Glaucius Oliva

Molecular Docking and Structure-Based Drug Design Strategies

Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. Today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.

Virtual Screening and Its Integration with Modern Drug Design Technologies

Drug discovery is a highly complex and costly process, which demands integrated efforts in several relevant aspects involving innovation, knowledge, information, technologies, expertise, R&D investments and management skills. The shift from traditional to genomics- and proteomics-based drug research has fundamentally transformed key R&D strategies in the pharmaceutical industry addressed to the design of new chemical entities as drug candidates against a variety of biological targets. Therefore, drug discovery has moved toward more rational strategies based on our increasing understanding of the fundamental principles of protein-ligand interactions. The combination of available knowledge of several 3D protein structures with hundreds of thousands of small-molecules have attracted the attention of scientists from all over the world for the application of structure- and ligand-based drug design approaches. In this context, virtual screening technologies have largely enhanced the impact of computational methods applied to chemistry and biology and the goal of applying such methods is to reduce large compound databases and to select a limited number of promising candidates for drug design. This review provides a perspective of the utility of virtual screening in drug design and its integration with other important drug discovery technologies such as high-throughput screening (HTS) and QSAR, highlighting the present challenges, limitations, and future perspectives in medicinal chemistry.

The reactivity of five-coordinate Ru(II) (1,4-bis(diphenylphosphino)butane) complexes with the N-donor ligands: ammonia, pyridine, 4-substituted pyridines, 2,2′-bipyridine, bis(o-pyridyl)amine, 1,10-phenanthroline, 4,7-diphenylphenanthroline and ethylenediamine

Abstract A series of Ru(II)(1,4-bis(diphenylphosphino)butane)(L)2 complexes was synthesized from [RuCl2(dppb) l2 (μ-dppb) or RuCl2 (dppb)- (PPh3); dppb = Ph2P(CH2)4PPH2, L = NH3, pyridine (py), 4-aminopyridine (4-NH2py), 4-cyanopyridine (4-CNpy), 4-dimethylaminopyridine (4-Me2Npy), 4-methylpyridine (4-Mepy), 4-phenylpyridine (4-Phpy), 4-vinylpyridine (4-Phy) and N-methylimidazole (Melm) and L2 = 2,2′-bipyridine (bipy), bis(o-pyridyl)amine (bpa), 1,10-phenanthroline (phen), 4,7-diphenylphenanthroline (or bathophenanthroline, batho) and ethylenediamine (en). The complexes were characterized by elemental analysis, cyclic voltametry, UV-Vis, NMR and IR spectroscopies. The structures of trans-RuCl2(dppb) (py)2 (3), cis-RuCl2(dppb)(bipy) (4) and cis-RuCl2(dppb) (phen) (5) were established by X-ray crystallographic analyses. Crystals of trans-3, cis-4-CH2Cl2 and cis-5-solvate are all monoclinic, space group P21/c, with Z=4; a = 12.946 (2), b = 14.204(3), c = 18.439(4) A , β = 90.08(2)° for trans-3; a=10.694(6), b=18.485(6), c=18.632(7) A , β = 90.26(3)° for cis-4·CH2Cl2; a = 17.094 (1), b = 9.923(2), c = 21.905(2) A , β = 98.883 (6)° for cis-5 solvate. The structures were solved by the heavy atom Patterson method and were refined by full-matrix least-squares procedures to R=0.069, 0.071 and 0.036 (Rw = 0.069, 0.076 and 0.039) for 1957, 4165 and 4824 reflections with l ≥ 3σ (l), respectively.

Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 å resolution

BACKGROUND Glucosamine 6-phosphate deaminase from Escherichia coli is an allosteric hexameric enzyme which catalyzes the reversible conversion of D-glucosamine 6-phosphate into D-fructose 6-phosphate and ammonium ion and is activated by N-acetyl-D-glucosamine 6-phosphate. Mechanistically, it belongs to the group of aldoseketose isomerases, but its reaction also accomplishes a simultaneous amination/deamination. The determination of the structure of this protein provides fundamental knowledge for understanding its mode of action and the nature of allosteric conformational changes that regulate its function. RESULTS The crystal structure of glucosamine 6-phosphate deaminase with bound phosphate ions is presented at 2.1 A resolution together with the refined structures of the enzyme in complexes with its allosteric activator and with a competitive inhibitor. The protein fold can be described as a modified NAD-binding domain. CONCLUSIONS From the similarities between the three presented structures, it is concluded that these represent the enzymatically active R state conformer. A mechanism for the deaminase reaction is proposed. It comprises steps to open the pyranose ring of the substrate and a sequence of general base-catalyzed reactions to bring about isomerization and deamination, with Asp72 playing a key role as a proton exchanger.

Structure of an Odorant-Binding Protein from the Mosquito Aedes aegypti Suggests a Binding Pocket Covered by a pH-Sensitive “Lid”

Background The yellow fever mosquito, Aedes aegypti, is the primary vector for the viruses that cause yellow fever, mostly in tropical regions of Africa and in parts of South America, and human dengue, which infects 100 million people yearly in the tropics and subtropics. A better understanding of the structural biology of olfactory proteins may pave the way for the development of environmentally-friendly mosquito attractants and repellents, which may ultimately contribute to reduction of mosquito biting and disease transmission. Methodology Previously, we isolated and cloned a major, female-enriched odorant-binding protein (OBP) from the yellow fever mosquito, AaegOBP1, which was later inadvertently renamed AaegOBP39. We prepared recombinant samples of AaegOBP1 by using an expression system that allows proper formation of disulfide bridges and generates functional OBPs, which are indistinguishable from native OBPs. We crystallized AaegOBP1 and determined its three-dimensional structure at 1.85 Å resolution by molecular replacement based on the structure of the malaria mosquito OBP, AgamOBP1, the only mosquito OBP structure known to date. Conclusion The structure of AaegOBP1 ( = AaegOBP39) shares the common fold of insect OBPs with six α-helices knitted by three disulfide bonds. A long molecule of polyethylene glycol (PEG) was built into the electron-density maps identified in a long tunnel formed by a crystallographic dimer of AaegOBP1. Circular dichroism analysis indicated that delipidated AaegOBP1 undergoes a pH-dependent conformational change, which may lead to release of odorant at low pH (as in the environment in the vicinity of odorant receptors). A C-terminal loop covers the binding cavity and this “lid” may be opened by disruption of an array of acid-labile hydrogen bonds thus explaining reduced or no binding affinity at low pH.

Development and characterization of an immobilized enzyme reactor based on glyceraldehyde-3-phosphate dehydrogenase for on-line enzymatic studies

The glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been extensively studied as a target for new drugs to be used in the treatment of various parasitic diseases. The standard approach to the determination of GAPDH activity utilizes solubilized free enzyme and is limited by the enzymes low stability. In the current study the stability of GAPDH was significantly increased through the covalent immobilization of the enzyme on a wide-pore silica support containing glutaraldehyde (Glut-P). The optimal conditions for the immobilization were: 100 mg Glut-P stationary phase, approximately 150 microg of enzyme dissolved in pyrophosphate buffer (15 mM, pH 8.5). The mixture was gently agitated for 6 h at 4 degrees C. Under these conditions 91.3% of protein was immobilized on 100 mg of Glut-P support with retention of 2.97% of the initial enzymatic activity. The activity of the immobilized GAPDH was stable for over 30 days. The GAPDH-Glut-P stationary phase was packed into a glass column to produce a GAPDH immobilized enzyme reactor (GAPDH-IMER). The activity and kinetic parameters of the GAPDH-IMER were investigated and the results demonstrated that the enzyme retained its activity and sensitivity to the competitive inhibitor agaric acid.

The protein crystallography beamline at LNLS, the Brazilian National Synchrotron Light Source

Abstract The Brazilian National Synchrotron Light Laboratory - LNLS, will have a dedicated protein crystallography beamline. The beamline under construction includes cylindrical mirror and bent crystal monochromator focusing the high flux of synchrotron radiation in the horizontal plane at the position of the sample. The monochromatic radiation will be tuneable between 2.0 and 1.0 A with the optimum wavelength at 1.3–1.6 A, chosen with the aim of maximizing the photon flux from the bending magnets of the storage ring (1.37 GeV). Diffraction images will be recorded on a commercial image plate detector system with on-line readout. The beamline set-up will include cooler/chiller for the samples and biochemical lab for crystallization, heavy-metal soaks, crystal storage and mounting at 22°C and 4°C, will also be available. The facility, intended to serve the national and international community, is planned to be brought into operation in the second half of 1997. It is foreseen that the commissioning of the first protein crystallography beamline in Latin America will boost the number of protein structures determined locally and will increase the general interest of the molecular biology and biochemical research community of Brazil in this area.

Synthesis and characterization of aquo[N,N′-ethylenebis(3-ethoxysalicylideneaminato)]dioxouranium(VI)

Abstract The synthesis, spectra and structure of [UO2(3-EtOsalen)(H2O) · H2O [where (3-EtOsalen) is the Schiff base N,N′-ethylenebis(3-ethoxysalicylidieniminato)] are reported. The IR spectra and 1H and 13C NMR spectra of the free ligand and the uranyl complex were recorded. Assignment of the IR bands and NMR chemical shifts are given. Four bands were observed for the complex, 455, 396, 341 and 267 nm in acetonitrile and 472, 396, 345 and 269 nm in dimethyl sulphoxide. The weak bands at 455 and 472 nm are assigned to the 1 E ∗ → 2 π u transition. The UO22+ ion is coordinated to two nitrogen and two oxygen atoms of the ligand, with a water molecule completing the characteristic seven-coordinate, pentagonal-bipyramidal geometry. Another water molecule completes the crystal structure and is involved in several intra- and intermolecular hydrogen bonds.

Novel ruthenium complexes as potential drugs for Chagas's disease: enzyme inhibition and in vitro/in vivo trypanocidal activity

Background and purpose:  The discovery of the pharmacological functions of nitric oxide has led to the development of NO donor compounds as therapeutic agents. A new generation of ruthenium NO donors, cis‐[Ru(NO)(bpy)2L]Xn, has been developed, and our aim was to show that these complexes are able to lyse Trypanosoma cruzi in vitro and in vivo.

Structure of Trypanosoma cruzi glycosomal glyceraldehyde-3-phosphate dehydrogenase complexed with chalepin, a natural product inhibitor, at 1.95 Å resolution

The structure of the glycosomal glyceraldehyde‐3‐phosphate dehydrogenase (gGAPDH) from Trypanosoma cruzi complexed with chalepin, a natural product from Pilocarpus spicatus, has been determined by X‐ray crystallography to 1.95 Å resolution. The structure is in the apo form without cofactors in the subunits of the tetrameric gGAPDH in the asymmetric unit. Unequivocal density corresponding to the inhibitor was clearly identified in one monomer. The final refined model of the complex shows extensive conformational changes when compared with the native structure. The mode of binding of chalepin to gGAPDH and its implications for inhibitor design are discussed.