Isosteric Replacement Research Articles

Proline isosteres in a series of 2,4-disubstituted pyrrolo[1,2- f][1,2,4]triazine inhibitors of IGF-1R kinase and IR kinase

Pyrrolidine, pyrrolidinone, carbocyclic, and acyclic groups were used as isosteric proline replacements in a series of insulin-like growth factor I receptor kinase/insulin receptor kinase inhibitors. Examples that were similar in potency to proline-containing reference compounds were shown to project a key fluoropyridine amide into a common space, while less potent compounds were not able to do so for reasons of stereochemistry or structural rigidity.

Library of 1,4-Disubstituted 1,2,3-Triazole Analogs of Oxazolidinone RNA-Binding Agents

The design and synthesis of small molecules that target RNA is immensely important in antibacterial therapy. We had previously reported on the RNA binding of a series of 4,5-disubstituted 2-oxazolidinones that bind to a highly conserved bulge region of bacterial RNA. This biological target T box antitermination system, which is found mainly in Gram-positive bacteria, regulates the expression of several amino acid related genes. In an effort to amplify our library, we have prepared a library of 1,4-disubstituted 1,2,3-triazole analogs that entails an isosteric replacement of the oxazolidinone nucleus. The synthesis of the new analogs was enhanced via copper(I) catalysis of an azide and alkyne cycloaddition reaction. A total of 108 1,4-disubstituted 1,2,3-triazole compounds have been prepared. All compounds were evaluated as RNA binding agents.

Diarylaniline Derivatives as a Distinct Class of HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors

By using structure-based drug design and isosteric replacement, diarylaniline and 1,5-diarylbenzene-1,2-diamine derivatives were synthesized and evaluated against wild type HIV-1 and drug-resistant viral strains, resulting in the discovery of diarylaniline derivatives as a distinct class of next-generation HIV-1 non-nucleoside reverse transcriptase inhibitor (NNRTI) agents. The most promising compound 37 showed significant EC(50) values of 0.003-0.032 microM against HIV-1 wild-type strains and of 0.005-0.604 microM against several drug-resistant strains. Current results also revealed important structure-activity relationship (SAR) conclusions for diarylanilines and strongly support our hypothesis that an NH(2) group on the central benzene ring ortho to the aniline moiety is crucial for interaction with K101 of the NNRTI binding site in HIV-1 RT, likely by forming H-bonds with K101. Furthermore, molecular modeling studies with molecular mechanism/general Born surface area (MM/GBSA) technology demonstrated the rationality of our hypothesis.

ChemInform Abstract: Synthesis and Use of Pseudopeptides Derived from 1,2,4-Oxadiazole-, 1,3,4-Oxadiazole-, and 1,2,4-Triazole-Based Dipeptidomimetics

This chapter focuses on the isosteric replacement of peptide bonds with three different types of heterocyclic ring systems (1); 1,2,4-oxadiazole (2), 1,3,4-oxadiazole (3), and 1,2,4-triazole rings (4-6). The ring systems are similar in size and shape but show variations in aromatic, electrostatic, and hydrogen bonding properties. These variations provide opportunities to study properties of importance for amide bond mimicry. The derivatives are synthesized from protected natural amino acids, and the reaction conditions have been chosen so that the enantiopurity is retained during the reaction sequences. Two series of mimetics will be described, one in which the carboxylic acid functionality is directly attached to the heterocyclic ring (1) and one series with a methylene group inserted between the ring and the carboxylic acid group (7). Since we have focused on the design and synthesis of Phe-Gly mimetics, the synthetic examples described here start from L: -phenylalanine. However, we have used the same synthetic scheme also for other amino acids and notes will be given when other derivatives require differences in reaction conditions (1). The use of the dipeptidomimetics as building blocks in pseudopeptide synthesis will also be described (7). These syntheses are performed on solid phase using Boc-chemistry. Also, the deprotection and purification of the pseudopeptides by reversed phase HPLC will be discussed.

Triazole-Linked Inhibitors of Inosine Monophosphate Dehydrogenase from Human and Mycobacterium tuberculosis

The modular nature of nicotinamide adenine dinucleotide (NAD)-mimicking inosine monophsophate dehydrogenase (IMPDH) inhibitors has prompted us to investigate novel mycophenolic adenine dinucleotides (MAD) in which 1,2,3-triazole linkers were incorporated as isosteric replacements of the pyrophosphate linker. Synthesis and evaluation of these inhibitors led to identification of low nanomolar inhibitors of human IMPDH and more importantly the first potent inhibitor of IMPDH from Mycobacterium tuberculosis (mtIMPDH). Computational studies of these IMPDH enzymes helped rationalize the observed structure-activity relationships. Additionally, the first cloning, expression, purification and characterization of mtIMPDH is reported.

ChemInform Abstract: Synthesis and Cytotoxic Activity of 2-Methylimidazo[1,2-a]pyridine- and Quinoline-Substituted 2-Aminopyrimidine Derivatives.

A series of 2-methylimidazo[1,2-a]pyridine- and quinoline-substituted 2-aminopyrimidines derivatives were synthesized using a convenient synthetic route. We evaluate the isosteric replacement of methyl groups in 4-(2-methylimidazo[1,2-a]pyridin-3-yl)-N-p-tolylpyrimidin-2-amine (compound 1) by trifluoromethyl groups and the isosteric substitution of the 2-methylimidazo[1,2-a]pyridin-3-yl scaffold by quinolin-4-yl or quinolin-3-yl moieties. The replacement of hydrogen by fluorine does not affect notably the cytotoxic activity and CDK inhibitor activity in this series. Quinolin-4-yl-substituted compound, 8, presents cytotoxic activity and is most effective and selective against CDK1/CycA than against CDK2/CycB. Compound 11, which has a quinolin-3-yl moiety is CDK inhibitor but presents null cytotoxic activity. Quinolin-4-yl-substituted compounds constitute a new lead of cytotoxic and CDK inhibitor compounds from which more compelling and selective inhibitors can be designed.

Abstract 756: Optimization of tetrahydroisoquinoline-based microtubule disruptors as anticancer agents

Abstract We outline the discovery and optimisation of new microtubule disruptors with in vivo anti-tumor activity. Translation of the SAR from a steroidal series of microtubule disruptors led us to identify a series of tetrahydroisoquinoline (THIQ) based systems which exhibit a similar activity profile. Of this new series, 2-(3′,4′,5′-Trimethoxybenzyl)-7-methoxy-6-O-sulfamoyl THIQ 1 proved especially potent in both in vitro (GI50 [DU-145] 297 nM) and in vivo experiments. Herein, we describe the results of optimisation at C-6 and C-7 of the THIQ core and assessment of other polymethoxylated N-benzyl systems. Variations at the N-2 and C-6 positions were achieved by alkylation, esterification and etherification. Friedel Crafts acylation of C-7 and functional group interconversion allowed access to various C-7 alkyl and alkoxy derivatives. The various dimethoxybenzyl compounds proved similar in activity to the lead compound 2 (GI50 2.1 μM) in the N-mono-methoxybenzyl series while, apart from the 3′,4′,5′-trimethoxybenzyl compound 1, only 2′,4′,5′-trimethoxybenzyl substitution delivered sub-micromolar activity. Investigations of the effect of C-6 substitution proved more fruitful. In contrast to the SAR observed for 2 where the sulfamate group is essential for activity, the 6-OH, with the 6-O-acyl and 6-O-mesyl derivatives of 1 displayed similar or improved activity to the parent compound (GI50s range from 650 to 220 nM). The 6-O-methyl derivative, in contrast, proved completely inactive, highlighting the importance of a H-bond donor directly attached to C-6 or a H-bond acceptor projecting further out from this position. The most pronounced improvement in activity was obtained from exploration of C-7 substitution. In the 3′,4′,5′-trimethoxybenzyl series isosteric replacement of methoxy with ethyl delivered a 7-fold improvement in activity (3 GI50 41 nM). Intriguingly, the corresponding phenol proved significantly active suggesting different binding modes operate for the phenol and sulfamate derivatives since the H-bond acceptor properties of the C-7 substituent of the former are clearly important. Incorporation of a C-7 ethoxy group meanwhile proved detrimental for both sulfamate and phenol derivatives. The same transformations were made to 2, though no improvement in activity was obtained. In order to establish the potential of these compounds as anti-tumor agents their activity in the RPMI-8226 multiple myeloma xenograft model was assessed. The >75% inhibition of tumor growth observed (3 p.o. 40 mg/kg, 28d) in this preliminary study augers well for the development of this class of anti-cancer agents. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 756.

2-Arylureidophenyl-4-(3-oxa-8-azabicyclo[3.2.1]octan-8-yl)triazines as highly potent and selective ATP competitive mTOR inhibitors: Optimization of human microsomal stability

Isosteric replacement of one of the 3,5-ethylene-bridged morpholines in 2-arylureidophenyl-4,6-di(3-oxa-8-azabicyclo[3.2.1]octan-8-yl)triazines led to significant improvements in human microsomal stability. 3- R-Me-morpholine and tetrahydropyran were identified as preferred isosteres for the bridged morpholine. Combination of tetrahydropyran substitution with an N-Me-piperazinophenylureido group led to 27, that selectively suppressed mTOR biomarkers in vivo and possessed excellent efficacy in a murine xenograft model.

Searching for multi-target antipsychotics: Discovery of orally active heterocyclic N-phenylpiperazine ligands of D 2- like and 5-HT 1A receptors

We described herein the design, synthesis, and pharmacological evaluation of N-phenylpiperazine heterocyclic derivatives as multi-target compounds potentially useful for the treatment of schizophrenia. The isosteric replacement of the heterocyclic ring at the biaryl motif generating pyrazole, 1,2,3-triazole, and 2-methylimidazole[1,2- a]pyridine derivatives resulted in 21 analogues with different substitutions at the para-biaryl and para-phenylpiperazine positions. Among the compounds prepared, 4 (LASSBio-579) and 10 (LASSBio-664) exhibited an adequate binding profile and a potential for schizophrenia positive symptoms treatment without cataleptogenic effects. Structural features of this molecular scaffold are discussed regarding binding affinity and selectivity for D 2- like, 5-HT 1A, and 5-HT 2A receptors.

Replacement of pyrazol-3-yl amine hinge binder with thiazol-2-yl amine: Discovery of potent and selective JAK2 inhibitors

Thiazol-2-yl amine was identified as an isosteric replacement for pyrazol-3-yl amine during our efforts to identify potent and selective JAK2 inhibitors. The rationale, synthesis and biological evaluation of several analogs is reported, along with the in vivo evaluation of the lead compounds.

A general approach to indole-7-yl derivatives of isoxazole, oxadiazole, thiadiazole and pyrazole

Isosteric replacement of the α,β-unsaturated amide at the C-7 position of indoles with a diverse set of five-membered amino-heterocycles including isoxazole, oxadiazole, thiadiazole and pyrazole followed by subsequent derivatization of the heterocyclic amino group to yield amides, sulfonamides and phosphoramides is described. Distinctive features of these procedures include the versatility and robust nature of the synthetic steps along with the high yields of the targeted molecules.

Synthesis and cytotoxic activity of 2-methylimidazo[1,2- a]pyridine- and quinoline-substituted 2-aminopyrimidine derivatives

A series of 2-methylimidazo[1,2- a]pyridine- and quinoline-substituted 2-aminopyrimidines derivatives were synthesized using a convenient synthetic route. We evaluate the isosteric replacement of methyl groups in 4-(2-methylimidazo[1,2- a]pyridin-3-yl)- N- p-tolylpyrimidin-2-amine (compound 1) by trifluoromethyl groups and the isosteric substitution of the 2-methylimidazo[1,2- a]pyridin-3-yl scaffold by quinolin-4-yl or quinolin-3-yl moieties. The replacement of hydrogen by fluorine does not affect notably the cytotoxic activity and CDK inhibitor activity in this series. Quinolin-4-yl-substituted compound, 8, presents cytotoxic activity and is most effective and selective against CDK1/CycA than against CDK2/CycB. Compound 11, which has a quinolin-3-yl moiety is CDK inhibitor but presents null cytotoxic activity. Quinolin-4-yl-substituted compounds constitute a new lead of cytotoxic and CDK inhibitor compounds from which more compelling and selective inhibitors can be designed.

Bioisosteric replacement of the hydrazide pharmacophore of the cannabinoid-1 receptor antagonist SR141716A. Part I: Potent, orally-active 1,4-disubstituted imidazoles

A new series of CB 1 receptor antagonists incorporating an imidazole-based isosteric replacement for the hydrazide moiety of rimonabant (SR141716) is disclosed. Members of this imidazole series possess potent/selective binding to the rCB 1 receptor and exhibit potent hCB 1 functional activity. Isopropyl analog 9a demonstrated activity in the tetrad assay and was orally-active in a food intake model.

Recent Advances in the Synthesis and Applications of Reduced Amide Pseudopeptides

Being one of the simplest and widely used isosteric replacements for the peptide bond, reduced amide has been successfully applied in the synthesis of many bioactive compounds. The introduction of reduced amide not only confers the pseudopeptide a higher enzymatic resistance and a linear and more flexible structure, but also increases its hydrophylicity due to the introduction of a protonable group. It has also proved adequate as a transition state mimetic for the tetrahedral intermediate formed during the hydrolysis of the peptide bond. Recent advances in the solution and solid-phase synthesis of reduced amides that emerged during the past ten years are presented. Most of them include the use of microwave irradiation to shorten the reaction times and improve the yields. The bioorganic chemistry of reduced-peptide-containing compounds represents an area of growing interest and it has recently been expanded to include analogues of endogenous peptides/ hormones that are resistant to hydrolysis by serum peptidases and enzyme inhibitors. Under certain conditions, synthetic peptides are highly immunogenic in animals, and might constitute chemically defined, safe and cheap vaccines. Linear pseudooligolysines, containing multiple adjacent CH2NH amide bond are potential candidates for future use as DNA carriers in gene delivery. Reduced amides have also seen use in the preparation of peptide nucleic acids and antibacterial peptides.

The development of biochemistry and molecular biology in China

The development of biochemistry and molecular biology in China

Design, synthesis and antimycobacterial activity of some novel imidazo[1,2- c]pyrimidines

Tuberculosis, due to its relentless nature, is now a major public health threat. The concomitant resurgence of TB with the MDR- or XDR-TB and HIV/AIDS pandemic has exposed the frailties of the current drug armatorium. Based on isosteric replacement and good 3D structural similarity between PA-824, a novel antimycobacterial agent undergoing clinical trials, and imidazo[1,2- c]pyrimidines, we have designed novel imidazo[1,2- c]pyrimidines. The designed molecules were synthesized by nucleophilic displacement of chloro group of various substituted 4-chloropyrimidines by ethanolamine followed by cyclisation of these 4-(2-hydroxyethyl)aminopyrimidines to imidazo[1,2- c]pyrimidines in good yield. All the compounds were screened for their antimycobacterial activity on Mycobacterium tuberculosis H37Rv strain by 1% proportion method. Some of the synthesized compounds exhibited potent antimycobacterial activity with MIC values in the range of 2–20 μg/mL.

Molecular modeling of tricyclic compounds with anilino substituents and their intercalation complexes with DNA sequences

Although 9-anilinoacridines are among the best studied antitumoral intercalators, there are few studies about the effect of isosteric substitution of a benzene moiety for a heterocycle ring in the acridine framework. According to these studies, this approach may lead to effective cytotoxic agents, but good cytotoxic activity depends on structural requirements in the aniline ring which differ from those in 9-anilinoacridines. The present paper deals with molecular modeling studies of some 9-anilino substituted tricyclic compounds and their intercalation complexes (in various DNA sequences) resulting from docking the compounds into various DNA sequences. As expected, the isosteric substitution in 9-anilinoacridines influences the LUMO energy values and orbital distribution, the dipole moment, electrostatic charges and the conformation of the anilino ring. Other important differences are observed during the docking studies, for example, changes in the spatial arrangement of the tricyclic nucleus and the anilino ring at the intercalation site. Semiempirical calculations of the intercalation complexes show that the isosteric replacement of a benzene ring in the acridine nucleus affects not only DNA affinity but also base pair selectivity. These findings explain, at least partially, the different structural requirements observed in several 9-anilino substituted tricyclic compounds for cytotoxic activity. Thus, the data presented here may guide the rational design of new agents with different DNA binding properties and/or a cytotoxic profile by isosteric substitution of known intercalators.

Synthesis and biological activities of linear and cyclic enkephalin analogues containing a psi (E,CH = CH) or psi (CH2CH2) isosteric replacement.

The peptide CO-NH function was replaced by a trans carbon-carbon double bond or by a CH2-CH2 isostere in enkephalin analogues of DADLE, DCDCE-NH2 or DPDPE. In DADLE the 2-3 and the 3-4 peptide bond was modified, whereas in the cyclic analogues the Gly3-Phe4 bond was replaced by the isosteres Gly psi (E,CH = CH)Phe [5-amino-2-(phenylmethyl)-3(E)-pentenoic acid] or Gly psi (CH2CH2)Phe [5-amino-2-(phenylmethyl)pentanoic acid]. In general, the modification results in a drop in potency which is the largest for the flexible CH2-CH2 replacement. The Gly3 psi (E,CH = CH)Phe4 DCDCE-NH2 analogue retains considerable potency. These results confirm the importance of the peptide function at the 2-3 and 3-4 position in enkephalin analogues for biological potency.

Solid phase synthesis and structural analysis of novel A-chain dicarba analogs of human relaxin-3 (INSL7) that exhibit full biological activity

Replacement of disulfide bonds with non-reducible isosteres can be a useful means of increasing the in vivo stability of a protein. We describe the replacement of the A-chain intramolecular disulfide bond of human relaxin-3 (H3 relaxin, INSL7), an insulin-like peptide that has potential applications in the treatment of stress and obesity, with the physiologically stable dicarba bond. Solid phase peptide synthesis was used to prepare an A-chain analogue in which the two cysteine residues that form the intramolecular bond were replaced with allylglycine. On-resin microwave-mediated ring closing metathesis was then employed to generate the dicarba bridge. Subsequent cleavage of the peptide from the solid support, purification of two isomers and their combination with the B-chain via two intermolecular disulfide bonds, then furnished two isomers of dicarba-H3 relaxin. These were characterized by CD spectroscopy, which suggested a structural similarity to the native peptide. Additional analysis by solution NMR spectroscopy also identified the likely cis/trans form of the analogs. Both peptides demonstrated binding affinities that were equivalent to native H3 relaxin on RXFP1 and RXFP3 expressing cells. However, although the cAMP activity of the analogs on RXFP3 expressing cells was similar to the native peptide, the potency on RXFP1 expressing cells was slightly lower. The data confirmed the use of a dicarba bond as a useful isosteric replacement of the disulfide bond.

Differences between High- and Low-Affinity Complexes of Enzymes and Nonenzymes

Physical differences in small molecule binding between enzymes and nonenzymes were found through mining the protein-ligand database, Binding MOAD (Mother of All Databases). The data suggest that divergent approaches may be more productive for improving the affinity of ligands for the two classes of proteins. High-affinity ligands of enzymes are much larger than those with low affinity, indicating that the addition of complementary functional groups is likely to improve the affinity of an enzyme inhibitor. However, this process may not be as fruitful for ligands of nonenzymes. High- and low-affinity ligands of nonenzymes are nearly the same size, so modest modifications and isosteric replacement might be most productive. The inherent differences between enzymes and nonenzymes have significant ramifications for scoring functions and structure-based drug design. In particular, nonenzymes were found to have greater ligand efficiencies than enzymes. Ligand efficiencies are often used to indicate druggability of a target, and this finding supports the feasibility of nonenzymes as drug targets. The differences in ligand efficiencies do not appear to come from the ligands; instead, the pockets yield different amino acid compositions despite very similar distributions of amino acids in the overall protein sequences.