Structure-activity relationships of bradykinin potentiating peptides

Ensemble QSAR: a QSAR method based on conformational ensembles and metric descriptors

Quantitative structure-activity relationship (QSAR) is the most versatile tool in computer-assisted molecular design. One conceptual drawback seen in QSAR approaches is the "one chemical-one structure-one parameter value" dogma where the model development is based on physicochemical description for a single molecular conformation, while ignoring the rest of the conformational space. It is well known that molecules have several low-energy conformations populated at physiological temperature, and each conformer makes a significant impact on associated properties such as biological activity. At the level of molecular interaction, the dynamics around the molecular structure is of prime essence rather than the average structure. As a step toward understanding the role of these discrete microscopic states in biological activity, we have put together a theoretically rigorous and computationally tractable formalism coined as eQSAR. In this approach, the biological activity is modeled as a function of physicochemical description for a selected set of low-energy conformers, rather than that's for a single lowest energy conformation. Eigenvalues derived from the "Physicochemical property integrated distance matrices" (PD-matrices) that encompass both 3D structure and physicochemical properties, have been used as descriptors; is a novel addition. eQSAR is validated on three peptide datasets and explicitly elaborated for bradykinin-potentiating peptides. The conformational ensembles were generated by a simple molecular dynamics and consensus dynamics approaches. The eQSAR models are statistically significant and possess the ability to select the most biologically relevant conformation(s) with the relevant physicochemical attributes that have the greatest meaning for description of the biological activity.

Descriptors for antimicrobial peptides

INTRODUCTION

A frightening increase in the number of isolated multidrug resistant bacterial strains linked to the decline in novel antimicrobial drugs entering the market is a great cause for concern. Cationic antimicrobial peptides (AMPs) have lately been introduced as a potential new class of antimicrobial drugs, and computational methods utilizing molecular descriptors can significantly accelerate the development of new peptide drug candidates.

AREAS COVERED

This paper gives a broad overview of peptide and amino-acid scale descriptors available for AMP modeling and highlights which of these are currently being used in quantitative structure-activity relationship (QSAR) studies for AMP optimization. Additionally, some key commercial computational tools are discussed, and both successful and less successful studies are referenced, illustrating some of the challenges facing AMP scientists. Through examples of different peptide QSAR studies, this review highlights some of the missing links and illuminates some of the questions that would be interesting to challenge in a more systematic fashion.

EXPERT OPINION

Computer-aided peptide QSAR using molecular descriptors may provide the necessary edge to peptide drug discovery, enabling successful design of a new generation anti-infective drug molecules. However, if this wonderful scenario is to play out, computational chemists and peptide microbiologists would need to start playing together and not just side by side.

Amino acid quantitative structure property relationship database: a web-based platform for quantitative investigations of amino acids

Here, we present the AA-QSPR Db (Amino Acid Quantitative Structure Property Relationship Database): a novel, freely available web-resource of data pertaining to amino acids, both engineered and naturally occurring. In addition to presenting fundamental molecular descriptors of size, charge and hydrophobicity, it also includes online visualization tools for users to perform instant, interactive analyses of amino acid sub-sets in which they are interested. The database has been designed with extensible markup language technology to provide a flexible structure, suitable for future development. In addition to providing easy access for queries by external computers, it also offers a user-friendly web-based interface that facilitates human interactions (submission, storage and retrieval of amino acid data) and an associated e-forum that encourages users to question and discuss current and future database contents.

A new set of amino acid descriptors and its application in peptide QSARs

In this work, a new set of amino acid descriptors, i.e., VHSE (principal components score Vectors of Hydrophobic, Steric, and Electronic properties), is derived from principal components analysis (PCA) on independent families of 18 hydrophobic properties, 17 steric properties, and 15 electronic properties, respectively, which are included in total 50 physicochemical variables of 20 coded amino acids. Using the stepwise multiple regression (SMR) method combined with partial least squares (PLS), the VHSE scales are then applied to QSAR studies of bitter-tasting dipeptides (BTD), angiotensin-converting enzyme (ACE) inhibitors, and bradykinin-potentiating pentapeptides (BPP). To validate the predictive power of resulting models, external validation are also performed. A comparison of the results to those obtained with z scores and other two-dimensional (2D) or three-dimensional(3D) descriptors shows that the VHSE scales are comparable for parameterizing the structural variability of the peptide series.

Hypothesized and found mechanisms for potentiation of bradykinin actions

Potentiation of hormone actions can occur by different mechanisms, including inhibition of degrading enzymes, interaction with the hormone receptor leading to stabilization of bioactive conformation or leading to receptor homo- and hetero-oligomerization, receptor phosphorylation and dephosphorylation or can occur by directly influencing the signal transduction and ion channels. In this review the potentiation of bradykinin actions in different systems by certain compounds will be reviewed. Despite many long years of experimental research and investigation the mechanisms of potentiating action remain not fully understood. One of the most contradictory findings are the distinct differences between the inhibition of the angiotensin I-converting enzyme and the potentiation of the bradykinin induced smooth muscle reaction. Contradictory findings and hypothesized mechanisms in the literature are discussed in this review and in some cases compared to own results. Investigation of potentiating actions was extended from hypotension, smooth muscle reaction and cellular actions to activation of immunocompetent cells. In our opinion the potentiation of bradykinin action can occur by different mechanisms, depending on the system and the applied potentiating factor used.

Potentiation of bradykinin actions by analogues of the bradykinin potentiating nonapeptide BPP9alpha

Synthetic analogues of the bradykinin potentiating nonapeptide BPP9alpha indicate significantly different structural requirements for potentiation of the bradykinin (BK)-induced smooth muscle contraction (GPI) and the inhibition of isolated somatic angiotensin I-converting enzyme (ACE). The results disprove the ACE inhibition as the only single mechanism and also the direct interaction of potentiating peptides with the bradykinin receptors in transfected COS-7 cells as molecular mechanism of potentiation. Our results indicate a stimulation of inositol phosphates (IPn) formation independently from the B2 receptor. Furthermore, the results with La3+ support the role of extracellular Ca2+ and its influx through corresponding channels. The missing effect of calyculin on the GPI disproves the role of phosphatases in the potentiating action. These experimental studies should not only contribute to a better understanding of the potentiating mechanisms but also incorporate a shift in the research towards the immune system, in particular towards the immunocompetent polymorphonuclear leukocytes. The chemotaxis of these cells can be potentiated most likely by exclusive inhibition of the enzymatic degradation of bradykinin. Thus the obtained results give evidence that the potentiation of the bradykinin action can occur by different mechanisms, depending on the system and on the applied potentiating factor.

A bradykinin potentiating peptide from Egyptian cobra venom strongly affects rat atrium contractile force and cellular calcium regulation

Peptide fractions were isolated from venoms of the Egyptian snake Naja haje haje (cobra BPP) and the scorpions Buthus occitanus (BPP(B)) and Leirus quenquestriatus (BPP(L)). The pharmacological effects of these peptides were bioassayed and showed bradykinin potentiating activities. Amino acid analysis revealed that 14 amino acids contribute to the structure of BPP(B) and 16 for BPP(L), while cobra BPP was composed of 15 amino acids. Treatment of rat atrial preparations with 50 microg/ml of cobra BPP caused a significant reduction (P<0.001) in myocardial force. Elevation of extracellular calcium concentration from 1.25 to 5 mM antagonized the effect of cobra BPP in a way that restored the atrial force development. Na(+)-channel blockers did not change the force development at 5 mM Ca(2+). Experiments with (45)Ca revealed that Ca(2+) uptake of cobra BPP treated atria was 0.52+/-0.07 microM/g wet mass and the force at the end of the uptake period was 55.0+/-2.0%. The corresponding values for non-treated preparations were 0.56+/-0.04 microM/g and 92.0%+/-3.0%, respectively. Our results revealed that cobra BPP did not exhibit any effect on Ca(2+) uptake by rat atrial preparations, but strongly affected cellular Ca(2+) regulation.

Flexsim-R: a virtual affinity fingerprint descriptor to calculate similarities of functional groups

Methods to describe the similarity of fragments occurring in drug-like molecules are of fundamental importance in computational drug design. In the early phase of lead discovery, they can help to select diverse building blocks for combinatorial compound libraries intended for broad screening. In lead optimization, such methods can guide bioisosteric replacements of one functional group by another or serve as descriptors for QSAR calculations. In this paper, we outline the development of a novel 3D descriptor, termed Flexsim-R, which is a further extension of our virtual affinity fingerprint idea. Descriptors are calculated based on docking of small fragments such as building blocks for combinatorial chemistry or functional groups of drug-like molecules into a reference panel of protein binding sites. The method is validated by examining the neighborhood behavior of the affinity fingerprints and by deriving predictive QSAR models for a couple of literature peptide data sets.

Exploration of sequence space for protein engineering

The process of protein engineering is currently evolving towards a heuristic understanding of the sequence-function relationship. Improved DNA sequencing capacity, efficient protein function characterization and improved quality of data points in conjunction with well-established statistical tools from other industries are changing the protein engineering field. Algorithms capturing the heuristic sequence-function relationships will have a drastic impact on the field of protein engineering. In this review, several alternative approaches to quantitatively assess sequence space are discussed and the relatively few examples of wet-lab validation of statistical sequence-function characterization/correlation are described.

A validation study of molecular descriptors for the rational design of peptide libraries

Important molecular descriptors used for establishing quantitative structure-activity relationships are investigated to classify similar versus dissimilar peptides. When searching new lead structures, synthesizing and testing compounds which are too similar wastes time and resources. In contrast, any lead optimization program requires the investigation of similar compounds to that lead. Thus, it is important to maximize or minimize the structural diversity of peptides to design useful compound libraries for lead finding or lead refinement projects. If a molecular descriptor is a useful measure of similarity for the design of peptide libraries, small differences in this descriptor for a pair of molecules should only translate into small biological differences. Using this paradigm as a basis for descriptor validation, it was possible to rank different molecular descriptors. Those physicochemical descriptors are 2D fingerprints and five experimentally or theoretically derived principal property scales. Some theoretically derived metrics are obtained by computing interaction energies or similarity indices on predefined 3D grid points using canonical conformations for individual amino acids. The resulting 3D data matrices are analyzed using a principal component analysis leading to three principal properties for CoMFA (Comparative Molecular Field Analysis) or CoMSIA (Comparative Molecular Similarity Index Analysis) derived molecular fields. The descriptor validation results reveal the applicability of design tools on peptide data sets. Experimentally derived descriptors, in general, are more acceptable than computationally derived metrics, while the latter provide a statistically valid alternative to characterize novel building blocks. The CoMSIA metrics perform slightly better than the CoMFA-based principal properties, while GRID-based descriptors are always less acceptable.

Isolation and characterization of a bradykinin-potentiating peptide from a bovine peptic hemoglobin hydrolysate

A bradykinin potentiating peptide was isolated from a peptic bovine hemoglobin hydrolysate, by the use of reversed-phase high-performance liquid chromatography (RP-HPLC). Its primary structure, determined by fast atom bombardment (FAB) and tandem mass spectrometry (MS/MS), was identical to fragment 129-134 of the alpha-chain of bovine hemoglobin. The bradykinin potency of this peptide, as exhibited by the guinea-pig ileum contraction, was significant and comparable with some others previously described.

Theoretical amino acid descriptors. Application to bradykinin potentiating peptides

A simple and computationally nonintensive technique based on principal component analysis of 3-dimensional fields to derive theoretical descriptors is presented. The descriptors are then applied to a quantitative structure-activity relationship study on bradykinin potentiating pentapeptides.

Pharmacological properties of a new kinin-potentiating peptide generated from human serum proteins

A kinin-potentiating peptide (KPP) generated from human plasma proteins on trypsin incubation was partially purified by ultrafiltration and ion-exchange chromatography and was characterized through some of its pharmacological properties. KPP itself was devoid of any action but it potentiated the guinea-pig ileum contractions elicited by several kinins, including an analog resistant to angiotensin-converting enzyme (ACE). In contrast, contractions induced by angiotensin II, histamine, acetylcholine, barium chloride and substance P were not potentiated. Not only did KPP have high specificity towards kinins, but its action started immediately and induced kinin potentiation in a dose-dependent and reversible manner. Furthermore KPP potentiated the bradykinin contracting effects on the rat uterus, a preparation with very poor ACE activity, and on guinea-pig ileum previously incubated with 1.10-phenanthroline, a metal chelator able to inhibit ACE and kininase I activities and with phosphoramidon, a specific inhibitor of neutral endopeptidase (NEP). The results suggest that the potentiating effect of KPP is due to a mechanism different from the inhibition of kinin metabolism by ACE, NEP and kininase I.

Further studies on the structure-activity relationships of bradykinin-potentiating peptides

Several pentapeptides were synthesized and tested for bradykinin-potentiating activity. From these and previous data it appeared that an (L)-aromatic amino acid residue (preferably Trp) in position 3 is essential for high activity. Position 3 represents a stereospecific pillar function, whereas the other positions and the lipophilicity/hydrophilicity balance are important for additional activity. So far, BPP5a seems to have the optimal structure for a bradykinin-potentiating pentapeptide.

Potentiation of bradykinin with synthetic peptides on guinea pig ileum

Potentiation of the activity of bradykinin on the isolated guinea pig ileum was studied using a designed test system with the synthetic peptides Leu-Val-Glu-Ser-Ser-Lys, Thr-Pro-Val-Ser-Glu-Lys, derivatives of the former coupled to the N- and C-terminals of bradykinin and two peptides with phenylalanine substituted with its isomer L-3-amino-3-phenylpropanoic acid in the 5- and 5,8-positions in bradykinin respectively. On average, two times potentiation effects were obtained at 10-6 to 10-8 M concentrations of the peptides. After elimination of the basic lysine no potentiation occurred with synthetic Leu-Val-Glu-Ser-Ser. With the [beta Phe5,8]-bradykinin a mixed sensitizing/potentiating effect was observed, suggesting that a separation of the two effects may be difficult with an intact receptor structure of this kind. This peptide was not hydrolyzed by carboxypeptidase B or chymotrypsin.