Aminodiol HIV protease inhibitors. Synthesis and structure-activity relationships of P1/P1' compounds: correlation between lipophilicity and cytotoxicity

Diazocarbonyl derivatives of amino acids: unique chiral building blocks for the synthesis of biologically active compounds

This review deals with applications of chiral α-amino diazoketones, α-amino acid derivatives, in the synthesis of various biologically active compounds. General approaches to the synthesis of chiral α-amino diazoketones, including the Arndt – Eistert reaction, acylation of trimethylsilyldiazomethanes, etc., are discussed. Due to the presence of three functional groups, these building blocks can be used to produce a wide range of organic compounds with potential physiological activity, ranging from various heterocyclic compounds to peptidomimetics. Methods for the synthesis of β-amino acid-containing peptides and depsipeptides, amino acid derivatives and heterocyclic compounds with three- to seven-membered rings are considered.

The bibliography includes 226 references.

Novel solid-phase parallel synthesis of N-substituted-2-aminobenzo [d]thiazole derivatives via cyclization reactions of 2-iodophenyl thiourea intermediate resin

A novel solid-phase methodology has been developed for the synthesis of N-alkyl, N-acyl, and N-sulfonyl-2-aminobenzo[d]thiazole derivatives. The key step in this procedure involves the preparation of polymer-bound 2-aminobenzo[d]thiazole resins 5 by cyclization reaction of 2-iodophenyl thiourea resin 3. The resin-bound 2-iodophenyl thiourea 3 is produced by addition of 2-iodophenyl isothiocyanate 2 to the amine-terminated linker amide resin 1. These core skeleton 2-aminobenzo[d]thiazole resins 5 undergo functionalization reactions with various electrophiles, such as alkyl halides, acid chlorides, and sulfonyl chlorides to generate N-alkyl, N-acyl, and N-sulfonyl-2-aminobenzo[d]thiazole resins 6, 7, and 8, respectively. Finally, N-alkyl, N-acyl, and N-sulfonyl-2-aminobenzo[d]thiazole derivatives 9, 10, and 11 are then generated in good yields and purities by cleavage of the respective resins 6, 7, and 8 using trifluoroacetic acid (TFA) in dichloromethane (DCM).

Molecular dynamics investigation on a series of HIV protease inhibitors: assessing the performance of MM-PBSA and MM-GBSA approaches

The binding free energies (ΔG(Bind)) obtained from molecular mechanics with Poisson-Boltzmann surface area (MM-PBSA) or molecular mechanics with Generalized Born surface area (MM-GBSA) calculations using molecular dynamics (MD) trajectories are the most popular procedures to measure the strength of interactions between a ligand and its receptor. Several attempts have been made to correlate the ΔG(Bind) and experimental IC(50) values in order to observe the relationship between binding strength of a ligand (with its receptor) and its inhibitory activity. The duration of MD simulations seems very important for getting acceptable correlation. Here, we are presenting a systematic study to estimate the reasonable MD simulation time for acceptable correlation between ΔG(Bind) and experimental IC(50) values. A comparison between MM-PBSA and MM-GBSA approaches is also presented at various time scales. MD simulations (10 ns) for 14 HIV protease inhibitors have been carried out by using the Amber program. MM-PBSA/GBSA based ΔG(Bind) have been calculated and correlated with experimental IC(50) values at different time scales (0-1 to 0-10 ns). This study clearly demonstrates that the MM-PBSA based ΔG(Bind) (ΔG(Bind)-PB) values provide very good correlation with experimental IC(50) values (quantitative and qualitative) when MD simulation is carried out for a longer time; however, MM-GBSA based ΔG(Bind) (ΔG(Bind)-GB) values show acceptable correlation for shorter time of simulation also. The accuracy of ΔG(Bind)-PB increases and ΔG(Bind)-GB remains almost constant with the increasing time of simulation.

Prediction of pesticides chromatographic lipophilicity from the computational molecular descriptors

Quantitative structure-property relationship models were developed for the prediction of pesticides and some PAH compounds lipophilicity based on a wide set of computational molecular descriptors and a set of experimental chromatographic data. The chromatographic lipophilicity of pesticides has been evaluated by high-performance liquid chromatography (HPLC) using different chemically bonded (C18, C8, CN and Phenyl HPLC columns) stationary phases and two different organic modifiers (methanol and acetonitrile, respectively) in the mobile phase composition. Through a systematic study, by using the classic multivariate analysis, several quantitative structure-property/lipophilicity multi-dimensional models were established. Multiple linear regression and genetic algorithm for the variable subset selection were used. The internal and external statistical evaluation procedures revealed some appropriate models for the chromatographic lipophilicity prediction of pesticides. Moreover, the statistical parameters of regression and those obtained by applying t-test for the intercept (a(0)) and for the slope (a(1)) in order to evaluate relationship between experimental and predicted octanol-water partition coefficients in case of the test set compounds, revealed two statistically valid models that can be successfully used in lipophilicity prediction of pesticides.

(1S,2R,4S)-1-[(Benzyl-amino)-meth-yl]-4-(prop-1-en-2-yl)cyclo-hexane-1,2-diol

The title compound, C₁₇H₂₅NO₂, was synthesized by epoxidation of the double bond of (S)-perillyl alcohol [(S)-4-isopropenyl-1-cyclo­hexenyl­methanol], followed by the oxirane ring-opening by benzyl­amine using [Ca(CF₃CO₂)₂] as catalyst under solvent-free condition at 313 K. The mol­ecular conformation is stabilized by an intra­molecular O—H⋯N hydrogen bond. In the crystal, mol­ecules are linked by inter­molecular N—H⋯O hydrogen bonds, forming chains parallel to the a axis, which are further connected by O—H⋯O hydrogen bonds into sheets parallel to (010). The absolute configuration of the mol­ecule is known from the synthetic procedure.

Stabilized (111)in-labeled sCCK8 analogues for targeting CCK2-receptor positive tumors: synthesis and evaluation

Radiolabeled cholecystokinin-8 (CCK8) peptide analogues can be used for peptide receptor radionuclide imaging and therapy for tumors expressing CCK2/gastrin receptors. Earlier findings indicated that sulfated CCK8 (sCCK8, Asp-Tyr(OSO(3)H)-Met-Gly-Trp-Met-Asp-Phe-NH(2)) may have better characteristics for peptide receptor radionuclide therapy (PRRT) than gastrin analogues. However, sCCK8 contains an easily hydrolyzable sulfated tyrosine residue and two methionine residues which are prone to oxidation. Here, we describe the synthesis of stabilized sCCK8 analogues, resistant to hydrolysis and oxidation. Hydrolytic stability was achieved by replacement of the Tyr(OSO(3)H) moiety by a robust isosteric sulfonate, Phe(p-CH(2)SO(3)H). Replacement of methionine by norleucine (Nle) or homopropargylglycine (HPG) avoided undesired oxidation side-reactions. The phenylalanine analogue Phe(p-CH(2)SO(3)H) of l-tyrosine, synthesized by a modification of known synthetic routes, was incorporated in three peptides: sCCK8[Phe(2)(p-CH(2)SO(3)H),Met(3,6)], sCCK8[Phe(2)(p-CH(2)SO(3)H),Nle(3,6)], and sCCK8[Phe(2)(p-CH(2)SO(3)H),HPG(3,6)]. All peptides were N-terminally conjugated with the macrocyclic chelator DOTA (1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid) and radiolabeled with In-111. In vitro binding assays on CCK2R-expressing HEK293 cells revealed that all three peptides showed specific binding and receptor-mediated internalization, with binding affinity values (IC(50)) in the nanomolar range. In vitro oxidation studies demonstrated that peptides with Nle or HPG indeed were resistant to oxidation. In vivo targeting studies in mice with AR42J tumors showed that tumor uptake was highest for (111)In-DOTA-sCCK8 and (111)In-DOTA-sCCK8[Phe(2)(p-CH(2)SO(3)H),Nle(3,6)] (4.78 +/- 0.64 and 4.54 +/- 1.15%ID/g, respectively, 2 h p.i.). The peptide with the methionine residues replaced by norleucine ((111)In-DOTA-sCCK8[Phe(2)(p-CH(2)SO(3)H), Nle(3,6)]) showed promising in vivo characteristics and will be further investigated for radionuclide imaging and therapy of CCK2R-expressing tumors.

Chiral-catalyst-based convergent synthesis of HIV protease inhibitor GRL-06579A

Catalytic asymmetric synthesis of GRL-06579A (1), an HIV-1 protease inhibitor effective against multi-protease-inhibitor-resistant viruses, is described. A convergent strategy that utilizes heterobimetallic multifunctional catalysts developed in our group is a key feature of the synthesis. The chirality of the bicyclic tetrahydrofuran unit of 1 was introduced through Al-Li-bis(binaphthoxide) (ALB) catalyst-controlled Michael addition of dimethyl malonate to racemic 4-O-protected cyclopentenone. ALB afforded not only the trans adduct with up to 96% ee from a matched substrate through kinetic resolution, but also the cis adduct with 99% ee through a catalyst-controlled Michael addition to a mismatched substrate. The Michael addition to produce the unusual cis adduct is described in detail. The framework of the bicyclic tetrahydrofuran was constructed by an intramolecular oxy-Michael reaction. The amino alcohol unit was constructed by an La-Li3-tris(binaphthoxide) (LLB)-catalyzed diastereoselective nitroaldol reaction of N-Boc aldehyde (Boc = tert-butoxycarbonyl) derived from L-phenylalanine. LLB promoted the nitroaldol reaction without racemization of the chiral aldehyde to give the nitroaldol adduct in 85% yield and with 93:7 diastereoselectivity and over 99% ee.

Solid-phase synthesis of the 2-aminobenzoxazole library using thioether linkage as the safety-catch linker

An efficient solid-phase methodology has been developed for the synthesis of 2-aminobenzoxazole derivatives. The key step in this procedure involves preparation of polymer-bound 2-mercaptobenzoxazole resins 3 by reaction of the Merrifield resin with 2-aminophenols and CS(2) in the presence of DIC in MeCN. Oxidation of the resulting resins followed by treatment with amines gives the desired 2-aminobenzoxazole products 5. Further diversification can be introduced to the key resin 11, derived from the nitro group containing resin 3c. This process produces the corresponding amine, which upon reaction with acid chlorides and isocyanates can be used to generate various 6-functionalized 2-aminobenzoxazole analogues 13 and 15.

Fluorogenic peptide substrates containing benzoxazol-5-yl-alanine derivatives for kinetic assay of cysteine proteases

New peptide substrates containing benzoxazol-5-yl-alanine derivatives for kinetic assay of cysteine proteases have been synthesized and characterized. The substrates are peptides internally quenched by the intramolecular fluorescence resonance energy transfer. The results demonstrate that the kind of donor-acceptor pair (D-A) significantly affects the kinetic parameters of the enzymatic process. The three longest peptides, Box-Lys-Phe-Gly-Gly-Ala-Ala-Tyr(NO2) containing Box-alanine derivative as a donor and nitro-tyrosine as an acceptor, show two times greater affinity to papain than does the one peptide possessing Dabcyl-Edans as a D-A pair. Kinetic parameters for the best papain substrate, Lys-Box(benzfur)-Gly-Gly-Ala-Ala-Tyr(NO2), are Km = 6.85+/-0.59 microM, kcat = 19.51 s(-1), and kcat/Km = 2.85 microM(-1) s(-1). It was found that the peptides Box(benzfur)-Lys-Phe-Gly-Gly-Tyr(NO2) and Box(benzfur)-Phe-Gly-Gly-Tyr(NO2) were also hydrolyzed by cathepsin B with the highest speed of hydrolysis as a result of carboxypeptidase activity of this enzyme. Moreover, these substrates show high affinity and selectivity to this enzyme.

Respiratory syncytial virus inhibitors. Part 2: Benzimidazol-2-one derivatives

Structure-activity relationships for a series of benzimidazol-2-one-based inhibitors of respiratory syncytial virus are described. These studies focused on structural variation of the benzimidazol-2-one substituent, a vector inaccessible in a series of benzotriazole derivatives on which 2 is based, and revealed a broad tolerance for substituent size and functionality.

In silico prediction of drug toxicity

It is essential, in order to minimise expensive drug failures due to toxicity being found in late development or even in clinical trials, to determine potential toxicity problems as early as possible. In view of the large libraries of compounds now being handled by combinatorial chemistry and high-throughput screening, identification of putative toxicity is advisable even before synthesis. Thus the use of predictive toxicology is called for. A number of in silico approaches to toxicity prediction are discussed. Quantitative structure-activity relationships (QSARs), relating mostly to specific chemical classes, have long been used for this purpose, and exist for a wide range of toxicity endpoints. However, QSARs also exist for the prediction of toxicity of very diverse libraries, although often such QSARs are of the classification type; that is, they predict simply whether or not a compound is toxic, and do not give an indication of the level of toxicity. Examples are given of all of these. A number of expert systems are available for toxicity prediction, most of them covering a range of toxicity endpoints. Those discussed include TOPKAT, CASE, DEREK, HazardExpert, OncoLogic and COMPACT. Comparative tests of the ability of these systems to predict carcinogenicity show that improvement is still needed. The consensus approach is recommended, whereby the results from several prediction systems are pooled.

Fundamental structure-activity relationships associated with a new structural class of respiratory syncytial virus inhibitor

Structure-activity relationships surrounding the dialkylamino side chain of a series of benzotriazole-derived inhibitors of respiratory syncytial virus fusion based on the screening lead 1a were examined. The results indicate that the topology of the side chain is important but the terminus element offers considerable latitude to modulate physical properties.

Symmetry-based inhibitors of HIV-1 protease. Design, synthesis and preliminary structure-activity studies of acylated 2,3-diamino-1-hydroxypropanes and 2,4 diamino-1-hydroxybutanes

Two series of peptidomimetics containing a novel C(2) pseudosymmetrical hydroxyalkyldiamino core structure were prepared from amino acid starting materials and tested for inhibitory activity against the HIV-1 protease (HIV-1 Pr) and the virus in cell culture. In the 2,3-diamino-1-hydroxypropane series, compound 6a, containing P1/P1(I) benzyl and P2/P2(I) Fmoc substituents, displayed modest HIV-1 Pr inhibition (IC(50) = 430 nM). The corresponding 2,4-diamino-1-hydroxybutane derivative (6b) was the best inhibitor of the series (IC(50) = 160 nM). Interestingly, 6a and 6b showed satisfactory inhibition of HIV replication in cell culture (ED(50) = 340 and 110 nM, respectively), a result which suggests good cell membrane penetration by this class of compounds.