Drug Design and Discovery (Drug Des Discov )

Description

Drug Design and Discovery is an international journal which publishes original work in aspects of drug design and discovery. The primary focus is on research which addresses the generation and optimization of new lead compounds through rational approaches such as structure-based drug design, molecular modelling, mechanism-based design, or application of structure-activity analysis. Papers which describe novel screening strategies or searching techniques for the discovery and optimisation of novel agents are also published. Research into novel, molecular approaches to the optimisation of drug delivery, pharmacokinetics, or modification of properties through manipulation of metabolism could be considered. The journal will publish full length research papers, short communications and reviews.

  • Impact factor
    0.00
  • 5-year impact
    0.00
  • Cited half-life
    0.00
  • Immediacy index
    0.00
  • Eigenfactor
    0.00
  • Article influence
    0.00
  • Website
    Drug Design and Discovery website
  • Other titles
    Drug design and discovery (Online), Drug design and discovery
  • ISSN
    1055-9612
  • OCLC
    51540689
  • Material type
    Document, Periodical, Internet resource
  • Document type
    Internet Resource, Computer File, Journal / Magazine / Newspaper

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Sulfonamide hydroxamate derivatives of anthranilic acids are known to be potent inhibitors of cell-free TACE enzyme. However, compounds of this structural class with both high potency and high selectivity for TACE over matrix metalloproteinases (MMPs) are uncommon. Replacement of the sulfonamide functionality with an isosteric sulfonate ester has resulted in a series of sulfonate ester hydroxamates, 2a-e, with excellent activity against TACE and excellent selectivity over MMP-1 and MMP-13. Although compounds 2a-e possess good permeability in a PAMPA assay, they are only weakly active as inhibitors of lipopolysaccharide (LPS)-stimulated tumor necrosis factor (TNF) production in human monocytic THP-1 cells. Protein binding affinity also does not predict the lack of cellular activity for these analogs.
    Drug Design and Discovery 02/2003; 18(4):123-6.
  • [Show abstract] [Hide abstract]
    ABSTRACT: Three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis was applied to a series of H(3) receptor antagonists characterized by an imidazole ring, an alkyl spacer, and a heterocyclic polar moiety containing an imidazole or a thiazole ring, with a view to investigate the requirements for H(3) receptor affinity on rat cortex membranes. The compounds were aligned based on the hypothesis that the presence of a H-bond donor group in the polar portion of the molecule can increase H(3) receptor affinity. The 3D-QSAR analysis, which was performed using both the CoMFA and CoMSIA protocols, revealed that the presence of a H-bond donor group is not statistically relevant for H(3) receptor affinity. Based on this result, another alignment was adopted that took into consideration the structural features common to all compounds, namely the imidazole ring and the N atom with a free lone pair in the polar portion. The 3D-QSAR models thus obtained showed that H(3) receptor affinity is modulated by the position and direction of the intermolecular interaction elicited by the polar group in the ligands.
    Drug Design and Discovery 02/2003; 18(2-3):65-79.
  • [Show abstract] [Hide abstract]
    ABSTRACT: 3-Deoxy-D-manno-octulosonate 8-phosphate (KDO8P) is the phosphorylated precursor of KDO, an essential sugar of the lipopolysaccharide of Gram negative bacteria. KDO8P is produced by a specific synthase (KDO8PS) by condensing arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP), with release of inorganic phosphate. As KDO8PS is present in bacteria and plants, but not in mammalian cells, and mutations that inactivate KDO8PS also block cell replication, KDO8PS is a promising target for the design of new antimicrobials that act by blocking lipopolysaccharide biosynthesis. Previous studies have shown that a compound mimicking an intermediate of the condensation reaction is a good ligand and a powerful inhibitor. Here we report on the crystallographic investigation of the binding to KDO8PS of new derivatives of this original inhibitor. The structures of the enzyme in complex with these compounds, and also with the PEP analogs, 2-phosphoglyceric acid (2-PGA) and Z-methyl-PEP, point to future strategies for the design of novel inhibitors of KDO8PS.
    Drug Design and Discovery 02/2003; 18(2-3):91-9.
  • [Show abstract] [Hide abstract]
    ABSTRACT: Globomycin (1), a 19-membered cyclic depsipeptide, exhibited an antibiotic activity against gram-negative bacteria by inhibiting signal peptidase II in the cytoplasmic membrane. Although only one conformation of 1 was observed for the crystal structure, it was revealed by 1H NMR spectroscopic analysis that 1 exists as a mixture of two rotational isomers in solution (CDCl3 and CD3OD). A conformational analysis of 1 was, therefore, performed by high-temperature molecular dynamics simulation in combination with 1H NMR analysis to elucidate the conformations in solution. The relative ratio of the major and minor isomers present, which differs depending on the solvent, was then derived from their relative energy differences obtained in the conformational analysis. The difference in the relative ratios corresponded with that calculated from the 1H NMR analysis. Finally, the predicted conformations in solution were compared with that of the X-ray crystal structure to find local and global differences that characterize these conformations.
    Drug Design and Discovery 02/2003; 18(4):109-16.
  • [Show abstract] [Hide abstract]
    ABSTRACT: Three series of anti-HIV data (reverse transcriptase inhibitory activity, cytopathicity data, and cytotoxicity data) of alkenyldiarylmethanes were modeled with physicochemical, topological and structural descriptors by multiple regression analysis using principal component factor analysis as the data pre-processing step. Molar refractivity was found to be a significant contributor in modeling all three data sets. Apart from this, partition coefficient, E-state index, valence connectivity and indicator parameters were important in modeling different activity series. The final relations were of moderate to good quality as evidenced from regression statistics (R2 values ranging 66-75%) and leave-one-out cross validation data (Q2 values ranging 54-70%).
    Drug Design and Discovery 02/2003; 18(4):165-80.
  • [Show abstract] [Hide abstract]
    ABSTRACT: Neonicotinoids are the most important class of synthetic insecticides increasingly used in agriculture and veterinary medicine. Fundamental differences between the nicotinic acetylcholine receptors (nAChRs) of insects and mammals confer remarkable selectivity of the neonicotinoids at insect nAChR over mammalian nAChR. To identify pharmacophoric requirements of azidopyridinyl neonicotinoids for their efficacy and selectivity towards the insect nAChR over the mammalian one, quantitative structure-activity relationship (QSAR) study was performed using electrotopological state atom (ETSA) indices. This study clearly showed that nitroimines, nitromethylenes, and cyanoimines are more selective to Drosophila nAChR and safe for human being, whereas N-substituted imines have affinity to mammalian receptor. Pharmacophore mapping for both the activities was done.
    Drug Design and Discovery 02/2003; 18(2-3):81-9.
  • [Show abstract] [Hide abstract]
    ABSTRACT: Strong hydrogen-bonding forces between the Thr26 and Thr26' of the protease stabilize the internal cage of the dimeric triad of the aspartyl HIV-1 protease (Asp25Thr26Gly27 and Asp25' Thr26'Gly27', respectively). The interaction of reversible inhibitors of HIV-1 protease is based on (i) strong hydrogen-bonding forces between the main chain (--CONH--) oxygen atoms of Gly27 and/or Gly27' and hydrogen-bond donating moieties of a drug, and (ii) hydrogen bonds between the oxygen of the catalytic Asp25 and/or Asp25' carboxylates and aliphatic hydroxyl groups of a drug. The free entry of natural substrates into the active-site cavity is sterically hindered by inhibitors, so that the catalytic Asp carboxylates cannot interact with natural substrates. Irreversible inhibitors interact with the nucleophilic carboxylate moiety of Asp25 of HIV-1 protease by covalent bonding.
    Drug Design and Discovery 02/2003; 18(2-3):53-64.
  • [Show abstract] [Hide abstract]
    ABSTRACT: Thromboxane A(2) receptor antagonists have attracted much attention in recent times in the design of new agents that could be active against diseases such as thrombosis, asthma and myocardial ischemia. 3D-QSAR studies have been performed on a series of [[1-aryl(or benzyl)-1-(benzenesulphonamido)methyl] phenyl] alkanoic acid derivatives by using the receptor surface analysis (RSA) method. The RSA analysis was carried out on 31 analogues of which 25 were used in the training set and the rest considered for the test set. This study produced reasonably good predictive models with good cross-validated and conventional r(2) values in both the models.
    Drug Design and Discovery 02/2003; 18(2-3):47-51.
  • [Show abstract] [Hide abstract]
    ABSTRACT: The methods of bioinformatics, molecular modelling, and quantitative structure-activity relationships (QSARs) using regression and artificial neural network (ANN) analyses were applied to develop safer aldoxime antidotes against poisoning by organophosphorus (OP) agents with high, mean, and low aging rates. We start here from a molecular modelling of the mouse AChE at an atomistic level. Aim is to predict qualitatively the structural requirements of an aldoxime that shows an unique reactivating activity against the three classes of OPs. An antidotal action should occur by a three-site mechanism: the aldoxime groups of the first pyridinium ring should point towards the catalytic site, and the second pyridinium ring and its substituents should be anchored at the peripherical and anionic subsites. Based on this model, it is predicted that a suitable substituent is based on an arginine-like moiety. Then, an ANN-based QSAR analysis using a training set of aldoximes with known structure and activities was applied. Its input layer consisted of seven nodes: the group-membership descriptors that parameterize the type of the OP, the logarithms of the distribution coefficients at pH 7.4 and their squared term, the lowest unoccupied molecular orbital (LUMO) energies, the scaled molar refractions of the substituents, and their squared term. It was shown that the qualitative prediction made by molecular modelling can be quantified by an ANN prediction.
    Drug Design and Discovery 02/2003; 18(4):127-50.
  • [Show abstract] [Hide abstract]
    ABSTRACT: Relationship between the topological indices and acyl-coenzyme A:cholesterol O-acyltransferase (ACAT) inhibitory activity of (aminosulfonyl)ureas has been investigated. Three topological indices, Wiener's index--a distance-based topological descriptor, molecular connectivity index--an adjacency-based topological index, and eccentric connectivity index--an adjacency-cum-distance-based topological descriptor, were used for the present investigations. A data set comprising 41 analogues of substituted (aminosulfonyl)ureas was selected for the present studies. The values of wiener's index, eccentric connectivity index, and molecular connectivity index for each of the 41 compounds comprising the data set were computed using an in-house computer program. Resultant data were analyzed and suitable models were developed after identification of active ranges. Subsequently, a biological activity was assigned to each compound using these models, which was then compared with the reported in vitro ACAT inhibitory activity. Accuracy of prediction using these models was found to vary from a minimum of approximately 83% to a maximum of approximately 91%.
    Drug Design and Discovery 02/2003; 18(4):117-22.
  • [Show abstract] [Hide abstract]
    ABSTRACT: Imidazole and oxazole derivatives 1 to 4 were designed and prepared as dipeptide mimetics to replace the Ser-Leu dipeptide sequence of Ro-25-9980 (Ac-(Cha)-RAMA-S-L-NH2), a peptidic inhibitor of antigen binding to major histocompatibility complex (MHC) class II DR molecules linked to rheumatoid arthritis (RA). The most potent analog in binding assays (IC50 = 30 nM in DRB1*0401 binding; 1.6 times as potent as Ro 25-9980) was 16, Ac-(Cha)RAMA-(S)S-psi(oxazole)-L-NH2. The SAR of peptide hybrids 10 to 24, prepared by incorporating the dipeptide mimetics 1 to 4 is discussed. Of these hybrids, 23 and 24, analogs that incorporated the imidazole and oxazole mimetics as well as optimized variants at positions 3 to 5, were found to have 70 to 80 nM binding affinity comparable to the parent peptide in DRB 1*0401 binding and were also active in DRB1*0101 binding, while being resistant to proteolysis by cathepsin B. Both of these compounds showed inhibitory activity in an antigen-stimulated T-cell proliferation assay, indicating their potential to suppress autoimmune responses and as leads for therapeutic agents to treat RA.
    Drug Design and Discovery 02/2002; 18(1):3-7.
  • [Show abstract] [Hide abstract]
    ABSTRACT: Quantitative structure-activity relationship (QSAR) study of human factor Xa inhibitor N2-aroylanthranilamides, recently reported by Yee et al. (J. Med. Chem., 43, 873-882), has been performed using principal component factor analysis as the preprocessing step. The study reveals that presence of electron-donating R2 substituent at the para position (with respect to the amide linkage) is conducive to the binding affinity, whereas a meta R2 substituent decreases the affinity. Again, electron-donating R1 substituents with less bulk and optimum hydrophilic-lipophilic balance (particularly, methyl and methoxy groups) favor the activity. The study further suggests that electron-withdrawing R3 substituents are detrimental for the activity, whereas bulkier R4 substituents (particularly NHSO2Me group) increase the activity.
    Drug Design and Discovery 02/2002; 18(1):23-31.
  • [Show abstract] [Hide abstract]
    ABSTRACT: Recently, N2-aroylanthranilamides have been reported as novel series of possible anticoagulant drug candidates and the two aryl rings (A and B) have been suggested to interact with S1 and S4 regions, respectively, of human factor Xa (hfXa). In the present effort, quantitative structure-activity relationship (QSAR) of the hfXa binding affinity of 32 N2-aroylanthranilamides have been attempted, in continuation of our previous report on the QSAR analysis of the data set using linear free energy related (LFER) model, with electrotopological state atom (ETSA) index (Kier and Hall, 1991, Adv. Drug Design., 22, 1-38), to explore the atoms/regions of the compounds that modulate the activity comparatively to the greater extent. The univariate and bivariate relations involving the ETSA values of different common atoms of the compounds show importance of the atom nos. 12, 3 and 17 (arbitrary numbering): B ring carbon bearing meta R2 substituents, C ring carbon bearing R4 substituent, and carbonyl oxygen of A ring amide linkage. The importance of atom 12 is suggested to be due to detrimental effects of meta R2 substituents (B ring) on the hfXa binding affinity, which may be owing to interference in the attainment of the proper orientation of the phenyl ring in the S4 site. Atom 3 signifies the impact of R4 substituents (central C ring) on the binding affinity. Again, atom 17 (carbonyl oxygen of A ring amide linkage) has been suggested to form hydrogen bonding with the NH group of the other amide linkage, producing a pseudo ring and thus stabilizing the structure. The relations were improved further using indicator and physicochemical variables and the present results are in good agreement with the previous findings of the Hansch analysis.
    Drug Design and Discovery 02/2002; 18(1):33-43.
  • [Show abstract] [Hide abstract]
    ABSTRACT: One hundred sixty-eight multiply substituted 1,4-benzodiazepines have been prepared by a five-step solid-phase combinatorial approach using syn-phase crowns as a solid support and a hydroxymethyl-phenoxy-acetamido linkage (Wang linker). The substituents of the 1,4-benzodiazepine scaffold have been varied in the -3, -5, -7, and 8-positions and the combinatorial library was evaluated in a chole cys to kinin (CCK) radioligand binding assay. 3-Alkylated 1,4-benzodiazepines with selectivity towards the CCK-B (CCK2) receptor have been optimized on the lipophilic side chain, the ketone moiety, and the stereochemistry at the 3-position. Various novel 3-alkylated compounds were synthesized and [S]3-propyl-5-phenyl-1,4-benzodiazepin-2-one, [S]NV-A, has shown a CCK-B selective binding at about 180 nM. Fifty-eight compounds of this combinatorial library were purified by preparative TLC and 25 compounds were isolated and fully characterized by TLC, IR, APCI-MS, and 1H/13C-NMR spectroscopy.
    Drug Design and Discovery 02/2002; 18(1):9-21.
  • [Show abstract] [Hide abstract]
    ABSTRACT: The SAR of Asperlicin analogues is reported, leading to bioactive 1,4-benzodiazepine-2-ones, which were prepared in a 3 step reaction sequence. The Asperlicin substructure was built up using Tryptophan and readily available 2-amino-acetophenones. This template, containing a 1,4-benzodiazepin-2-one moiety with a 3-indolmethyl side chain, was transformed into mono- and di-substituted 3-indol-3'-yl-methyl-1,4-benzodi-azepine-2-ones by selective alkylation and acylation reactions. The SAR optimization of the 1,4-benzodiazepine scaffold has included variations at the 5-, 7-, 8-position, at the N1, N-indole nitrogen and the configuration of the C3-position. The most active Asperlicin analogue, having an IC50 of 1.6 microM on the CCKA receptor subtype, was obtained from Tryptophan in only 3 steps in an overall yield of 48%.
    Drug Design and Discovery 02/2001; 17(3):219-30.
  • [Show abstract] [Hide abstract]
    ABSTRACT: In protein X-ray crystallography, it is sometimes impossible to distinguish N and O in amide side chains and N and C in His side chains, resulting in the 'flipped' conformations in these side chains. We have developed a simple, but effective, approach to assess the side chain orientations of His. Asn, and Gln as well as the protonation forms of His in protein structures. This method finds the most favorable side chain orientation and His form by calculating the van der Waals interaction and hydrogen bonding energies around each residue in question. This evaluation is repeated until consistent results are obtained. Our approach was applied to four proteins and in overall approximately 25% of His, Asn, and Gln were evaluated as 'flipped' and 63% of the imidazole rings were suggested to have a polar hydrogen atom only on N epsilon2. In the individual cases, it was found that our results were comparable to or even better than those obtained by a traditional method. The present approach is therefore quite useful to construct initial protein structures for the molecular modeling studies.
    Drug Design and Discovery 02/2001; 17(3):231-41.
  • [Show abstract] [Hide abstract]
    ABSTRACT: Hansch analysis of recently reported antitumor activities of novel N-(7-indolyl)benzenesulfonamide derivatives against KB human nasopharynx carcinoma, colon 38 murine adenocarcinoma and P388 murine leukemia cell lines reveals that the pattern of receptor interactions in human KB cells differs from that in murine (colon 38 and P388 leukemia) cells. The latter two activities are autocorrelated and show similar receptor specificity. It seems that two binding sites, one interacting with the indole fragment and another with phenyl fragment of the indolylbenzenesulfonamide compounds, are present on the murine cell receptors (colon 38 and P388 leukemia) while only the latter binding site is active on the human KB cell receptors. For the activity against KB cells, a para-methyl or paramethoxy substituent on the phenyl ring of benzenesulfonamide moiety greatly enhances the activity. For the other two activities, a 3-chloro or 3-cyano substituent on indole nucleus enhances activities, while presence of bulkier meta or para substituent on the phenyl ring decreases activities. Presence of an ortho substituent on the phenyl ring appears to be detrimental for all the three activities. Equations generated by both QSAR and QAAR studies are quite robust as evidenced from cross-validation by 'leave-one-out' technique.
    Drug Design and Discovery 02/2001; 17(3):199-206.