Peptide reagent design based on physical and chemical properties of amino acid residues

It has tremendous values for both drug discovery and basic research to develop a solid bioinformatical tool for guiding peptide reagent design. Based on the physical and chemical properties of amino acids, a new strategy for peptide reagent design, the so-called AABPD (amino acid based-peptide design), is proposed. The peptide samples in a training dataset are described by a series of HMLP (heuristic molecular lipophilicity potential) parameters and other physicochemical properties of amino acid residues that form a three-dimensional data matrix where each component is defined by three indexes: the first index refers to the peptide samples, the second to the amino acid positions, and the third to the amino acid parameters. The binding free energy between a peptide ligand and its protein receptor is calculated by a linear free energy equation through the physicochemical parameters, resulting in a set of simultaneous linear equations between the bioactivity of the peptides and the physicochemical properties of amino acids. An iterative double least square technique is developed for the solution of the three-dimensional simultaneous linear equation set to determine the amino acid position coefficients of peptide sequence and the physicochemical parameter coefficients of amino acid residues alternately. The two sets of coefficients thus obtained are used for predicting the bioactivity of other query peptide reagents. Two calculation examples, the peptide substrate specificity of the SARS coronavirus 3C-like proteinase and the affinity prediction for epitope-peptides with Class I MHC molecules are studied by using the peptide reagent design strategy.     

Recent advances in QSAR and their applications in predicting the activities of chemical molecules, peptides and proteins for drug design

This review is to summarize three new QSAR (quantitative structure-activity relationship) methods recently developed in our group and their applications for drug design. Based on more solid theoretical models and advanced mathematical techniques, the conventional QSAR technique has been recast in the following three aspects. (1) In the fragment-based two dimensional QSAR, or abbreviated as FB-QSAR, the molecular structures in a family of drug candidates are divided into several fragments according to the substitutes being investigated. The bioactivities of drug candidates are correlated with physicochemical properties of the molecular fragments through two sets of coefficients: one is for the physicochemical properties and the other for the molecular fragments. (2) In the multiple field three dimensional QSAR, or MF-3D-QSAR, more molecular potential fields are integrated into the comparative molecular field analysis (CoMFA) through two sets of coefficients: one is for the potential fields and the other for the Cartesian three dimensional grid points. (3) In the AABPP (amino acid-based peptide prediction), the bioactivities of peptides or proteins are correlated with the physicochemical properties of all or partial residues of the sequence through two sets of coefficients: one is for the physicochemical properties of amino acids and the other for the weight factors of the residues. Meanwhile, an iterative double least square (IDLS) technique is developed for solving the two sets of coefficients in a training dataset alternately and iteratively. Using the two sets of coefficients, one can predict the bioactivity of a query peptide, protein, or drug candidate. Compared with the old methods, the new QSAR approaches as summarized in this review possess machine learning ability, can remarkably enhance the prediction power, and provide more structural information. Meanwhile, the future challenge and possible development in this area have been briefly addressed as well.     

Design,structure-based focusing and in silico screening of combinatorial library of peptidomimetic inhibitors of Dengue virus NS2B-NS3 protease

Abstract  

Serine protease activity of the NS3 protein of Dengue virus is an important target of antiviral agents that interfere with the viral polyprotein precursor processing catalyzed by the NS3 protease (NS3pro), which is important for the viral replication and maturation. Recent studies showed that substrate-based peptidomimetics carrying an electrophilic warhead inhibit the NS2B-NS3pro cofactor-protease complex with inhibition constants in the low micromolar concentration range when basic amino acid residues occupy P₁ and P₂ positions of the inhibitor, and an aldehyde warhead is attached to the P₁. We have used computer-assisted combinatorial techniques to design, focus using the NS2B-NS3pro receptor 3D structure, and in silico screen a virtual library of more than 9,200 peptidomimetic analogs targeted around the template inhibitor Bz-Nle-Lys-Arg-Arg-H (Bz—benzoyl) that are composed mainly of unusual amino acid residues in all positions P₁–P₄. The most promising virtual hits were analyzed in terms of computed enzyme-inhibitor interactions and Adsorption, Distribution, Metabolism and Excretion (ADME) related physico-chemical properties. Our study can direct the interest of medicinal chemists working on a next generation of antiviral chemotherapeutics against the Dengue Fever towards the explored subset of the chemical space that is predicted to contain peptide aldehydes with NS3pro inhibition potencies in nanomolar range which display ADME-related properties comparable to the training set inhibitors.     

Rational design of hirulog-type inhibitors of thrombin

Summary The two crystal structures of thrombin complexed with its most potent natural inhibitor hirudin and with the active-site inhibitor d-Phe-Pro-Arg-CH₂Cl [Rydel, T.J. et al., J. Mol. Biol., 221 (1991) 583; Bode, W. et al., EMBO J., 8 (1989) 3467] were used as a basis to design a new inhibitor, combining the high specificity of the polypeptide hirudin with the simpler chemistry of an organic compound. In the new inhibitor, the C-terminal amino acid residues 53–65 of hirudin are linked by a spacer peptide of four glycines to the active-site inhibitor NAPAP (N-(2-naphthyl-sulfonyl-glycyl)-dl-p-amidinophenylalanyl-piperidine). Energy minimization techniques served as a tool to determine the preferred configuration at the amidinophenylalanine and the modified piperidine moiety of the inhibitor. The predictions are supported by the interaction energies determined for d- and l-NAPAP in complex with thrombin, which are in good agreement with experimentally determined dissociation constants. The conformational flexibility of the linker peptide in the new inhibitors was investigated with molecular dynamics techniques. A correlation between the P1 position and the interactions of the linker peptide with the protein is suggested. Modifications of the linker peptide are proposed based on the distribution of its main-chain torsion angles in order to enhance its binding to thrombin.     

Factors affecting immonium ion intensities in the high-energy collision-induced decomposition spectra of peptides

Each amino acid in a peptide has a characteristic immonium ion (H₂N⁺?CHR), the presence of which in a mass spectrum can indicate the presence of that amino acid. High-energy collision-induced decomposition studies on small peptide ions formed by fast atom bombardment showed the relative intensities of these immonium ions to be dependent on the relative positions of the amino acids in the peptide chain: C-terminal, N-terminal or in-chain. Evidence in favour of competition in the formation of immonium ions is presented.     

Stapled SC34EK fusion inhibitors with high potency against HIV-1 and improved protease resistance

A single all-hydrocarbon staple introduction in SC34EK can afford a potent HIV inhibitor with high protease resistance for ADIS treatment.     

Benchmarking and validating algorithms that estimate p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values of drugs based on their molecular structures

The REGDIA regression diagnostics algorithm in S-Plus is introduced in order to examine the accuracy of pK _a predictions made with four updated programs: PALLAS, MARVIN, ACD/pKa and SPARC. This report reviews the current status of computational tools for predicting the pK _a values of organic drug-like compounds. Outlier predicted pK _a values correspond to molecules that are poorly characterized by the pK _a prediction program concerned. The statistical detection of outliers can fail because of masking and swamping effects. The Williams graph was selected to give the most reliable detection of outliers. Six statistical characteristics (F _exp, R ², , MEP, AIC, and s(e) in pK _a units) of the results obtained when four selected pK _a prediction algorithms were applied to three datasets were examined. The highest values of F _exp, R ², , the lowest values of MEP and s(e), and the most negative AIC were found using the ACD/pK _a algorithm for pK _a prediction, so this algorithm achieves the best predictive power and the most accurate results. The proposed accuracy test performed by the REGDIA program can also be applied to test the accuracy of other predicted values, such as log P, log D, aqueous solubility or certain physicochemical properties of drug molecules.     

Thermodynamics of the Interaction of a Homologous Series of Amino Acids with Sorbitol

The apparent molar volumes V _2,φ , apparent molar isentropic compressibilities K _S,2,φ , and enthalpies of dilution of aqueous glycine, alanine, α-amino butyric acid, valine, and leucine have been determined in aqueous 1.0 and 2.0 mol⋅dm⁻³ sorbitol solutions at 298.15 K. These data have been used to calculate the infinite dilution standard partial molar volumes V_2,m⁰V_{2,m}^{0}, partial molar isentropic compressibilities K_S,2,m⁰K_{S,2,m}^{0}, and enthalpies of dilution Δ_dil H ⁰ of the amino acids in aqueous sorbitol, along with the standard partial molar quantities of transfer of the amino acids from water to aqueous sorbitol. The linear correlation of V_2,m⁰V_{2,m}^{0} for this homologous series of amino acids has been utilized to calculate the contribution to V₂⁰V_{2}^{0} of the charged end groups (NH₃⁺\mathrm{NH}_{3}^{+}, COO⁻), the CH₂ group, and other alkyl chains of the amino acids. The results for the standard partial molar volumes of transfer, compressibilites and enthalpies of dilution from water to aqueous sorbitol solutions have been correlated and interpreted in terms of ion–polar, ion–hydrophobic, and hydrophobic–hydrophobic group interactions. A comparison of these thermodynamic properties of transfer suggest that an enhancement of the hydrophilic/polar group interactions is operating in ternary systems of amino acid, sorbitol, and water.     

Solute–Solvent Interactions of Amino Acids in Aqueous 1-Propyl-3-Methylimidazolium Bromide Ionic Liquid Solutions at 298.15 K

Densities, viscosities, and refractive indices of three amino acids (glycine, L-alanine, and L-valine) in aqueous solutions of an ionic liquid, 1-propyl-3-methylimidazolium bromide, have been measured at 298.15 K. These data have been used to calculate apparent molar volumes (V _φ ), viscosity B-coefficients, and molar refractions of these mixtures. The standard partial molar volumes (V_f⁰V_{\phi}^{0}) and standard partial molar volumes of transfer (D_trV_f⁰\Delta_{\mathrm{tr}}V_{\phi}^{0}) have been determined for these amino acid solutions from these density data. The resulting values of V_f⁰V_{\phi}^{0} and D_trV_f⁰\Delta_{\mathrm{tr}}V_{\phi}^{0} for transfer of amino acids from water to aqueous ionic liquid solutions have been interpreted in terms of solute + solvent interactions. These data also indicate that hydrophobic interactions predominate in L-alanine and L-valine solutions. Linear correlations were found for both V_f⁰V_{\phi}^{0} and the viscosity B-coefficient with the number of carbon atoms in the alkyl chain of the amino acids, and have been used to estimate the contribution of the charged end groups (NH₃⁺\mathrm{NH}_{3}^{+}, COO⁻), the CH₂ group, and other alkyl chains of the amino acids. The viscosity and molar refractivity results have been used to confirm the conclusions obtained from volumetric properties.     

Quantum chemical modelling of the effect of proline residues on peptide conformation

Semiempirical AM1 calculations were performed for quantum chemically optimized minimum-energy conformations of L -alanine oligomers (A)_n at n = 7 and their derivatives containing one, two, or three proline residues at various positions along the peptide chain. The effect of proline residues on the peptide conformation was quantified in terms of the conformational “strain energy” and also analyzed in terms of the spatial compatibility of peptides. The defined “strain energy” corresponds to the transformation of the polyalanine peptide from its minimum conformation to the conformation corresponding to that of the proline-containing peptide. The results of calculations indicate that the “strain effect” of proline residues is additive at all locations along the peptide chain, except at the first and the second positions of its N-terminal part. Also, the regular α-helical polyalanine structure was most significantly altered by the presence of some specific motifs around the proline location in the peptide. This, in turn, has its implications in the prediction of the protein secondary structure, as well as in the design of peptide inhibitors and substrates for enzymes and receptors. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 391–396, 1998     

Conformational analysis of thiopeptides: (ϕ,ψ) maps of thio‐substituted dipeptides

Noncoded amino acids such as isobutyric acid have been used extensively in the process of drug design and protein engineering. This article focuses on a noncoded amino acid where the oxygen in the peptide unit is replaced with a sp² sulfur. It was hypothesized that the conformational space as well as the conformational preferences of thiopeptides will be more restricted and altered by the bulkier atom with different electrostatic properties. In vacuo conformational minima as well as associated energies for the thio‐substituted alanine dipeptides were calculated at the ab initio HF/6‐31G* level. When the bulkier sulfur atom acts as a hydrogen bond acceptor in the C₅ conformation or in the C$^{\mathrm{axial}}_{7}$ and C$^{\mathrm{equatorial}}_{7}$ conformations, the hydrogen bond lengths are much longer than that of normal peptides. Consequently, the ?, ψ dihedral angles of the C₅, C$^{\mathrm{axial}}_{7}$, and C$^{\mathrm{equatorial}}_{7}$ conformations change to accommodate the longer hydrogen bonds. The thiopeptide group is a poorer hydrogen bond acceptor and a better hydrogen bond donor than the normal peptide group. Therefore, thio‐substitution at the amino terminal leads to disfavoring of the C₇ conformations relative to the C₅ conformations and thio‐substitution at the carboxyl terminal leads to favoring of the C₇ conformations relative to the C₅ conformation. To simulate the conformations in solution, (?,ψ) conformational energy maps were calculated for the glycine and alanine dipeptides at various dielectric constants using the CFF91 force field with our previously derived parameters for the thioamide group. The results show that thio‐substitution does restrict the conformations available to amino acids residues in peptides. Thio substitution at the amino terminal introduces unfavorable interactions near ?=?120 and 120, where there are increased overlaps between S_n?1?H_β, and S_n?1?C_β atoms, respectively. Thio substitution at the carboxyl terminal restricts the conformations near ψ=60, ?60, and 180, which correspond with increase overlaps between S_n?C_β, S_n?H_β′ and S_n?N_n atoms, respectively. The effects of dithio substitutions of either the alanine or the glycine dipeptides are similar to the combined effects of the two single thio substitutions. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1026–1037, 2001     

Prediction of different antibacterial activity in a new set of formyl hydroxyamino derivatives with potent action on peptide deformylase using structural information

Due to the essential role of peptide deformylase (PDF) at the bacterial growth cycle, it is a noteworthy target for developing a novel antibacterial agent. In the current study, the antibacterial activities of a set of 44 new structures of formyl hydroxyamino derivatives as PDF inhibitors were quantified using quantitative structure–activity relationship (QSAR). Artificial neural networks (ANN) were used as a chemometrics tool for QSAR modeling. Three quantitative models were suggested to relate the chemical structural features of the formyl hydroxyamino derivatives to their antibacterial activities (pIC₅₀) against Staphylococcus aureus, methicillin-susceptible S. aureus (MSSA), and methicillin-resistant S. aureus (MRSA) peptide deformylase. The sufficiency of the model for prediction of the antibacterial activities of the desired PDF inhibitor compounds against S. aureus, MSSA, and MRSA was statistically demonstrated according to the validation parameters such as coefficient of determination (R²), mean square error (MSE) in training, validation, and prediction sets, and also using applicability domain (AD) and randomization test.

     

Synthesis of the human adrenal cortex hormone ( h ACTH) with a revised amino acid sequence

We demonstrated recently that the amino acid sequence of human ACTH (α_h-ACTH¹) differs in four positions from the structure reported in 1961 by Lee and coworkers. The synthesis of the revised sequence and a method of verifying the identity of the synthetic peptide with the naturally occurring hormone are described. The two preparations can most readily be compared by examining the mixture of fragments obtained upon degradation with trypsin. In this mixture, fragments 22–39 of natural α_h-ACTH and of the synthetic peptide are identical and easily distinguishable from the corresponding synthetic fragment of the previously postulated sequence. This is demonstrated by thin layer-chromatography and -electrophoresis as well as by reference to the rate of deamidation under alkaline conditions.     

QSAR modeling and design of cationic antimicrobial peptides based on structural properties of amino acids

Drug resistance to existing antibiotics poses alarming threats to global public health, which inspires heightened interests in searching for new antibiotics, including antimicrobial peptides (AMPs). Accurate prediction of antibacterial activities of AMPs may expedite novel AMP design and reduce the costs and efforts involved in laboratory screening. In the present study, a novel quantitative prediction method of AMP was established by quantitative structure-activity relationship (QSAR) modeling based on the physicochemical properties of amino acids. The indices of these physicochemical properties were used to define AMP. The structural variables were optimized by stepwise regression (STR). Three series of AMPs from the QSAR model were constructed by multiple linear regressions (MLR). These QSAR models showed good performance in reliability and predictability. The normalized regression coefficients of the QSAR model and the contribution of amino acids at each position of AMP may determine the suitableness of a particular residue at any given position. QSAR models constructed by STR-MLR should prove to be useful tools in peptide design with respect to the calculation, explanation, good and reliable performance, and definition of physiochemical properties.     

多级质谱法测定Axinastatin 1环肽序列及其断裂机理研究

对具有抗癌活性的海洋环肽Axinastatin 1进行化学合成. 采用多级质谱法对合成环肽进行序列测定. 线性前体测序依据b_x－y_z断裂路径, 在同一张MS²谱中利用b和y离子所提供序列信息的互补来实现. 环肽测序依据b_x→b_x－1断裂路径, 每一级MS由b离子的C端碰撞掉一个氨基酸残基直到MS⁶, 得到2套b离子, 根据它们所提供序列信息的互补可准确测定环肽序列并推断其环结构, 同时观察到b离子重排现象. 讨论了上述断裂与重排的路径和机理, 并利用半经验量子化学PM3和AM1两种算法计算了碎片的生成焓, 验证了路径的合理性. 由离子b_5PN的生成焓偏高和其重排间的联系尝试提出过渡结构假设.     

Conformationally Constrained Peptidomimetics as Inhibitors of the Protein Arginine Methyl Transferases

Protein arginine N‐methyl transferases (PRMTs) belong to a family of enzymes that modulate the epigenetic code through modifications of histones. In the present study, peptides emerging from a phage display screening were modified in the search for PRMT inhibitors through substitution with non‐proteinogenic amino acids, N‐alkylation of the peptide backbone, and incorporation of constrained dipeptide mimics. One of the modified peptides ( 23 ) showed an increased inhibitory activity towards several PRMTs in the low μm range and the conformational preference of this peptide was investigated and compared with the original hit using circular dichroism and NMR spectroscopy. Introducing two constrained tryptophan residue mimics (l ‐Aia) spaced by a single amino acid was found to induce a unique turn structure stabilized by a hydrogen bond and aromatic π‐stacking interaction between the two l ‐Aia residues.     

Acidity,lipophilicity, solubility,absorption, and polar surface area of some ACE inhibitors

Computational chemical methods have been used to correlate the molecular properties of the 10 ACE inhibitors (captopril, enalapril, perindopril, lisinopril, ramipril, trandolapril, quinapril, fosinopril, benazepril, and cilazapril) and some of their active metabolites (enalaprilat, perindoprilat, ramiprilat, trandolaprilat, quinaprilat, fosinoprilat, benazeprilat, and cilazaprilat). The computed pK _a values correlate well with the available experimental values. In the dicarboxylic ACE inhibitors, the carboxyalkyl carboxylate group of the ACE inhibitors studied is more acidic than the C-terminal carboxylate. However, at physiological pH = 7.4 both carboxyl groups of ACE inhibitors are completely ionized and the dicarboxyl-containing ACE inhibitors behave as strong acids. The available experimental partition coefficients of these ACE inhibitors investigated are well reproduced by the neural network-based ALOGPs and the fragment-based KoWWiN methods. All parent drugs (and prodrugs), with the exception of fosinopril, are compounds with low lipophilicity. Calculated pK _a, lipophilicity, solubility, absorption, and polar surface area of the most effective ACE inhibitors for the prevention of myocardial infarction, perindopril and ramipril, were found similar. Therefore, it is probable that the experimentally observed differences in the survival benefits in the first year after acute myocardial infarction in patients 65 years of age or older correlate closely to the physicochemical and pharmacokinetic characteristics of the specific ACE inhibitor that is used.     

Engineered Peptide Macrocycles Can Inhibit Matrix Metalloproteinases with High Selectivity

Matrix metalloproteinases (MMPs) are zinc‐dependent endopeptidases at the intersection of health and disease due to their involvement in processes such as tissue repair and immunity as well as cancer and inflammation. Because of the high structural conservation in the catalytic domains and shallow substrate binding sites, selective, small‐molecule inhibitors of MMPs have remained elusive. In a tour‐de‐force peptide engineering approach combining phage‐display selections, rational design of enhanced zinc chelation, and d ‐amino acid screening, we succeeded in developing a first synthetic MMP‐2 inhibitor that combines high potency (K_i=1.9±0.5 nm ), high target selectivity, and proteolytic stability, and thus fulfills all the required qualities for in cell culture and in vivo application. Our work suggests that selective MMP inhibition is achievable with peptide macrocycles and paves the way for developing specific inhibitors for application as chemical probes and potentially therapeutics.     

Influence of amino acid side chains on apparent selective opening of cyclic <Emphasis Type="Italic">b</Emphasis><Subscript>5</Subscript> ions

In this study, the possible influence of acidic, basic, and amide side chains on the opening of a putative macrocyclic b ion (b ₅⁺) intermediate was investigated. Collision induced dissociation (CID) of b ₅ ions was studied using a group of hexapeptides in which amino acids with the side chains of interest occupied internal sequence positions. Further experiments were performed with permuted isomers of glutamine (Q) containing peptides to probe for sequence scrambling and whether the specific sequence site of the residues influences opening of the macrocycle. Overall, the trend for (apparent) preferential/selective opening of the cyclic b ₅⁺, presumably due to the side chain, followed by the loss of the amino acid with active side group is: Q > K > D > N ∼ E.     

A Versatile Strategy for Screening Custom-Designed Warhead-Armed Cyclic Peptide Inhibitors

Demand for peptide-based pharmaceuticals has been steadily increasing, but only limited success has been achieved to date. To expedite peptide-based drug discovery, we developed a general scheme for cell-based screening of cyclic peptide inhibitors armed with a user-designed warhead. We combined unnatural amino acid incorporation and split intein-mediated peptide cyclization techniques and integrated a yeast-based colorimetric screening assay to generate a new scheme that we call the custom-designed warhead-armed cyclic peptide screening platform (CWCPS). This strategy successfully discovered a potent inhibitor, CY5-6Q, that targets human histone deacetylase 8 (HDAC8) with a K_D value of 15 nM. This approach can be a versatile and general platform for discovering cyclic peptide inhibitors.