2'-Deoxyribosyltransferase from Leishmania mexicana, an efficient biocatalyst for one-pot, one-step synthesis of nucleosides from poorly soluble purine bases.

Processes catalyzed by enzymes offer numerous advantages over chemical methods although in many occasions the stability of the biocatalysts becomes a serious concern. Traditionally, synthesis of nucleosides using poorly water-soluble purine bases, such as guanine, xanthine, or hypoxanthine, requires alkaline pH and/or high temperatures in order to solubilize the substrate. In this work, we demonstrate that the 2'-deoxyribosyltransferase from Leishmania mexicana (LmPDT) exhibits an unusually high activity and stability under alkaline conditions (pH 8-10) across a broad range of temperatures (30-70 °C) and ionic strengths (0-500 mM NaCl). Conversely, analysis of the crystal structure of LmPDT together with comparisons with hexameric, bacterial homologues revealed the importance of the relationships between the oligomeric state and the active site architecture within this family of enzymes. Moreover, molecular dynamics and docking approaches provided structural insights into the substrate-binding mode. Biochemical characterization of LmPDT identifies the enzyme as a type I NDT (PDT), exhibiting excellent activity, with specific activity values 100- and 4000-fold higher than the ones reported for other PDTs. Interestingly, LmPDT remained stable during 36 h at different pH values at 40 °C. In order to explore the potential of LmPDT as an industrial biocatalyst, enzymatic production of several natural and non-natural therapeutic nucleosides, such as vidarabine (ara A), didanosine (ddI), ddG, or 2'-fluoro-2'-deoxyguanosine, was carried out using poorly water-soluble purines. Noteworthy, this is the first time that the enzymatic synthesis of 2'-fluoro-2'-deoxyguanosine, ara G, and ara H by a 2'-deoxyribosyltransferase is reported.

Epigenetic regulation of ID4 in the determination of the BRCAness phenotype in breast cancer.

BRCAness breast tumors represent a group of sporadic tumors characterized by a reduction in BRCA1 gene expression. As BRCA1 is involved in double-strand breaks (DSBs) repair, dysfunctional BRCA pathway could make a tumor sensitive to DNA damaging drugs (e.g., platinum agents). Thus, accurately identifying BRCAness could contribute to therapeutic decision making in patients harboring these tumors. The purpose of this study was to identify if BRCAness tumors present a characteristic methylation profile and/or were related to specific clinico-pathological features. BRCAness was measured by MLPA in 63 breast tumors; methylation status of 98 CpG sites within 84 cancer-related genes was analyzed by MS-MLPA. Protein and mRNA expressions of the selected genes were measured by quantitative real-time PCR and Western Blot. BRCAness was associated with younger age, higher nuclear pleomorphism, and triple-negative (TN) status. Epigenetically, we found that the strongest predictors for BRCAness tumors were the methylations of MLH1 and PAX5 plus the unmethylations of CCND2 and ID4. We determined that ID4 unmethylation correlated with the expression levels of both its mRNA and protein. We observed an inverse relation between the expressions of ID4 and BRCA1. To the best of our knowledge, this is the first report suggesting an epigenetic regulation of ID4 in BRCAness tumors. Our findings give new information of BRCAness etiology and encourage future studies on potential drug targets for BRCAness breast tumors.

Synthesis and evaluation of hybrid molecules targeting the vinca domain of tubulin.

Some hybrids of vinca alkaloids and phomopsin A, linked by a glycine pattern, have been synthesized in one or two steps, by an insertion reaction and shown to inhibit microtubule assembly. These compounds have been elaborated in order to interact with both the "vinca site" and the "peptide site" of the vinca domain in tubulin. Two out of three hybrids are potent inhibitors of microtubules assembly and they present good cytotoxicity against different cell lines. Molecular modelling studies show that they could bind, within the vinca domain, in similar spatial regions as those of vinca and phomopsin thanks to the flexibility provided by the glycine linker used to elaborate these hybrids.

Urinary and fecal incontinence in patients with advanced ovarian cancer treated with CRS + HIPEC.

PURPOSE: The objective of this work was to analyze the long-term prevalence of urinary and fecal incontinence and their impact on quality of life in patients with advanced and recurrent ovarian cancer treated with cytoreductive surgery and hyperthermic intraoperative intraperitoneal chemotherapy (CRS + HIPEC). METHODS: This cross-sectional study included a series of patients with advanced and recurrent ovarian cancer treated by CRS + HIPEC, with a disease-free period of at least 12 months after the procedure. Urinary incontinence was evaluated using the International Consultation on Incontinence Questionnaire - Short Form (ICIQ-SF), fecal incontinence using the Wexner test and the Fecal Incontinence Quality of Life (FIQL) questionnaire and global quality of life using the Short Form 36 (SF-36) survey. RESULTS: A total of 64 patients were included in the study, with a median age of 55 years (range 28-78). The urinary incontinence rate was 45% and the fecal incontinence rate was 20%. Up to 14% of the patients presented both types of incontinence. The presence of urinary or fecal incontinence generated a significant negative impact on quality of life in relation to patients without incontinence. DISCUSSION: Urinary and fecal incontinence is frequent in the follow-up of ovarian cancer patients treated with CRS + HIPEC. Reconsidering the approach to the pelvis without peritoneal metastases in the peritoneum could modify the incidence of these pelvic floor dysfunctions.

Risk factors and management of incisional hernia after cytoreduction and hyperthermic intraperitoneal chemotherapy (HIPEC) in patients with peritoneal surface malignancies.

BACKGROUND: The incidence of incisional hernia in patients with peritoneal surface malignancies treated by cytoreduction plus hyperthermic intraperitoneal chemotherapy (HIPEC) remains unclear, and the criteria commonly used to indicate their repair cannot be applied in these patients. The objective of this work was to analyze the incidence of incisional hernias in these patients, identify the risk factors associated with their appearance, and propose an algorithm for their management. METHODS: We analyzed a series of patients with malignant pathologies of the peritoneal surface treated by cytoreduction with peritonectomy and HIPEC procedures between January 2008 and June 2017. Only patients with a minimum postoperative follow-up period of 12 months were included. RESULTS: Our series included 282 patients, 28 (10%) of whom developed an incisional hernia during the follow-up period. Fifty-one patients, all with ovarian cancer with peritoneal dissemination, did not receive HIPEC after cytoreduction as they were part of the control arm of the CARCINOHIPEC clinical trial (NCT02328716) or because they did not provide specific informed consent. In the multivariate analysis, treatment with HIPEC (OR 2.56, 95% CI [1.57, 4.31], p = 0.032) and the administration of preoperative systemic chemotherapy (OR = 1.59, 95% CI [1.26, 3.58], p = 0.041) were found to be independent factors related to the appearance of an incisional hernia. CONCLUSIONS: The incidence of incisional hernia after cytoreduction and HIPEC is within the ranges described in the literature for other abdominal surgery procedures. The use of systemic chemotherapy and treatment with HIPEC, in particular, were identified as factors related to their occurrence.

A functional BH3 domain in an aquaporin from Leishmania infantum.

Despite the absence of sequences showing significant similarity to any of the members of the Bcl-2 family of proteins in protozoa, experiments carried out in yeast or trypanosomatids have demonstrated that ectopic expression of some of these members alters their response to different death stimuli. Because the BH3 domain is the smallest common signature in all the proteins of this family of apoptosis regulators and also because they are essential for molecular interactions between antagonistic members, we looked for sequences with significant similarity to the BH3 motif in the Leishmania infantum genome. Among the top scoring ones, we found the MYLALQNLGDEV amino-acid stretch at the C terminus of a previously described aquaporin, now renamed as Li-BH3AQP. This motif is highly conserved in homologous proteins from other species of the Leishmania genus. The association of Li-BH3AQP with human Bcl-XL was demonstrated by both co-immunoprecipitation and yeast two-hybrid experiments. Ectopic expression of Li-BH3AQP reduced viability of HeLa cells and this deleterious effect was abrogated by the simultaneous overexpression of Bcl-XL. Although we were not able to demonstrate a reduction in parasite viability when the protein was overexpressed in Leishmania promastigotes, a prodeath effect could be observed when the parasites overexpressing Li-BH3AQP were treated with staurosporine or antimycin A. Surprisingly, these parasites were more resistant, compared with wild-type parasites, to hypotonic stress or nutrient deprivation. The prodeath activity was abolished upon replacement of two highly conserved amino acids in this BH3 domain. Taken together, these results point to Li-BH3AQP as the first non-enzymatic protein ever described in trypanosomatids that is involved in cell death.

One left-handed strand in DNA-oligonucleotide complexes?

A single strand of oligonucleotide can bind to double helical DNA under certain conditions. This must involve some unwinding of the original double helix in a process leading to the formation of a three-stranded region. The free energy for such an entropically unlikely reaction may come from a change in the degree of supercoiling of the original DNA. The conformation of the triple strand is investigated here using computer graphics and molecular mechanics calculations. It is suggested that on binding the oligonucleotide (strand 3) to two paired strands (1 and 2) in a supercoiled DNA molecule, strand 2 might adopt a left-handed conformation whilst strand 1 and strand 3 pair in the normal Watson-Crick B-configuration.

Advances in the chemistry and pharmacology of ecteinascidins, a promising new class of anti-cancer agents.

Ecteinascidins are marine natural products consisting of two or three linked tetrahydroisoquinoline subunits and an active carbinolamine functional group. Their potent antiproliferative activity against a variety of tumor cells has made them attractive candidates for development as anticancer agents. The lead compound, ecteinascidin 743 (ET 743), is currently in phase II clinical trials but the low amounts present in its natural source, the tunicate Ecteinascidia turbinata, made it necessary to develop efficient synthetic procedures. Recent improvements on the original synthesis are reviewed as well as new strategies starting from readily available cyanosafracin B. ET 743 is known to bind to the minor groove of DNA giving rise to a covalent adduct with the exocyclic amino group at position 2 of a guanine in a fashion similar to saframycin antibiotics. Some of the resulting complexes have been studied by a variety of biochemical and spectroscopic methods and also by computer simulations. The rules for sequence specificity have been well established (preferred targets are RGC and YGG, where R and Y stand for purine and pyrimidine, respectively), and it has been shown that binding of ET 743 to DNA is accompanied by minor groove widening and DNA bending towards the major groove. Although the precise target for antitumor action remains to be unambiguously defined, a role in affecting the transcriptional regulation of some inducible genes is rapidly emerging.

Molecular model of the interaction of bee venom phospholipase A2 with manoalide.

A molecular model of the interaction between manoalide (MLD) and bee venom phospholipase A2 (bv-PLA2) has been derived making use of a combination of computational methods. MLD was built in its open form and simulated by using molecular dynamics techniques. It is shown that the polar part of the molecule, which is thought to be the reactive region, is endowed with considerable conformational flexibility whereas the apolar region is rather rigid. The proposed active conformation of MLD and the main putative binding site for MLD on this enzyme were identified by matching potential energy GRID maps for both ligand and receptor with the chemical structure of the respective counterpart. The binding site is found in the C-terminal region of bv-PLA2, forming part of the proposed interfacial surface for binding to aggregated substrates, and comprises two distinct regions: (i) a hydrophobic cavity delimited by the C-terminal beta-sheet and the antiparallel beta-sheet, which interacts with the apolar zone of MLD, and (ii) a cationic site made up of residues Arg-58 and Lys-94, which interacts with the polar zone. Molecular dynamics and molecular orbital calculations indicate that the most likely initial reaction between MLD and bv-PLA2 is formation of a Schiff base between Lys-94 and the aldehyde generated upon opening of MLD's gamma-lactone ring, supporting recent model reaction studies. The inhibition seems to be a consequence of the occupation by MLD of a site overlapping a phosphocholine binding site in bv-PLA2 presumably involved in the interface desolvation process. The present model represents a starting point for further structural studies on the mechanism of phospholipases A2 inactivation by MLD and MLD-like compounds.

A molecular dynamics study of the bis-intercalation complexes of echinomycin with d(ACGT)2 and d(TCGA)2: rationale for sequence-specific Hoogsteen base pairing.

The behavior of the complexes of echinomycin with the DNA tetramers d(ACGT)2 and d(TCGA)2, in which the terminal AT base pairs are in either a Hoogsteen or a Watson-Crick conformation, has been explored by molecular dynamics taking into account experimental data from NMR studies (Gao and Patel. Biochemistry 1988, 27, 1744-1751). The DNA binding specificity of echinomycin appears to be the result of a subtle balance between stabilizing and destabilizing forces. Among the former is a number of hydrogen bonds between the alanine residues of echinomycin and both the N3 and 2-amino groups of the guanine bases which decisively determine the strong affinity of the antibiotic for CpG steps. On the other hand, there appears to be an unfavorable dipolar interaction between the chromophores of the antibiotic and the CpG step. This electrostatic component of the stacking interactions also contributes to explaining the conformational preferences of the flanking sequences: upon Hoogsteen pairing, the dipole moment of an AT base pair is found to increase significantly and alter its relative orientation. In the d(ACGT)2:echinomycin complex, this arrangement helps to improve the stacking interactions with the quinoxaline-2-carboxamide system, but would lead to unfavorable dipolar interactions in the d(TCGA)2 complex. The bearing of these findings on the binding of echinomycin to several sequences as well as on the altered binding selectivity of other members of the quinoxaline family of antibiotics is also discussed.

Assessment of solvation effects on calculated binding affinity differences: trypsin inhibition by flavonoids as a model system for congeneric series.

On the basis of molecular models of the interaction between trypsin and a series of seven structurally congeneric bioflavonoid inhibitors, the influence of solvation effects in the calculation of binding free energy differences in congeneric series has been assessed. The models were derived by making use of the X-ray crystal structure of bovine trypsin and the DOCK program, and the complementarity of the interactions between the functional groups of the docked molecules and the binding site region was corroborated independently with the GRID program. Interaction energies calculated for the complexes using molecular mechanics were found to correlate with the experimental inhibitory activities, although the quality of the correlation was dependent on the molecular modeling protocol. To understand why such correlations could be obtained in the absence of an explicit description of solvent effects, the in vitro activities were transformed into binding free energies, and continuum electrostatic theory was used to incorporate solvent effects by approximating them to the electrostatic contribution to the binding free energies. The results of our calculations show that, within this congeneric series, the cost in electrostatic free energy of desolvating both the enzyme binding site and the buried part of the inhibitors (delta Gdesolv) is roughly constant within the series. On the other hand, the electrostatic interaction energy (EeleLR) varies only slightly along the series in comparison with the van der Waals interaction (EVDWLR), and this variation is mostly solvent-independent, i.e., the reaction field energy of the solvent in the bound state (EsrfLR) makes almost a negligible contribution to the binding free energy differences. As a result, differences in binding free energy are dominated by the van der Waals term, while the electrostatic contribution is, to a good approximation, solvent-independent. A similar scenario may account for the good correlations frequently found between ligand activities and ligand-receptor interaction energies derived using plain molecular mechanics, although generality remains to be determined.

Prediction of drug binding affinities by comparative binding energy analysis.

A new computational method for deducing quantitative structure-activity relationships (QSARs) using structural data from ligand-macromolecule complexes is presented. First, the ligand-macromolecule interaction energy is computed for a set of ligands using molecular mechanics calculations. Then, by selecting and scaling components of the ligand-macromolecule interaction energy that show good predictive ability, a regression equation is obtained in which activity is correlated with the interaction energies of parts of the ligands and key regions of the macromolecule. Application to the interaction of the human synovial fluid phospholipase A2 with 26 inhibitors indicates that the derived QSAR has good predictive ability and provides insight into the mechanism of enzyme inhibition. The method, which we term comparative binding energy (COMBINE) analysis, is expected to be applicable to ligand-receptor interactions in a range of contexts including rational drug design, host-guest systems, and protein engineering.

Molecular dynamics simulations of the bis-intercalated complexes of ditercalinium and Flexi-Di with the hexanucleotide d(GCGCGC)2: theoretical analysis of the interaction and rationale for the sequence binding specificity.

The X-ray crystal structures of the complexes of ditercalinium and Flexi-Di with d(CGCG)2 have been studied by computational chemistry methods in an attempt to rationalize their distinct structural features. In addition, the complexes of these two bisintercalating drugs with d(GCGCGC)2 have been modeled and subjected to 0.5 ns of molecular dynamics simulations in explicit solvent with the aim of evaluating the relative importance of hydrogen bonding and stacking interactions in the sequence binding specificity of these compounds. According to our calculations, the electrostatic term is attractive for the stacking interactions between the pyridocarbazole chromophores of these drugs and the base pairs that make up the sandwiched GpC step. On the contrary, this energy term is repulsive for the base pairs that make up the boundaries of the bisintercalation site. This differential electrostatic binding energy component, which is shown to have a strong orientational dependence, could lie at the origin of the observed binding preferences of these drugs. In addition, both the Lennard-Jones and the electrostatic energy terms contribute to stabilizing the underwound central GpC step. The attractive electrostatic interactions between the linkers and the major groove are in concert with the stacking specificities for the sandwiched GpC step, which is thus very effectively stapled by the drugs. The hydrogen-bonding potential of the linkers, however, appears to be reduced in an aqueous medium due to competing interactions with water. Binding of either ditercalinium or Flexi-Di to d(GCGCGC)2 appears to favor the A-type conformation that this DNA molecule most likely adopts in the free state. The possible relevance of these findings to the process of bis-intercalation and to the pharmacological action of these compounds is discussed.

Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design.

A comparative binding energy (COMBINE) analysis (Ortiz et al. J. Med. Chem. 1995, 38, 2681-2691) has been performed on a training set of 33 HIV-1 protease inhibitors, and the resulting regression models have been validated using an additional external set of 16 inhibitors. This data set was originally reported by Holloway et al. (J. Med. Chem. 1995, 38, 305-317), who showed the usefulness of molecular mechanics interaction energies for predicting the activity of novel HIV-1 protease inhibitors within the framework of the MM2X force field and linear regression techniques. We first used the AMBER force field on the same set of three-dimensional structures to check up on any possible force-field dependencies. In agreement with the previous findings, the calculated raw ligand-receptor interaction energies were highly correlated with the inhibitory activities (r2 = 0.81), and the linear regression model relating both magnitudes had an acceptable predictive ability both in internal validation tests (q2 = 0.79, SDEPcv = 0.61) and when applied to the external set of 16 different inhibitors (SDEPex = 1.08). When the interaction energies were further analyzed using the COMBINE formalism, the resulting PLS model showed improved fitting properties (r2 = 0.89) and provided better estimations for the activity of the compounds in the external data set (SDEPex = 0.83). Computation of the electrostatic part of the ligand-receptor interactions by numerically solving the Poisson-Boltzmann equation did not improve the quality of the linear regression model. On the contrary, incorporation of the solvent-screened residue-based electrostatic interactions and two additional descriptors representing the electrostatic energy contributions to the partial desolvation of both the ligands and the receptor resulted in a COMBINE model that achieved a remarkable predictive ability, as assessed by both internal (q2 = 0.73, SDEPcv = 0.69) and external validation tests (SDEPex = 0.59). Finally, when all the inhibitors studied were merged into a single expanded set, a new model was obtained that explained 91% of the variance in biological activity (r2 = 0.91), with very high predictive ability (q2 = 0.81, SDEPcv = 0.66). In addition, the COMBINE analysis provided valuable information about the relative importance of the contributions to the activity of individual residues that can be fruitfully used to design better inhibitors. All in all, COMBINE analysis is validated as a powerful methodology for predicting binding affinities and pharmacological activities of congeneric ligands that bind to a common receptor.

Reliability of comparative molecular field analysis models: effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors.

The effects of data pretreatment, data scaling, and variable selection on three-dimensional quantitative structure-activity relationships derived by comparative molecular field analysis (CoMFA) using the GRID energy function were studied in detail for a set of inhibitors of the human synovial fluid phospholipase A2 (HSF-PLA2). The quality of the models was evaluated for predictive power and ability to map the receptor binding site by (a) comparison of predicted and experimental activities using cross-validation and external validation sets and (b) comparison of the regions selected in space in the CoMFA models with a crystal structure of a HSF-PLA2-inhibitor complex, with optimized comparative binding energy analysis (COMBINE) models (Ortiz et al., 1995) and with structure-activity relationships derived previously for different sets of compounds. It is found that (1) data scaling and dielectric modeling strongly influence CoMFA results. Unscaled data and a uniform dielectric constant of 4 are well suited to GRID-CoMFA studies for the present compound set. (2) The GOLPE and Q2-GRS variable selection methods select variables in roughly the same regions in Cartesian space, but they produce different models in chemometric space and differ in their sensitivity to data scaling and pretreatment and their tendency to overfitting. (3) CoMFA models are consistent with COMBINE models in that they identify approximately the same intermolecular interactions as relevant for activity. Our study provides support for the qualitative receptor-mapping properties of CoMFA models and for the validity of variable selection when applied with care and also provides guidelines for how to evaluate the quality of CoMFA models.

The binding of benzenesulfonamides to carbonic anhydrase enzyme. A molecular mechanics study and quantitative structure-activity relationships.

Molecular mechanics methods have been applied to study the interaction between a series of 20 deprotonated benzenesulfonamides and the enzyme carbonic anhydrase. The different contributions to the binding energy have been evaluated and correlated with experimental inhibition data and molecular orbital indices of the sulfonamides in their bound conformation. The results suggest that the discrimination shown by the enzyme toward these inhibitors is dominated by the short-range van der Waals forces.

DNA sequence-specific reading by echinomycin: role of hydrogen bonding and stacking interactions.

The binding of echinomycin to DNA hexamers of the form GpApXpZpTpC, where the central XpZ step can be CpG, TpA, GpC, or ApT, has been studied by molecular modeling and molecular mechanics techniques. Interaction energies have also been calculated for the complexation of echinomycin with sequences containing the preferred central CpG step and different flanking base pairs. Besides, two more sets of sequences incorporating either 2,6-diaminopurine (DAP) or hypoxanthine in place of adenine or guanine, respectively, have been examined. The aim of this work was to evaluate the relative importance of hydrogen-bonding and stacking interactions in the association of echinomycin with DNA and further rationalize the experimental evidence. The results of these calculations are in consonance with available data from footprinting experiments and appear to support our previous hypothesis that, in addition to the crucial intermolecular hydrogen bonds in the central region, the stacking interactions involving the quinoxaline-2-carboxamide chromophores of the drug and the DNA base pairs play an important role in modulating the binding specificity of this bisintercalating antitumor antibiotic. This is most clearly seen when sequences with similar minor-groove environments are compared (e.g. CpI vs TpA or CpG vs TpDAP). The dipole moment of N-methylquinoxaline-2-carboxamide has been measured (mu = 4.15 +/- 0.03 D) and compares very well with the calculated value (mu = 4.14 D). The fact that G:C, I:C, A:T, and DAP:T base pairs are shown to be endowed with distinct van der Waals and electrostatic stacking properties with respect to this heteroaromatic ring system could have important implications for the design of novel DNA mono- and bis-intercalating agents.

Abasic analogues of TSAO-T as the first sugar derivatives that specifically inhibit HIV-1 reverse transcriptase.

With the aim of assessing the role that the thymine base of TSAO-T may play in the interaction of TSAO compounds with HIV-1 reverse transcriptase (RT), we have designed, synthesized, and evaluated for their anti-HIV-1 activity a series of 3-spiro sugar derivatives substituted at the anomeric position with nonaromatic rings or with amine, amide, urea, or thiourea moieties that mimic parts or the whole thymine base of TSAO-T. Also, a dihydrouracil TSAO analogue and O-glycosyl 3-spiro sugar derivatives substituted at the anomeric position with methyloxy or benzyloxy groups have been prepared. Compounds substituted at the anomeric position with an azido, amino, or methoxy group, respectively, were devoid of marked antiviral activity (EC50: 10-200 microM). However, the substituted urea sugar derivatives led to an increase in antiviral potency (EC50: 0.35-4 microM), among them those urea derivatives that mimic most closely the intact TSAO-T molecule retained the highest antiviral activity. Also, the dihydrouracil TSAO derivative retained pronounced anti-HIV-1 activity. None of the compounds showed any anti-HIV-2 activity. The results described herein represent the first examples of sugar derivatives that interact in a specific manner with HIV-1 RT. Molecular modeling studies carried out with a prototype urea derivative indicate that a heteroaromatic ring is not an absolute requirement for a favorable interaction between TSAO-T and HIV-1 RT. Urea derivatives, which can mimic to a large extent both the shape and the electrostatic potential of a thymine ring, can effectively replace this nucleic acid base when incorporated into a TSAO molecular framework with only moderate loss of activity.

Identification of a putative binding site for [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]-3'-spiro-5''-(4''-amino-1'',2''-oxathiole-2'',2''-dioxide)thymine (TSAO) derivatives at the p51-p66 interface of HIV-1 reverse transcriptase.

A binding site for TSAO-m(3)T at the interface between the p66 and p51 subunits of HIV-1 reverse transcriptase (RT) and distinct from that of "classical" HIV-1 non-nucleoside inhibitors is proposed. The feasibility of the binding mode was assessed by carrying out nanosecond molecular dynamics simulations for the complexes of TSAO-m(3)T with reduced models of both the wild-type enzyme and a more sensitive R172A mutant. The molecular model is in agreement with a previous proposal, with known structure-activity and mutagenesis data for this unique class of inhibitors, and also with recent biochemical evidence indicating that TSAO analogues can affect enzyme dimerization. The relative importance of residues involved in dimer formation and TSAO-RT complex stabilization was assessed by a combination of surface area accessibility, molecular mechanics, and continuum electrostatics calculations. A structure-based modification introduced into the lead compound yielded a new derivative with improved antiviral activity.

Exploring the role of the 5'-position of TSAO-T. Synthesis and anti-HIV evaluation of novel TSAO-T derivatives.

Various analogues of the anti-HIV-1 agent TSAO-T, [1-[2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]thymine]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide) have been synthesized in which the 5'-TBDMS group has been replaced by alkyl-, alkenyl- or aromatic ether groups, substituted amines, carbamoyl or (thio)acyl groups. The compounds synthesized were evaluated for their inhibitory effect on HIV-1 and HIV-2 replication in cell culture. Replacement of the 5'-TBDMS group by an acyl, aromatic or a cyclic moiety markedly diminish or even eliminate the anti-HIV activity. However, the presence at that position of an alkyl or alkenyl chain, partially retain antiviral activity. These observations suggest that the 5'-TBDMS group of the TSAO molecule plays a crucial role.