CoMFA and CoMSIA 3D-QSAR analysis on hydroxamic acid derivatives as urease inhibitors

Urease (EC 3.5.1.5) serves as a virulence factor in pathogens that are responsible for the development of many diseases in humans and animals. Urease allows soil microorganisms to use urea as a source of nitrogen and aid in the rapid break down of urea-based fertilizers resulting in phytopathiCIT000y. It has been well established that hydroxamic acids are the potent inhibitors of urease activity. The 3D-QSAR studies on thirty five hydroxamic acid derivatives as known urease inhibitors were performed by Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) methods to determine the factors required for the activity of these compounds. The CoMFA model produced statistically significant results with cross-validated (q²) 0.532 and conventional (r²) correlation coefficients 0.969.The model indicated that the steric field (70.0%) has greater influence on hydroxamic acid inhibitors than the electrostatic field (30.0%). Furthermore, five different fields: steric, electrostatic, hydrophobic, H-bond donor and H-bond acceptor assumed to generate the CoMSIA model, which gave q² 0.665 and r² 0.976.This model showed that steric (43.0%), electrostatic (26.4%) and hydrophobic (20.3%) properties played a major role in urease inhibition. The analysis of CoMFA and CoMSIA contour maps provided insight into the possible modification of the hydroxamic acid derivatives for improved activity.     

3D-QSAR study of adamantyl N-benzylbenzamides as melanogenesis inhibitors

Three-dimensional quantitative structure–activity relationship (3D-QSAR) modeling, comparative molecular field analysis (CoMFA), and comparative molecular similarity indices analysis (CoMSIA) of polyhydroxylated N-benzylbenzamide derivatives containing an adamantyl moiety were performed to understand the mechanism of action and structure–activity relationship of these compounds. Contour map analysis indicated that steric contributions of the adamantyl moiety and electrostatic contributions of the hydroxyl group at the 3-position are important in the activity. Activities of the training set and test sets predicted by CoMFA fit well with actual activities, demonstrating that CoMFA, along with the best calculated q² value, has the best predictive ability.     

Interactions of chiral molecules with an (r)-n-(3,5-dinitrobenzoyl) phenylglycine HPLC stationary phase

Forty different chiral molecules were studied by liquid chromatography with a Pirkle-type, (R)-N-(3,5-dinitrobenzoyl) phenylglycine (DNBPG), chiral stationary phase column. The dramatic effect of a small molecular change on chiral recognition was demonstrated using DL-amino acid derivatives. The inductive effect on chiral recognition was also studied using trifluoro-, trichloro-, dichloro-, monochloroacetyl, and acetyl derivatives of four different chiral amines. The study of the enantiomer separation of 11 different crown ethers of 2,2′-binaphthyldiyl showed that the rigidity of the chiral center can be an additional parameter in chiral recognition for the DNBPG phase but not for a β-cyclodextrin bonded chiral phase. It is apparent from this study that steric effects, inductive effects, and molecular rigidity play important roles in chiral recognition with DNBPG chiral stationary phases.     

Chiral discrimination by albumin: A mechanistic study of liquid chromatographic optical resolution of nonaromatic carboxylic acids

In order to get further insight into the mechanism by which bovine serum albumin (BSA) discriminates between enantiomers of organic acids, some radioisotopically labeled, nonaromatic carboxylic acids were studied under varying mobile phase conditions. It was found for a series of N-alkanoyl-DL -[³H]leucines that the D -enantiomers were much more strongly retained and that the composition of the mobile phase could be adjusted to give very large (α > 20) enantiomeric separation factors. The elution order was consistent with what has been found earlier for other N-acyl derivatives as well as for N-arylcarbamoyl derivatives of simple aliphatic amino acids. A marked increase in the hydrophobic interaction of the D -enantiomers with the chiral phase was found upon a lowering of the mobile phase strength, conditions under which the L -form was only slightly influenced. These and other results are consistent with a chiral recognition model by which inclusion of the compound in a hydrophobic chiral cavity of BSA with simultaneous charge interaction is assumed to take place and whereby discrimination is determined by the steric bulk and orientation of the α-substituent. © 1993 Wiley-Liss, Inc.     

Three-dimensional quantitative structure–farnesyltransferase inhibition analysis for some diaminobenzophenones

A 3D-QSAR investigation of 95 diaminobenzophenone yeast farnesyltransferase (FT) inhibitors selected from the work of Schlitzer et al. showed that steric, electrostatic, and hydrophobic properties play key roles in the bioactivity of the series. A CoMFA/CoMSIA combined model using the steric and electrostatic fields of CoMFA together with the hydrophobic field of CoMSIA showed significant improvement in prediction compared with the CoMFA steric and electrostatic fields model. The similarity of the 3D-QSAR field maps for yeast FT inhibition activity (from this work) and for antimalarial activity data (from previous work) and the correlation between those activities are discussed.     

3D-QSAR studies of substituted 1-(3, 3-diphenylpropyl)-piperidinyl amides and ureas as CCR5 receptor antagonists

3D-QSAR studies on the derivatives of 1-(3,3-diphenylpropyl)-piperidinyl amide and urea as CCR5 receptor antagonists were performed by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices (CoMSIA) methods to rationalize the structural requirements responsible for the inhibitory activity of these compounds. The global minimum energy conformer of the template molecule, the most active and pharmacokinetically stable molecule of the series, was obtained by systematic search and used to build structures of the molecules in the dataset. The best predictions for the CCR5-receptor were obtained with the CoMFA standard model (q ² = 0.787, r ² = 0.962) and CoMSIA model combined steric, electrostatic and hydrophobic fields (q ² = 0.809, r ² = 0.951). The predictive ability of CoMFA and CoMSIA were determined using a test set of 12 compounds giving predictive correlation coefficients of 0.855 and 0.83, respectively, indicating good predictive power. Further, the robustness of the model was verified by bootstrapping analysis. The contour maps produced by the CoMFA and CoMSIA models were used to identify the structural features relevant to the biological activity in this series. Based on the CoMFA and CoMSIA analysis, we have identified some key features in the series that are responsible for CCR5 antagonistic activity which may be used to design more potent 1-(3,3-diphenylpropyl)-piperidinyl derivatives and predict their activity prior to synthesis. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Steric hindrance influence on the enantiorecognition ability of tyrosine-derived chiral stationary phases

Four chiral stationary phases (CSPs) derived from N-(3,5-dinitrobenzoyl)tyrosine have been synthesized. They differ by the substituent nature (methyl, ethyl, isopropyl, tert-butyl) of the aliphatic amide function. The enantiorecognition ability of these CSPs was evaluated with 10 racemates. For the majority of them, the stereoselectivity increases with the steric hindrance of the substituent. The chiral selector enantiomeric separation on the resulting CSPs has evidenced a reversal of elution order only for CS 4 on CSP 4 (tert-butyl substituent), suggesting a change in its conformation.     

Three-dimensional quantitative structure-activity relationships of pyrrolopyridinone as cell division cycle kinase inhibitors by CoMFA and CoMSIA

Seventy-five 1,5,6,7-tetrahydro-pyrrolo[3,2-C]pyridinone derivatives displaying potent activities against Cdc7 kinase were selected to establish 3D-QSAR models using CoMFA and CoMSIA methods. Internal and external cross-validation techniques were investigated as well as some measures including region focusing, progressive scrambling, bootstraping and leave-group-out. The satisfactory CoMFA model predicted a q ² value of 0.836 and an r ² value of 0.950, indicating that electrostatic and steric properties play a significant role in potency. The best CoMSIA model, based on a combination of steric, electrostatic and H-bond acceptor effects, predicted a q ² value of 0.636 and an r ² value of 0.907. The models were graphically interpreted using contour plots which provided insight into the structural requirements for increasing the activity of a compound. The final 3D-QSAR results could be used for rational design of potent inhibitors against Cdc7 kinase.     

Molecular similarity analysis on biologically active macrocyclic bis(bibenzyls)

Conformational analysis of marchantin A (1), a bis(diarylether) type, and riccardin A (2), a diarylether-biphenyl type macrocyclic bis(bibenzyl) was carried out by systematic unbounded multiple minimum search (SUMM). Mobility of the macrocyclic rings was analysed by variable temperature ¹H-NMR study. Molecular similarity analysis was performed on the minimum energy conformers of 1 and 2 comparing their steric, electrostatic and hydrophobic properties. Correlation between complexation properties and calmodulin inhibitor activity was established. Differences in steric and electrostatic profiles may be responsible for the reduced Ca²⁺ affinity and activity of 2.     

Molecular docking and 3D-QSAR studies on β-phenylalanine derivatives as dipeptidyl peptidase IV inhibitors

Three-dimensional quantitative structure-activity relationship (3D-QSAR) and molecular docking studies were carried out to explore the binding of 73 inhibitors to dipeptidyl peptidase IV (DPP-IV), and to construct highly predictive 3D-QSAR models using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The negative logarithm of IC₅₀ (pIC₅₀) was used as the biological activity in the 3D-QSAR study. The CoMFA model was developed by steric and electrostatic field methods, and leave-one-out cross-validated partial least squares analysis yielded a cross-validated value (r_cv² {\hbox{r}}_{{\rm{cv}}}^{\rm{2}} ) of 0.759. Three CoMSIA models developed by different combinations of steric, electrostatic, hydrophobic and hydrogen-bond fields yielded significant r_cv² {\hbox{r}}_{{\rm{cv}}}^{\rm{2}} values of 0.750, 0.708 and 0.694, respectively. The CoMFA and CoMSIA models were validated by a structurally diversified test set of 18 compounds. All of the test compounds were predicted accurately using these models. The mean and standard deviation of prediction errors were within 0.33 and 0.26 for all models. Analysis of CoMFA and CoMSIA contour maps helped identify the structural requirements of inhibitors, with implications for the design of the next generation of DPP-IV inhibitors for the treatment of type 2 diabetes.     

A new class of network-polymeric chiral stationary phases

A strategy based on the use of homo bi- and multifunctional building blocks for the synthesis of a new class of network-polymeric chiral stationary phases has been evaluated. The key steps comprise acylation of N,N′-diallyl-L-tartardiamide (DATD) and reaction with a multifunctional hydrosilane, yielding a network polymer incorporating the bifunctional C₂-symmetric chiral selector. Covalent bonding to a functionalized silica takes place during the latter process. Many of these chiral sorbents show interesting enantioselective properties toward a wide variety of racemic solutes under normal-phase (hexane-based) conditions. The retention is mainly caused by the hydrogen-bonding ability of the analyte, which is regulated by mobile phase additives like alcohol or ether cosolvents. The most interesting chiral stationary phases, in terms of broad enantioselectivity, were obtained from O,O′-diaryol-DATD-derivatives, particularly those containing the 3,5-dimethylbenzoyl and the 4-(tert-butyl)benzoyl moieties. Since high column efficiencies can be obtained with these chiral sorbents, an α-value of ca. 1.2 is usually sufficient to produce baseline separation. A large number of neutral as well as acidic or basic drug racemates are resolved without derivatization. © 1995 Wiley-Liss, Inc.     

Liquid chromatographic separation of chiral diarylcarbinols

The direct HPLC separation of three chiral carbinols of general formula Mesityl-CH(OH)-Aryl has been achieved using Pirkle (R)-DNBPG ionic or covalent columns and, for Aryl = o-tolyl, on a Chiralpak OP(+) phase. It is apparent that steric hindrance and hydrogen bonding play important roles in chiral recognition. Two compounds structurally very similar but lacking the hydroxyl group were not resolved in their enantiomeric pairs. © 1992 Wiley-Liss, Inc.     

Synthesis and Chiral Recognition of Nickel(II) Macrocyclic Complex with (R)‐Naphthylethyleneamine Pendant Groups and its Self‐Assembled Framework

A novel nickel(II) hexaaza macrocyclic complex, [Ni(L^R,R)](ClO₄)₂ ( 1 ), containing chiral pendant groups was synthesized by an efficient one‐pot template condensation and characterized (L^R,R═1,8‐di((R)‐α‐methylnaphthyl)‐1,3,6,8,10,13‐hexaazacyclotetradecane). The crystal structure of compound 1 was determined by single‐crystal X‐ray analysis. The complex was found to have a square‐planar coordination environment for the nickel(II) ion. Open framework [Ni(L^R,R)]₃[C₆H₃(COO)₃]₂ ( 2 ) was constructed from the self‐assembly of compound 1 with deprotonated 1,3,5‐benzenetricarboxylic acid, BTC^3?. Chiral discrimination of rac‐1,1′‐bi‐2‐naphthol and rac‐2,2,2‐trifluoro‐1‐(9‐anthryl)ethanol was performed to determine the chiral recognition ability of the chiral complex ( 1 ) and its self‐assembled framework ( 2 ). Binaphthol showed a good chiral discrimination on the framework ( 2 ). The optimum experimental conditions for the chiral discrimination were examined by changing the weight ratio between the macrocyclic complex 1 or self‐assembled framework 2 and racemates. The detailed synthetic procedures, spectroscopic data including single‐crystal X‐ray analysis, and the results of the chiral recognition for the compounds are described. Chirality, 25:54‐58, 2013 © 2012 Wiley Periodicals, Inc.     

Effect of Chromatographic Conditions on Enantioseparation of Bovine Serum Albumin Chiral Stationary Phase in HPLC and Thermodynamic Studies

Twelve chiral compounds were enantiomerically resolved on bovine serum albumin chiral stationary phase (BSA‐CSP) by high‐performance liquid chromatography (HPLC) in reversed‐phase modes. Chromatographic conditions such as mobile phase pH, the percentage of organic modifier, and concentration of analyte were optimized for separation of enantiomers. For N‐(2, 4‐dinitrophenyl)‐serine (DNP‐ser), the retention factors (k) greatly increase from 0.81 to 6.23 as the pH decreasing from 7.21 to 5.14, and the resolution factor (R_s) exhibited a similar increasing trend (from 0 to 1.34). More interestingly, the retention factors for N‐(2, 4‐dinitrophenyl)‐proline (DNP‐pro) decrease along with increasing 1‐propanol in mobile phase (3%, 5%, 7% and 9% by volume), whereas the resolution factor shows an upward trend (from 0.96 to 2.04). Moreover, chiral recognition mechanisms for chiral analytes were further investigated through thermodynamic methods. Chirality 25:487–492, 2013. © 2013 Wiley Periodicals, Inc.     

3D–QSAR studies of orvinol analogs as κ-opioid agonists

Orvinols are potent analgesics that target opioid receptors. However, their analgesic mechanism remains unclear and no significant preference for subtype opioid receptor has been achieved. In order to find new orvinols that target the κ-receptor, comparative 3D–QSAR studies were performed on 26 orvinol analogs using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The best predictions for the κ-receptor were obtained with the CoMFA standard model (q ²=0.686, r ²=0.947) and CoMSIA model combined steric, electrostatic, hydrophobic, and hydrogen bond donor/acceptor fields (q ²=0.678, r ²=0.914). The models built were further validated by a test set made up of seven compounds, leading to predictive r ² values of 0.672 for CoMFA and 0.593 for CoMSIA. The study could be helpful for designing and prepare new category κ-agonists from orvinols.      

Evaluation of π-acid chiral stationary phases deriving from tyrosine and related amino acids for the chromatographic resolution of racemates: Specific requirements for enantiorecognition ability

Chromatographic applications of three novel chiral stationary phases (CSPs) deriving from (S)-(N)-(3,5-dinitrobenzoyl)tyrosine are reported, under liquid chromatographic (LC) and subscritical fluid chromatographic (SubFC) conditions. Two grafting modes of the chiral moiety have been experimented starting either from γ-mercaptopropyl-silanized (type 1) or γ-aminopropyl-silanized (type 2) silica gels. For type 2 CSPs an evaluation of the stability of the amide linkage was achieved by means of SubFC; the relative contriution of ionic and covalent bindings to the ciral recognitio aility was then outlined. The chromatographic properties of these CSPs were compared with those of the corresponding CSPs deriving from phenylglycine, p-hydroxyphenylglycine, and phenylalanine for the resolution of some tertiary phosphine oxide, naphthoyl amide, and α-methylene γ-lactam enantiomers. Some simple requirements regarding the solute and CSP structures for chiral recognition ability can be inferred from these results. In addition, the resolutio of π-acid α-N-(3,5-dinitrobenzoyl)amino esters was investigated on these π-acid CSPs. An example of preparative scale chromatography is also presented.     

Design of novel quinazolinone derivatives as inhibitors for 5HT7 receptor

To study the pharmacophore properties of quinazolinone derivatives as 5HT₇ inhibitors, 3D QSAR methodologies, namely Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) were applied, partial least square (PLS) analysis was performed and QSAR models were generated. The derived model showed good statistical reliability in terms of predicting the 5HT₇ inhibitory activity of the quinazolione derivative, based on molecular property fields like steric, electrostatic, hydrophobic, hydrogen bond donor and hydrogen bond acceptor fields. This is evident from statistical parameters like q² (cross validated correlation coefficient) of 0.642, 0.602 and r² (conventional correlation coefficient) of 0.937, 0.908 for CoMFA and CoMSIA respectively. The predictive ability of the models to determine 5HT₇ antagonistic activity is validated using a test set of 26 molecules that were not included in the training set and the predictive r² obtained for the test set was 0.512 & 0.541. Further, the results of the derived model are illustrated by means of contour maps, which give an insight into the interaction of the drug with the receptor. The molecular fields so obtained served as the basis for the design of twenty new ligands. In addition, ADME (Adsorption, Distribution, Metabolism and Elimination) have been calculated in order to predict the relevant pharmaceutical properties, and the results are in conformity with required drug like properties.     

A New Biosensor for Chiral Recognition Using Goat and Rabbit Serum Albumin Self‐Assembled Quartz Crystal Microbalance

Quartz crystal microbalance (QCM) biosensor was used for the chiral recognition of five pairs of enantiomers by using goat serum albumin (GSA) and rabbit serum albumin (RbSA) as chiral selectors. Serum albumin (SA) was immobilized on the QCM through the self‐assembled monolayer technique, and the surface concentration of GSA and RbSA were 8.8 × 10^?12 mol cm^?2 and 1.2 × 10^?11 mol cm^?2, respectively. The QCM biosensors showed excellent sensitivity and selectivity. Meanwhile, the chiral recognition of SA sensors was quite species dependent. There were differences between GSA and RbSA sensors in the ability and the preference of chiral recognition. To R,S‐1,2,3,4‐tetrahydro‐1‐naphthylamine (R,S‐1‐TNA), R,S‐1‐(4‐methoxyphenyl)ethylamine (R,S‐4‐MPEA), and R,S‐1‐(3‐methoxyphenyl)ethylamine (R,S‐3‐MPEA), the preference of the stereoselective SA‐drug binding of the two kinds of SA sensors were consistent. However, to R,S‐2‐octanol (R, S‐2‐OT) and R,S‐methyl lactate (R,S‐MEL), the two kinds of SA sensors had opposite chiral recognition preference. Moreover, the interactions of SA and the five pairs of enantiomers have been further investigated through ultraviolet (UV) and fluorescent (FL) spectra. The UV/FL results were in accordance with the consequence of QCM. Chirality 24:804–809, 2012. © 2012 Wiley Periodicals, Inc.