Crystallographic analysis of human hemoglobin elucidates the structural basis of the potent and dual antisickling activity of pyridyl derivatives of vanillin.

Vanillin has previously been studied clinically as an antisickling agent to treat sickle-cell disease. In vitro investigations with pyridyl derivatives of vanillin, including INN-312 and INN-298, showed as much as a 90-fold increase in antisickling activity compared with vanillin. The compounds preferentially bind to and modify sickle hemoglobin (Hb S) to increase the affinity of Hb for oxygen. INN-312 also led to a considerable increase in the solubility of deoxygenated Hb S under completely deoxygenated conditions. Crystallographic studies of normal human Hb with INN-312 and INN-298 showed that the compounds form Schiff-base adducts with the N-terminus of the α-subunits to constrain the liganded (or relaxed-state) Hb conformation relative to the unliganded (or tense-state) Hb conformation. Interestingly, while INN-298 binds and directs its meta-positioned pyridine-methoxy moiety (relative to the aldehyde moiety) further down the central water cavity of the protein, that of INN-312, which is ortho to the aldehyde, extends towards the surface of the protein. These studies suggest that these compounds may act to prevent sickling of SS cells by increasing the fraction of the soluble high-affinity Hb S and/or by stereospecific inhibition of deoxygenated Hb S polymerization.

Structure-based drug design strategies in medicinal chemistry.

A broad variety of medicinal chemistry approaches can be used for the identification of hits, generation of leads, as well as to accelerate the development of high quality drug candidates. Structure-based drug design (SBDD) methods are becoming increasingly powerful, versatile and more widely used. This review summarizes current developments in structure-based virtual screening and receptor-based pharmacophores, highlighting achievements as well as challenges, along with the value of structure-based lead optimization, with emphasis on recent examples of successful applications for the identification of novel active compounds.

Structure of relaxed-state human hemoglobin: insight into ligand uptake, transport and release.

Hemoglobin was one of the first protein structures to be determined by X-ray crystallography and served as a basis for the two-state MWC model for the mechanism of allosteric proteins. Since then, there has been an ongoing debate about whether Hb allostery involves the unliganded tense T state and the liganded relaxed R state or whether it involves the T state and an ensemble of liganded relaxed states. In fact, the former model is inconsistent with many functional observations, as well as the recent discoveries of several relaxed-state Hb structures such as RR2, R3 and R2. One school of thought has suggested the R2 state to be the physiologically relevant relaxed end state, with the R state mediating the T-->R2 transition. X-ray studies have been performed on human carbonmonoxy Hb at a resolution of 2.8 A. The ensuing liganded quaternary structure is different from previously reported liganded Hb structures. The distal beta-heme pocket is the largest when compared with other liganded Hb structures, partly owing to rotation of betaHis63(E7) out of the distal pocket, creating a ligand channel to the solvent. The structure also shows unusually smaller alpha- and beta-clefts. Results from this study taken in conjunction with previous findings suggest that multiple liganded Hb states with different quaternary structures may be involved in ligand uptake, stabilization, transport and release.

Pyridyl derivatives of benzaldehyde as potential antisickling agents.

Compounds that bind to sickle hemoglobin (Hb S) producing an allosteric shift to the high-affinity Hb S that does not polymerize are being developed to treat sickle cell anemia (SCA). In this study, three series of pyridyl derivatives of substituted benzaldehydes (Classes I-III) that combine structural features of two previously determined potent antisickling agents, vanillin and pyridoxal, were synthesized. When analyzed with normal human whole blood, the compounds form Schiff-base adducts with Hb and left shift the oxygen equilibrium curve (OEC) to the more soluble high-affinity Hb, more than vanillin or pyridoxal. Generally, Class-I compounds with an aromatic aldehyde located ortho to the pyridyl substituent are the most potent, followed by the Class-II compounds with the aldehyde at the meta-position. Class-III compounds with the aldehyde at the para position show the weakest activity. The structure-activity studies of these pyridyl derivatives of substituted benzaldehydes demonstrate significant allosteric potency that may be useful for treating SCA.

Identification of novel allosteric regulators of human-erythrocyte pyruvate kinase.

Erythrocyte pyruvate kinase (PK) is an important glycolytic enzyme, and manipulation of its regulatory behavior by allosteric modifiers is of interest for medicinal purposes. Human-erythrocyte PK was expressed in Rosetta cells and purified on an Ni-NTA column. A search of the small-molecules database of the National Cancer Institute (NCI), using the UNITY software, led to the identification of several compounds with similar pharmacophores as fructose-1,6-bisphosphate (FBP), the natural allosteric activator of the human kinases. The compounds were subsequently docked into the FBP binding site using the programs FlexX and GOLD, and their interactions with the protein were analyzed with the energy-scoring function of HINT. Seven promising candidates, compounds 1-7, were obtained from the NCI, and subjected to kinetics analysis, which revealed both activators and inhibitors of the R-isozyme of PK (R-PK). The allosteric effectors discovered in this study could prove to be lead compounds for developing medications for the treatment of hemolytic anemia, sickle-cell anemia, hypoxia-related diseases, and other disorders arising from erythrocyte PK malfunction.

The consequences of scoring docked ligand conformations using free energy correlations.

Ligands from a set of 19 protein-ligand complexes were re-docked with AutoDock, GOLD and FlexX using the scoring algorithms native to these programs supplemented by analysis using the HINT free energy force field. A HINT scoring function was calibrated for this data set using a simple linear regression of total HINT score for crystal-structure complexes vs. measured free energy of binding. This function had an r(2) of 0.84 and a standard error of +/-0.42 kcal mol(-1). The free energies of binding were calculated for the best poses using the AutoDock, GOLD and FlexX scoring functions. The AutoDock and GoldScore algorithms estimated more than half of the binding free energies within the reported calibration standard errors for these functions, while that of FlexX did not. In contrast, the calibrated HINT scoring function identified optimized poses with standard errors near +/-0.5 kcal mol(-1). When the metric of success is minimum RMSD (vs. crystallographic coordinates) the three docking programs were more successful, with mean RMSDs for the top-ranking poses in the 19 complexes of 3.38, 2.52 and 2.62 A for AutoDock, GOLD and FlexX, respectively. Two key observations in this study have general relevance for computational medicinal chemistry: first, while optimizing RMSD with docking score functions is clearly of value, these functions may be less well optimized for free energy of binding, which has broader applicability in virtual screening and drug discovery than RMSD; second, scoring functions uniquely calibrated for the data set or sets under study should nearly always be preferable to universal scoring functions. Due to these advantages, the poses selected by the HINT score also required less post-docking structure optimization to produce usable molecular models. Most of these features may be achievable with other scoring functions.

Identification of a series of tetrahydroisoquinoline derivatives as potential therapeutic agents for breast cancer.

A series of tetrahydroisoquinoline-N-phenylamide derivatives were designed, synthesized, and tested for their relative binding affinities, and antagonistic activities against estrogen receptor (ER). Compound 1f (relative binding affinity, RBA=5) showed higher binding affinity than tamoxifen (RBA=1), a potent ER antagonist and currently being used for breast cancer therapy. Compound 1f also exerted optimal antagonistic activity against ER in reporter and cell proliferation assays. Interestingly, compound 1j, which only has a minor agonistic effect against ER, acted as a progesterone receptor (PR) antagonist and exerted agonistic activity against AP-1 through ER pathway. Our results show that these new compounds can be employed as leading pharmacophore for further development of potent selective ER and/or PR modulators or antagonists.

Identification of a lead pharmacophore for the development of potent nuclear receptor modulators as anticancer and X syndrome disease therapeutic agents.

A series of tetrahydroisoquinoline-N-phenylamide derivatives were designed, synthesized, and tested for their relative binding affinity and antagonistic activity against androgen receptor (AR). Compound 1b (relative binding affinity, RBA = 6.4) and 1h (RBA = 12.6) showed higher binding affinity than flutamide (RBA = 1), a potent AR antagonist. These two compounds also exerted optimal antagonistic activity against AR in reporter assays. The derivatives were also tested for their activities against another nuclear receptor, farnesoid x receptor (FXR), with most compounds acting as weak antagonists, however, compound 1h behaved as a FXR agonist with activity slightly less than that of chenodeoxycholic acid (CDCA), a natural FXR agonist.

Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules.

The energetics and hydrogen bonding pattern of water molecules bound to proteins were mapped by analyzing structural data (resolution better than 2.3A) for sets of uncomplexed and ligand-complexed proteins. Water-protein and water-ligand interactions were evaluated using hydropatic interactions (HINT), a non-Newtonian forcefield based on experimentally determined logP(octanol/water) values. Potential water hydrogen bonding ability was assessed by a new Rank algorithm. The HINT-derived binding energies and Ranks for second shell water molecules were -0.04 kcal mol(-1) and 0.0, respectively, for first shell water molecules -0.38 kcal mol(-1) and 1.6, for active site water molecules -0.45 kcal mol(-1) and 2.3, for cavity water molecules -0.55 kcal mol(-1) and 3.3, and for buried water molecules -0.56 kcal mol(-1) and 4.4. For the last four classes, similar energies indicate that internal and external water molecules interact with protein almost equally, despite different degrees of hydrogen bonding. The binding energies and Ranks for water molecules bridging ligand-protein were -1.13 kcal mol(-1) and 4.5, respectively. This energetic contribution is shared equally between protein and ligand, whereas Rank favors the protein. Lastly, by comparing the uncomplexed and complexed forms of proteins, guidelines were developed for prediction of the roles played by active site water molecules in ligand binding. A water molecule with high Rank and HINT score is unlikely to make further interactions with the ligand and is largely irrelevant to the binding process, while a water molecule with moderate Rank and high HINT score is available for ligand interaction. Water molecule displaced for steric reasons were characterized by lower Rank and HINT score. These guidelines, tested by calculating HINT score and Rank for 50 water molecules bound in the active site of four uncomplexed proteins (for which the structures of the liganded forms were also available), correctly predicted the ultimate roles (in the complex) for 76% of water molecules. Some failures were likely due to ambiguities in the structural data.

Tools for building a comprehensive modeling system for virtual screening under real biological conditions: The Computational Titration algorithm.

Computational tools utilizing a unique empirical modeling system based on the hydrophobic effect and the measurement of logP(o/w) (the partition coefficient for solvent transfer between 1-octanol and water) are described. The associated force field, Hydropathic INTeractions (HINT), contains much rich information about non-covalent interactions in the biological environment because of its basis in an experiment that measures interactions in solution. HINT is shown to be the core of an evolving virtual screening system that is capable of taking into account a number of factors often ignored such as entropy, effects of solvent molecules at the active site, and the ionization states of acidic and basic residues and ligand functional groups. The outline of a comprehensive modeling system for virtual screening that incorporates these features is described. In addition, a detailed description of the Computational Titration algorithm is provided. As an example, three complexes of dihydrofolate reductase (DHFR) are analyzed with our system and these results are compared with the experimental free energies of binding.

Structures of R- and T-state hemoglobin Bassett: elucidating the structural basis for the low oxygen affinity of a mutant hemoglobin.

The crystal structures of R- and T-state hemoglobin (Hb) Bassett have been determined to 2.15 and 1.80 A resolution, respectively. Physiologically, Hb Bassett (alphaAsp94-->Ala) is characterized by a low affinity for oxygen, a reduced Bohr effect and low cooperativity, as well as being slightly unstable (compared with normal adult hemoglobin; HbA). Comparisons between the Hb Bassett structures and previously determined R- and T-state HbA structures revealed that this mutant shares similar tertiary and quaternary structures with other Hbs. However, this analysis did identify localized structural differences between R-state Hb Bassett and R-state HbA at the alpha1beta2 (alpha2beta1) dimer interface and at the beta-cleft. Specifically, the beta-FG corner has shifted closer to the alpha-C helix in the mutant R structure. In addition, four intersubunit hydrogen bonds found at the alpha1beta2 interfaces of native R-state Hb structures are abolished or weakened and subsequently replaced by two new intersubunit hydrogen bonds in R-state Hb Bassett. Remarkably, the newly formed hydrogen bonds in the R-state mutant structure are also observed in T-state Hb structures. At the beta-cleft, betaHis46, which is known to contribute to the Bohr effect in Hb, makes a unique hydrogen-bonding interaction with betaAsn139 in the R-state Hb Bassett. Unlike the R-state mutant, the T-state Hb Bassett structure does not display any significant structural changes at both the alpha1beta2 (alpha2beta1) dimer interface and the beta-cleft. Quite significantly, the mutation has led to removal of an interdimer repulsion involving alpha1Asp94 and beta2Asp99. The R- and T-state structures of Hb Bassett suggest a stereochemical basis for the observed functional properties of this mutant.

5-hydroxymethyl-2-furfural modifies intracellular sickle haemoglobin and inhibits sickling of red blood cells.

In an attempt to find new types of anti-sickling agents that specifically bind to intracellular sickle haemoglobin (HbS) without inhibition by plasma and tissue proteins or other undesirable consequences, we identified 5-hydroxymethyl-2-furfural (5HMF), a naturally occurring aromatic aldehyde, as an agent that fulfils this criterion. Preliminary studies in vitro showed that 5HMF forms a high-affinity Schiff-base adduct with HbS and inhibits red cell sickling by allosterically shifting oxygen equilibrium curves towards the left. Further studies with transgenic (Tg) sickle mice showed that orally administered 5HMF was rapidly absorbed into the bloodstream from the gastrointestinal tract without being destroyed, traversed the red blood cell membrane and specifically bound with, and modified, HbS molecules at levels as high as 90%. Pretreatment of Tg sickle mice with 5HMF inhibited the formation of sickle cells and significantly prolonged survival time under severe hypoxia, compared with untreated mice, which died within 15 min because of sickling-dependent pulmonary sequestration. These results indicate the feasibility of 5HMF as an attractive potential candidate for therapy of sickle cell disease.

Free energy of ligand binding to protein: evaluation of the contribution of water molecules by computational methods.

One of the more challenging issues in medicinal chemistry is the computation of the free energy of ligand binding to macromolecular targets. This allows for the screening of libraries of chemicals for fast and inexpensive identification of lead compounds. Many attempts have been made and several algorithms have been developed for this purpose. Whereas enthalpic contributions are evaluated using methods and equations for which there is a reasonable consensus among researchers, the entropic contribution is evaluated using very different, and, in some cases, very approximate methods, or it is entirely ignored. Entropic contributions are of primary importance in the formation of many ligand-protein complexes, as well as in protein folding. The hydrophobic interaction, associated with the release of water molecules from the protein active site and the ligand, plays a significant role in complex formation, predominantly contributing to the total entropy change and, in some cases, to the total free energy of binding. There are distinct approaches for the evaluation of the contribution of water molecules to the free energy of binding based on Newtonian mechanics force fields, multi-parameter empirical scoring functions and experimental force fields. This review describes these methods -- discussing both their advantages and limitations. Particular emphasis will be placed on HINT (Hydropatic INTeractions), a "natural" force field that takes into account in a unified way enthalpic and entropic contributions of all interacting atoms in protein-ligand complexes, including released and structured water molecules. As a case-study, the contribution of water molecules to the binding free energy of HIV-1 protease inhibitors is evaluated.

Characterization of hemoglobin bassett (alpha94Asp-->Ala), a variant with very low oxygen affinity.

Hemoglobin (Hb) Bassett, an abnormal Hb variant with a markedly reduced oxygen affinity, was discovered in a Caucasian (Anglo-Saxon) male child who experienced episodes of cyanosis. Cation-exchange and reversed-phase (RP) high-performance liquid chromatography (HPLC) showed that the patient has an abnormal Hb, with a mutation in the alpha-globin. Tryptic peptide digest of the abnormal alpha-globin with subsequent HPLC analysis revealed abnormal elution of the alpha-T11 peptide. Further studies with Edman sequencing and electrospray mass spectrometry of tryptic peptide alpha-T11, as well as structural analysis by X-ray crystallography revealed an Asp-->Ala substitution at the alpha94 (G1) position, a match for Hb Bassett. Detailed functional studies showed that this Hb variant had a markedly reduced oxygen affinity (P(50) at pH 7.0 = 22 mmHg; Hb A P(50) = 10.5 mmHg), reduced Bohr effect (-0.26 compared to - 0.54 in Hb A), and low subunit cooperativity (n = 1.4, compared to 2.6 in Hb A). X-ray crystallography results explain the probable effects of the structural modification on the oxygen-binding properties of this Hb variant.

Computational titration analysis of a multiprotic HIV-1 protease-ligand complex.

A new computational method for analyzing the protonation states of protein-ligand complexes with multiple ionizable groups is applied to the structurally characterized complex between the peptide Glu-Asp-Leu and HIV-1 protease. This complex has eight ionizable groups at the active site: four from the ligand and four Asp residues on the protein. Correlation, with an error of ca. 0.6 kcal mol-1, is made between the calculated titration curve and the experimental titration curve. The analysis suggests that between four and five of the eight ionizable groups are protonated at the pH of crystallization.

Structural basis for the potent antisickling effect of a novel class of five-membered heterocyclic aldehydic compounds.

Naturally occurring five-membered heterocyclic aldehydes, including 5-hydroxymethyl-2-furfural, increase the oxygen affinity of hemoglobin (Hb) and strongly inhibit the sickling of homozygous sickle red blood (SS) cells. X-ray studies of Hb complexed with these compounds indicate that they form Schiff base adducts in a symmetrical fashion with the N-terminal alphaVal1 nitrogens of Hb. Interestingly, two cocrystal types were isolated during crystallization experiments with deoxygenated Hb (deoxyHb): one crystal type was composed of the low-affinity or tense (T) state Hb quaternary structure; the other crystal type was composed of high-affinity or relaxed state Hb (with a R2 quaternary structure). The R2 crystal appears to be formed as a result of the aldehydes binding to fully or partially ligated Hb in the deoxyHb solution. Repeated attempts to crystallize the compounds with liganded Hb failed, except on rare occasions when very few R state crystals were obtained. Oxygen equilibrium, high performance liquid chromatography (HPLC), antisickling, and X-ray studies suggest that the examined heterocyclic aldehydes may be acting to prevent polymerization of sickle hemoglobin (HbS) by binding to and stabilizing liganded Hb in the form of R2 and/or various relaxed state Hbs, as well as binding to and destabilizing unliganded T state Hb. The proposed mechanism may provide a general model for the antisickling effects of aldehyde containing small molecules that bind to N-terminal alphaVal1 nitrogens of Hb. The examined compounds also represent a new class of potentially therapeutic agents for treating sickle cell disease (SCD).

Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 3. The free energy contribution of structural water molecules in HIV-1 protease complexes.

Structural water molecules within protein active sites are relevant for ligand-protein recognition because they modify the active site geometry and contribute to binding affinity. In this work an analysis of the interactions between 23 ligands and dimeric HIV-1 protease is reported. The X-ray structures of these complexes show the presence of four types of structural water molecules: water 301 (on the symmetry axis), water 313, water 313bis, and peripheral waters. Except for water 301, these are generally complemented with a symmetry-related set. The GRID program was used both for checking water locations and for placing water molecules that appear to be missing from the complexes due to crystallographic uncertainty. Hydropathic analysis of the energetic contributions using HINT indicates a significant improvement of the correlation between HINT scores and the experimentally determined binding constants when the appropriate bridging water molecules are taken into account. In the absence of water r2 = 0.30 with a standard error of +/- 1.30 kcal mol(-1) and when the energetic contributions of the constrained waters are included r2 = 0.61 with a standard error of +/- 0.98 kcal mol(-1). HINT was shown to be able to map quantitatively the contribution of individual structural waters to binding energy. The order of relevance for the various types of water is water 301 > water 313 > water 313bis > peripheral waters. Thus, to obtain the most reliable free energy predictions, the contributions of structural water molecules should be included. However, care must be taken to include the effects of water molecules that add information value and not just noise.

A nonpeptidic sulfonamide inhibits the p53-mdm2 interaction and activates p53-dependent transcription in mdm2-overexpressing cells.

The evaluation of a sulfonamide inhibitor of the p53-mdm2 interaction is presented. The compound was identified using 3D database searching techniques based on a computationally derived pharmacophore model of mdm2 binding. It inhibits the physical interaction of recombinant p53 and mdm2 in vitro and increases p53-dependent transcription in an mdm2-overexpressing cell line.

Getting it right: modeling of pH, solvent and "nearly" everything else in virtual screening of biological targets.

"Getting it right" refers to the careful modeling of all elements in the living system, i.e. biological macromolecules, ligands and water molecules. In addition, careful attention should be paid to the protonation state of ionizable functional groups on the ligands and residues at the active site. Computational technology based on the empirical HINT program is described to: (1) calculate free energy scores for ligand binding; (2) include the implicit and explicit effects of water in and around the ligand binding site; and (3) incorporate the effects of global and local pH in molecular models. This last point argues for the simultaneous consideration of a number of molecular models, each with different protonation profiles. Data from recent studies of protein-ligand systems (trypsin, thrombin, neuraminidase, HIV-1 protease and others) are used to illustrate the concepts in the paper. Also discussed are experimental factors related to accurate free energy predictions with this and other computational technologies.