and the aryl groups form pi-pi interactions with some aryl residues of the receptor around ligand.

CONCLUSION

Our ligand-receptor interaction models should be helpful for rational design of more potent drugs.

QSAR of 3-methylfentanyl derivatives studied with neural networks method

AIM

To use neural networks, which simulate the functions of living nervous systems, in QSAR studies;

METHODS

Using the back-propagation neural networks program devised by us, combining with partial least squares (PLS) method, we studied the relationships of quantum chemical indices and analgesic activities of 25 3-methylfentanyl derivatives;

RESULTS

Through learning process, a good QSAR model was established, and the activities of these compounds were predicted; the correlation between the activities and quantum chemical indices: the net charge of the atom N1, the net charge of the atom O16, the torsional angle of atoms C10-C9-N8-C4, the interatomic distance between atom C7 and the center of phenyl plane C9-14 (PhA), is quite well-matched. Based on these results, an interactive pattern between 3-methylfentanyl derivatives and opioid receptors was suggested;

CONCLUSION

Not only are the results of neural networks superior to those of PLS method but they also provide accurate predictions of the activity of the compounds and also combine the PLS method with neural networks.

3D-QSAR study on ether and ester analogs of artemisinin with comparative molecular field analysis

Comparative molecular field analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) paradigm, was used to study the correlations between the physicochemical properties and the in vitro activities of a series of ether and ester analogs of artemisinin. Four alignment models were used in the CoMFA investigation. The correlations derived from CoMFA analysis with the four alignments proved all to have good predictive values. The steric field predictive model of alignment B is accordant with the experimental results of Avery M A, et al: J Med Chem 1993; 36: 4264-75. The electrostatic field predictive results of alignments A, B, and C are consistent with our previous result of quantum chemical calculation. The highest rcross2 of alignment D, indicated that the side chain of -C6-O2-O1-C10-O3-C7-O4-C12-O5- and atom C16 are important groups of artemisinin analogs for antimalarial activity.

Microsurgical replantation of the avulsed scalp: report of six cases

This article reports the successful microsurgical replantation of six scalps avulsed for over 3 to 11 hr, after trauma and before repair, including five total and one partial avulsion. The authors believe that one key to successful replantation is effective vessel anastomoses. In the reported series, three scalps were reconstructed with two superficial temporal vessels and in five cases, with a 1:1 ratio between arteries and veins. The partially avulsed scalp was replanted successfully with only one artery and one vein. The management of postoperative complications is discussed.

Modelling basic features of specificity in DNA-aureolic acid-derived antibiotic interactions

The nonintercalative groove binding of a simplified model of olivomycin, to sequences d(CGCGCGC)2, d(TATATAT)2, and d(CICICIC)2 is investigated. A significant preference is displayed for the minor groove of the d(CG) sequence. This is due predominantly to the formation of H-bonds between the hydroxyl groups on the aglycone of the drug and the 2-amino group of the central guanine of the oligonucleotide.

Energetics and stereochemistry of DNA complexation with the antitumor AT specific intercalators tilorone and m-AMSA

Computations by the SIBFA method on the intercalative interaction energies of tilorone and m-AMSA with B-DNA representative oligonucleotides account for the specificity of these antitumor drugs for AT sites and minor groove intercalation. In tilorone this specificity is due to the strong preference of the side chains for the minor groove, which overcomes the preference of the chromophore for a GC intercalation site. In m-AMSA the specificity is due to the combined preference of both the chromophore and the anilino side chain for AT intercalation site and minor groove, respectively. o-AMSA is shown to manifest a similar (although significantly less pronounced specificity) as m-AMSA but a higher affinity for DNA. A comparison of the energetics and stereochemistry of intercalative binding to DNA of m-AMSA (AT minor groove specific) and 9-aminoacridine-4-carboxamide (GC major groove specific), which possess the same chromophore and differ only by the nature and position of the side chains, shows the possibility of important variations in the intercalative behaviour of chromophoric drugs as a function of the substituent groups attached to them.

Groove selectivity in the interaction of 9-aminoacridine-4-carboxamide antitumor agents with DNA

Theoretical quantitative evaluation of the intercalative binding to DNA of the new antitumor drug 9-aminoacridine-4-carboxamide indicates that, in contradiction with a recently proposed model, the compound should show specificity for interaction with the major (and not minor) groove of GC sequences.

A study on configuration-activity relationship of diamminedichloroplatinum (II) by the pseudopotential valence electron-only ab initio calculation method

We investigated the cis- and trans-isomers of Pt(NH3)2Cl2 and [Pt(NH3)2]2+ using a quantum chemical non-empirical calculation method, the pseudopotential valence electron-only ab initio method. The electronic structure and electrostatic potential counter maps were in turn determined through the wave functions so obtained. There was a sharp difference between the dipole moments of the cis- and trans-isomers. The electrostatic counter maps of the isomers also had remarkably different features. Based on the interaction between the platinum (II) coordination compound and the base pairs of nucleic acid, the difference in antitumour activity of the isomeric compounds was discussed. It is pointed out that the key factor for antitumour activity is that the platinum (II) coordination compound must be mutually complementary with the target acceptor in both configuration and bonding activity. This mutual-complementary requirement includes a bonding ability of the platinum complex with two negative centers in DNA, so as to form an intrastrand crosslink with two neighbouring guanines.

A theoretical study of the intercalative binding of the anti-tumour drug anthrapyrazole to double-stranded oligonucleotides

Theoretical computations have been performed on the intercalative binding of anthrapyrazole to the double-stranded tetranucleotides d(GCGC)2 and d(ATAT)2, intercalation taking place in the central pyrimidine-(3',5')-purine sequences, with an unwinding angle of 29 degrees. The complex is principally stabilized by hydrogen-bonds of the two side chains with the ionic oxygens of the two central phosphates. In marked contrast with the corresponding complexes of the related compound mitoxantrone, the N7 atoms of the two central purines do not participate in hydrogen-bonding interactions with the dimethylamino fragments of the side chains. Side chain A of the anthrapyrazole, which is on the imino nitrogen side, is located farther away from the core of the major groove, closer to the phosphate backbone. Compared to the mitoxantrone complexes, there is a considerable decrease in the difference of interaction energy between the d(GCGC)2 and the d(ATAT)2 complexes. This is in line with the experimental results indicating that, compared to mitoxantrone, anthrapyrazole manifests little or no GC sequence selectivity.

A tentative model of the intercalative binding of the neocarzinostatin chromophore to double-stranded tetranucleotides

Theoretical computations are performed of the intercalative binding of the neocarzinostatin chromophore (NCS) with the double-stranded oligonucleotides d(CGCG)2, d(GCGC)2, d(TATA)2 and d(ATAT)2. Minor groove binding is preferred over major groove binding. It is found that the long axis of the stacked naphtoate ring lies approximately parallel to the long axis of the base pairs of the intercalation site. The galactosamine ammonium group interacts with specific sites of the groove (O2/N3 of bases 2 and O1' of sugar S3), whereas the dodecadyine ring system wraps around the groove towards the backbone. An overall AT versus GC preference is derived. Intercalation in a central purine-(3', 5')-pyrimidine sequence appears to be preferred over that in a central pyrimidine-(3', 5')-purine sequence.

A theoretical study of anthracene and phenanthrene derivatives acting as A-T specific intercalators

Theoretical computations are performed on the comparative A-T versus G-C binding selectivities of two DNA intercalating molecules recently synthesized by Wilson et al. These are derivatives of phenanthrene and anthracene with side chains containing an hydroxy group bound to its C alpha carbon and a cationic amino group bound to its C beta carbon. We have optimized the binding energies of these phenanthrene and anthracene derivatives (1 and 2, respectively) to the double-stranded tetramers d(ATAT)2 and d(GCGC)2, the intercalation occurring in the central pyrimidine (3'-5') purine sequence. The sum of the intercalator-oligonucleotide intermolecular interaction energy plus the conformational energy variation of the intercalator upon binding were computed by the SIBFA procedures, which use empirical formulas based on ab initio SCF computations. Both compounds are found to bind more favourably to the AT sequence than to the GC one. Moreover, the affinity of 1 for the AT oligomer is computed to be larger than that of 2, whereas conversely that of 2 is larger than that of 1 for the GC oligomer. The AT versus GC binding selectivity of 1 is significantly larger than that of 2. These results are in excellent agreement with the experimental findings of Wilson et al. However, contrary to the suggestion of these authors the alpha-hydroxy group of the side chain of the intercalators does not seem to play a decisive role in determining the A-T specificity.

A theoretical study of the comparative binding affinities of daunomycin derivatives to a double-stranded oligomeric DNA. Proposal for new high affinity derivatives

Theoretical computations were performed on the comparative binding affinities of daunomycin (DM, 1) and seven derivatives related to the double-stranded oligonucleotide d(CGATCG)2. The compounds investigated were 4-demethoxy DM (2), and its beta-anomer (3), 4-demethoxy-7,9-bis-epi DM (4) and its beta anomer (5), a derivative with glucosamine instead of daunosamine (6), and two additional hypothetical DM derivatives in which the cationic NH3+ group of the daunosamine moiety is replaced by either a CH2--NH3+ group (7) or a CH2CH2NH3+ group (8), so as to indicate the effect on the binding affinity of interposing one- or two-methylene groups between the sugar and the cationic charge. The conformational angles of the hexanucleotide are fixed in values found in the representative crystal structure of the d(CGTACG)2-DM complex. The intermolecular drug-hexanucleotide interaction energies and the conformational energy changes of the drug upon binding are computed and optimized in the framework of the SIBFA procedure (sum of interactions between fragments computed ab initio), which uses empirical formulas based on ab initio SCF computations. The overall binding affinity ordering of compounds 1-6 compares satisfactorily with the ordering of available experimental affinity constants. The binding affinities of compounds 7 and 8, for which no experimental results seem to be available yet, are predicted to be significantly higher than those of the parent compound DM, with the greatest affinity found for 7. Because of the overall correlation between binding affinity of anthracyclines to DNA and their antitumor activity, these last two compounds deserve an exploration of their chemotherapeutic efficiency.

A theoretical investigation on the sequence selective binding of mitoxantrone to double-stranded tetranucleotides

Theoretical computations are performed on the comparative binding energetics of mitoxantrone (MX), a newly synthesized intercalating anthraquinone antitumor drug, to six representative double-stranded tetranucleotides: d(GCGC)2, d(CGCG)2, d(ATAT)2, d(TATA)2, d(GTGT), d(ACAC), and d(CCGG)2. The computations are performed with the SIBFA procedure, which uses empirical formulas based on ab initio SCF computations. The best binding configuration of mitoxantrone locates its two side chains in the major groove. A considerable preference is elicited for intercalation of the chromophore ring in a pyrimidine (3'-5') purine sequence rather than the isomeric purine (3'-5') pyrimidine sequence. Contrary to the situation encountered with "simple" intercalators, in which this preference is generally attributed solely to differences in the energies of unstacking necessary to generate the intercalation sites, the preference is dictated in MX to a large extent by the intermolecular interaction energy term. This result is imposed by the interactions of the side chains of MX with the oligonucleotide.

A theoretical investigation on the sequence selective binding of daunomycin to double-stranded polynucleotides

Theoretical computations are performed on the structural and energetical factors involved in the sequence selective binding of daunomycin (DNM) to six representative self-complementary double-stranded hexanucleotides: d(CGTACG)2,d(CGATCG)2,d(CITACI)2, d(TATATA)2, d(CGCGCG)2 and d(TACGTA)2. The conformational angles of the hexanucleotides are fixed in values found in the representative crystal structure of the d(CGTACG)2-DNM complex. The intermolecular DNM-hexanucleotide interaction energies and the conformational energy changes of DNM upon binding are computed and optimized in the framework of the SIBFA procedure, which uses empirical formulas based on ab initio SCF computations. Among the two regularly alternating hexanucleotides, d(TATATA)2 and d(CGCGCG)2, a stronger binding is predicted for the former, in agreement with experimental results obtained with poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC). Altogether, however, among the six investigated sequences, the strongest complexes are computed for the mixed hexanucleotides d(CGATCG)2 and d(CGTACG)2, containing the intercalation site between two CG base pairs and an adjacent TA base pair. This situation may be related to the increased affinity of DNM for GC rich DNA's and to the situation in the crystal structure of the DNM-d(CGTACG)2 complex. Analysis of the intrinsic base sequence preferences expressed by the individual constituents of DNM, namely the daunosamine side chain, the chromophore ring and its two 9-hydroxyl and 9-acetoxy substituents, reveals that the overall sequence preference found is the result of a rather intricate interplay of intrinsic sequence preferences, in particular at the level of daunosamine and the 9-hydroxyl substituent.(ABSTRACT TRUNCATED AT 250 WORDS)