Experimental validation of specificity of the squamous cell carcinoma antigen-immunoglobulin M (SCCA-IgM) assay in patients with cirrhosis

Background: Squamous cell carcinoma antigen-immunoglobulin M (SCCA-IgM) is a useful biomarker for the risk of development of hepatocellular carcinoma (HCC) in patients with cirrhosis due to its progressive increase associated to HCC evolution. In patients with cirrhosis, other assays have been affected by interfering reactivities of IgM. In this study, the analytical specificity of the SCCA-IgM assay was assessed by evaluating SCCA-IgM measurement dependence on different capture phases, and by measuring the recovery of SCCA-IgM reactivity following serum fractionation. Methods: Serum samples from 82 patients with cirrhosis were analyzed. SCCA-IgM was measured using the reference test (Hepa-IC, Xeptagen, Italy) that is based on rabbit oligoclonal anti-squamous cell carcinoma antigen (SCCA) and a dedicated ELISA with a mouse monoclonal anti-SCCA as the capture antibody. Results: SCCA-IgM concentrations measured with the reference assay (median value=87 AU/mL) were higher than those measured with the mouse monoclonal test (median value=78 AU/mL). However, the differences in the SCCA-IgM distribution were not statistically significant (p>0.05). When SCCA-IgM concentrations measured with both tests were compared, a linear correlation was found (r=0.77, p<0.05). Fractionation of the most reactive sera by gel-filtration chromatography showed that total recovery of SCCA-IgM reactivity was seen only in the fractions corresponding to components with a molecular weight higher than IgM and SCCA (>2000 kDa) with both tests. Conclusions: The equivalence of both SCCA-IgM assays and the absence of reactivity not related to immune complexes support the analytical specificity of SCCA-IgM measurements. The results validate the assessment of SCCA-IgM for prognostic purposes in patients with cirrhosis. Clin Chem Lab Med 2010;48:217–23.Peer Reviewe

Calculation of Quantitative Structure-Activity Relationship Descriptors of Artemisinin Derivatives

Quantitative structure-activity relationships are based on the construction of predictive models using a set of known molecules and associated activity value. This accurate methodology, developed with adequate mathematical and computational tools, leads to a faster, cheaper and more comprehensive design of new products, reducing the experimental synthesis and testing on animals. Preparation of the QSAR models of artemisinin derivatives was carried out by the genetic function algorithm (GFA) method for 91 molecules. The results show some relationships to the observed antimalarial activities of the artemisinin derivatives. The most statistically signi fi cant regression equation obtained from the fi nal GFA relates to two molecular descriptors

Inhibitors of HIV-Protease from Computational Design. A History of Theory and Synthesis Still to be Fully Appreciated

Despite the fact that HIV-Protease is an over 20 years old target, computational approaches to rational design of its inhibitors still have a great potential to stimulate the synthesis of new compounds and the discovery of new, potent derivatives, ever capable to overcome the problem of drug resistance. This review deals with successful examples of inhibitors identified by computational approaches, rather than by knowledge-based design. Such methodologies include the development of energy and scoring functions, docking protocols, statistical models, virtual combinatorial chemistry. Computations addressing drug resistance, and the development of related models as the substrate envelope hypothesis are also reviewed. In some cases, the identified structures required the development of synthetic approaches in order to obtain the desired target molecules; several examples are reported

A Molecular Reactivity Template for Cannabinoid Analgesic Activity

The methods of theoretical chemistry were used to characterize the molecular structure and some reactivity properties of (–)-9-nor-9β-hydroxyhexahydrocannabinol (9-nor-9β-OH-HHC), our template molecule for cannabinoid analgesia. This characterization is part of a project whose ultimate goal is the design of cannabinoid analgesics with reduced psychoactive liabilities. Our working hypothesis is that the analgesic activity of 9-nor-9β-OH-HHC is due to the presence and relative location of two regions of negative potential in the top half of the molecule. A complete conformational study of the fused ring structure of 9-nor-9β-OH-HHC was performed using the technique of molecular mechanics as encoded in the MMP2(85) program. This study revealed six accessible conformers of 9-nor-9β-OH-HHC. All six conformers were found to have the same fused ring conformation, but to differ in the position of the phenol and 9β-hydroxyl groups. Molecular electrostatic potential (MEP) maps of each accessible conformer were calculated from molecular wave functions obtained with the LP-3G basis set implemented into the Gaussian 80 program. The MEP maps calculated at distances of 1.5 and 3.3 Å from the molecular plane defined by the aromatic ring serve as a discriminative factor for the conformers of the studied compound. In order to quantiate the spatial relationship of the potential minima in the MEPs of each accessible conformer, points of minimum potential associated with the 9β-hydroxyl oxygen (X1 at –1.5 Å and X2 at –3.3 Å) and with the phenol oxygen (Y1 at 1.5 Å and Y2 at –1.5 Å) were identified in the MEP maps of each conformer. The distances, |;XnYn|, and the nonbonded torsion angles, Yn–O–C9–Xn, were then measured for all conformers. The accessible conformations of 9-nor-9β-OH-HHC along with their MEPs and the measurements |XnYn| and Yn–O–C9–Xn form our preliminary template for cannabinoid analgesia. Future comparisons of this template with the properties of active and inactive cannabinoid analgesics should permit the identification of the relevant conformer at the site of action of these compounds and permit the formulation of an interaction site model for the cannabinoid analgesics

Synthesis and evaluation of 5'-modified thymidines and 5-hydroxymethyl-2'-deoxyuridines as Mycobacterium tuberculosis thymidylate kinase inhibitors

International audienceWe report the synthesis of 5'-modified thymidines (16, 18, 21, 23) and 5,5'-bis-substituted 2'-deoxyuridine analogues (30, 47) as inhibitors of thymidine monophosphate kinase of Mycobacterium tuberculosis (TMPKmt). These analogues were evaluated for their capacity to inhibit TMPKmt and solely two 5'-modified thymidines were found to possess moderate inhibitory activity. In addition, a feasibility study of protecting groups for the 5-CH(2)OH moiety of 2'-deoxyuridines is described that enables to introduce the desired 5'-modification

The Effects of Combinatorial Chemistry and Technologies on Drug Discovery and Biotechnology – a Mini Review

The review will focus on the aspects of combinatorial chemistry and technologies that are more relevant in the modern pharmaceutical process. An historical, critical introduction is followed by three chapters, dealing with the use of combinatorial chemistry/high throughput synthesis in medicinal chemistry; the rational design of combinatorial libraries using computer-assisted combinatorial drug design; and the use of combinatorial technologies in biotechnology. The impact of “combinatorial thinking” in drug discovery in general, and in the examples reported in details, is critically discussed. Finally, an expert opinion on current and future trends in combinatorial chemistry and combinatorial technologies is provided

Design of Thymidine Analogues Targeting Thymidilate Kinase of Mycobacterium tuberculosis

We design here new nanomolar antituberculotics, inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase (TMPKmt), by means of structure-based molecular design. 3D models of TMPKmt-inhibitor complexes have been prepared from the crystal structure of TMPKmt cocrystallized with the natural substrate deoxythymidine monophosphate (dTMP) (1GSI) for a training set of 15 thymidine analogues (TMDs) with known activity to prepare a QSAR model of interaction establishing a correlation between the free energy of complexation and the biological activity. Subsequent validation of the predictability of the model has been performed with a 3D QSAR pharmacophore generation. The structural information derived from the model served to design new subnanomolar thymidine analogues. From molecular modeling investigations, the agreement between free energy of complexation (ΔΔGcom) and Ki values explains 94% of the TMPKmt inhibition (pKi=-0.2924ΔΔGcom+3.234;R2=0.94) by variation of the computed ΔΔGcom and 92% for the pharmacophore (PH4) model (pKi=1.0206×pKipred-0.0832,  R2=0.92). The analysis of contributions from active site residues suggested substitution at the 5-position of pyrimidine ring and various groups at the 5′-position of the ribose. The best inhibitor reached a predicted Ki of 0.155 nM. The computational approach through the combined use of molecular modeling and PH4 pharmacophore is helpful in targeted drug design, providing valuable information for the synthesis and prediction of activity of novel antituberculotic agents