Structure activity of 3-aryl-1,3-diketo-containing compounds as HIV-1 integrase inhibitors

The Integrase: An Overview of a Key Player Enzyme in the Antiviral Scenario

Integration of a desossiribonucleic acid (DNA) copy of the viral ribonucleic acid (RNA) into host genomes is a fundamental step in the replication cycle of all retroviruses. The highly conserved virus-encoded Integrase enzyme (IN; EC 2.7.7.49) catalyzes such a process by means of two consecutive reactions named 3'-processing (3-P) and strand transfer (ST). The Authors report and discuss the major discoveries and advances which mainly contributed to the development of Human Immunodeficiency Virus (HIV) -IN targeted inhibitors for therapeutic applications. All the knowledge accumulated over the years continues to serve as a valuable resource for the design and development of effective antiretroviral drugs.

An MCM-41-immobilized dichloro(pyridine-2-carboxylato)gold(III) complex: an efficient and recyclable catalyst for the annulation of anthranils and ynamides

A new mesoporous MCM-41-immobilized dichloro(pyridine-2-carboxylato)gold(III) complex [MCM-41-PicAuCl₂] was synthesized via an addition reaction of a dichloro(3-hydroxypyridine-2-carboxylato)gold(III) complex to triethoxy(3-isocyanatopropyl)silane, followed by immobilization on MCM-41 and was characterized by different physico-chemical techniques. In the presence of 5 mol% of MCM-41-PicAuCl₂, the annulation reaction between anthranils and ynamides proceeded smoothly under mild conditions to afford diverse 6- or 5-formylindoles with high atom economy and good to excellent yields. This new heterogenized gold(III) complex can be easily recovered through a simple filtration process and recycled more than seven times without any apparent loss of its catalytic efficiency.

Visible-light-induced indole synthesis via intramolecular C-N bond formation: desulfonylative C(sp2)-H functionalization

Despite significant advances made on the synthesis of indole derivatives through photochemical strategies during the past several years, the requirement of equivalent amounts of oxidants, bases or other additional additives has limited their practical applications in the synthesis of natural products and pharmaceuticals as environment-friendly processes. Herein, we report LED visible-light-induced redox neutral desulfonylative C(sp2)-H functionalization for the synthesis of N-substituted indoles with a broad scope through γ-fragmentation under mild conditions in the absence of any additional additive. The reaction mechanism paradigm has been investigated on the basis of deuterium labeling experiments, kinetic analysis, Hammett plotting analysis and DFT calculations.

Synthesis and Antiviral Properties against SARS-CoV-2 of Epoxybenzooxocino[4,3-b]Pyridine Derivatives

The COVID-19 pandemic is ongoing as of mid-2022 and requires the development of new therapeutic drugs, because the existing clinically approved drugs are limited. In this work, seven derivatives of epoxybenzooxocinopyridine were synthesized and tested for the ability to inhibit the replication of the SARS-CoV-2 virus in cell cultures. Among the described compounds, six were not able to suppress the SARS-CoV-2 virus’ replication. One compound, which is a derivative of epoxybenzooxocinopyridine with an attached side group of 3,4-dihydroquinoxalin-2-one, demonstrated antiviral activity comparable to that of one pharmaceutical drug. The described compound is a prospective lead substance, because the half-maximal effective concentration is 2.23 μg/μL, which is within a pharmacologically achievable range.

Uncommon Terpenoids from Salvia Species: Chemistry, Biosynthesis and Biological Activities

The search for new bioactive compounds from plant sources has been and continues to be one of the most important fields of research in drug discovery. However, Natural Products research has continuously evolved, and more and more has gained a multidisciplinary character. Despite new developments of methodologies and concepts, one intriguing aspect still persists, i.e., different species belonging to the same genus can produce different secondary metabolites, whereas taxonomically different genera can produce the same compounds. The genus Salvia L. (Family Lamiaceae) comprises myriad distinct medicinal herbs used in traditional medicine worldwide that show different pharmacological activities due to the presence of a variety of interesting specialized metabolites, including mono-, sesqui-, di-, sester-, tri-, tetra-, and higher terpenoids as well as phenylpropanoids, phenolic acid derivatives, lignans, flavonoids, and alkaloids. We herein summarize the research progress on some uncommon terpenoids, isolated from members of the genus Salvia, which are well recognized for their potential pharmacological activities. This review also provides a current knowledge on the biosynthesis and occurrence of some interesting phytochemicals from Salvia species, viz. C₂₃-terpenoids, sesterterpenoids (C₂₅), dammarane triterpenoids (C₃₀), and uncommon triterpenoids (C₂₀+C₁₀). The study was carried out by searching various scientific databases, including Elsevier, ACS publications, Taylor and Francis, Wiley Online Library, MDPI, Springer, Thieme, and ProQuest. Therefore, 106 uncommon terpenoids were identified and summarized. Some of these compounds possessed a variety of pharmacological properties, such as antibacterial, antiviral, antiparasitic, cytotoxic and tubulin tyrosine ligase inhibitory activities. Due to the lack of pharmacological information for the presented compounds gathered from previous studies, biological investigation of these compounds should be reinvestigated.

Heck Reaction Boosted Heterocycle Ring-Closing and Ring-Opening Rearrangement: A Strategy for the Synthesis of Indolyl-Type Ligands

A novel method for P-involved heterocycle ring-closing-ring-opening rearrangement (HRR) via the Heck reaction is disclosed. The approach enables direct installation of a phosphorus-containing aryl group onto the C2 position of indole. This new rearrangement directly transforms easily prepared indole derivatives into indolyl-derived phosphonates and phosphinic acids with high yields, and many of the products are difficult to obtain by using established methods. This new HRR reaction provides an extremely simple and step-economic method to induce C-C bond formation and P-N bond cleavage for the synthesis of a variety of indolyl-type ligands.

Rapid Cesium Fluoride Catalyzed Synthesis of 5-Aryloxy-1-phenyl-1Htetrazoles via Nucleophilic Aromatic Substitution

Abstract:

A nucleophilic aromatic substitution via a new and facile cesium fluoride catalyzed synthetic approach to get 5-aryloxy-1-phenyl-1H-tetrazoles was developed. Dual usage of cesium fluoride as a nucleophilic catalyst as well as an electrophilic catalyst afforded the desired products at room temperature in a short reaction time without purification in high yields. This simple but useful reaction may be a rapid and reliable strategy for the synthesis of tetrazolyl ethers.

Rapid access to 3-acyl indoles using ethyl acetate/triflic acid couple as the acylium donor and Cu(OAc)2 catalysed aerial oxidation of indole benzoins

Esters are potential acyl donors but are relatively unexplored for that purpose. A facile installation of acyl groups at the C-3 position of indoles under triflic acid catalysed conditions with easily available and cheap esters as new acylating agents is described herein. Furthermore, heterocycles like N-protected pyrrole, furan and thiophene were also suitable substrates for similar C-2 acylation. Analogous C-3 benzoylated products of indole were obtained, albeit in lower yields, by using methyl benzoate as a benzoyl donor. The benzoylated products were synthesised in much better yields via a copper(ii) catalysed aerial oxidation of indole containing benzoins.

Synthesis of 3-acylindoles via copper-mediated oxidative decarbethoxylation of ethyl arylacetates

An efficient regioselective C-3 acylation of free indoles (N-H) has been accomplished via oxidative decarbethoxylation of easily available ethyl arylacetates using Cu(OAc)2 and KOtBu in DMSO.

A competitive and highly selective 7-, 6- and 5-annulation with 1,3-migration through C-H and N-H - alkyne coupling

We demonstrated a highly competitive and selective C-C and N-C cross-coupled 7-, 6- and 5-annulation utilizing 2-ethynylanilides to afford functionalized 1H-benzo[b]azepin-2(5H)-ones, 2-quinolinones, and 3-acylindoles in high yield. ZnCl2 was found to be the smart catalyst for 7- and 5-annulation with 1,3-migration through C-H and N-H functionalization, respectively, whereas molecular iodine performed the C-H functionalized 6-annulation with a nonconventional 1,3 H-shift. The mechanism was investigated by intermediate trapping, control, and labeling experiments.

Evolution of HIV-1 reverse transcriptase and integrase dual inhibitors: Recent advances and developments

HIV infection is a major challenge to mankind and a definitive cure or a viable vaccine for HIV is still elusive. HIV-1 is constantly evolving and developing resistant against clinically used anti-HIV drugs thus posing serious hurdles in the treatment of HIV infection. This prompts the need to developed new anti-HIV drugs; preferentially adopting intelligent ways to counteract an evolving virus. Highly Active Anti-Retroviral Therapy (HAART): a strategy involving multiple targeting through various drugs has proven beneficial in the management of AIDS. However, it is a complex regimen with high drug load, increased risk of drug interactions and adverse effects, which lead to poor patient compliance. Reverse transcriptase (RT) and Integrase (IN) are two pivotal enzymes in HIV-1 lifecycle with high structural and functional analogy to be perceived as drug-able targets for novel dual-purpose inhibitors. Designed multi-functional ligand (DML) is a modern strategy by which multiple targets can be exploited using a single chemical entity. A single chemical entity acting on multiple targets can be much more effective than a complex multi-drug regimen. The development of such multifunctional ligands is highly valued in anti-HIV drug discovery with the proposed advantage of being able to stop two or more stages of viral replication cycle. This review will encompass the evolution of the RT-IN dual inhibitory scaffolds reported so far and the contribution made by the leading research groups over the years in this field.

Zinc Mediated Selective Acylation of Ferrocene under Solvent-Free Conditions

A simple, convenient and environmentally-friendly method for selective acylation of ferrocene to monoacylferrocene in the presence of Zn metal under solvent-free conditions is described. The protocol requires mild operating conditions, affording higher yields of desired products both with acyl chloride/carboxylic acid within a short reaction time (15–30 min).

Enhanced taxonomy annotation of antiviral activity data from ChEMBL

The discovery of antiviral drugs is a rapidly developing area of medicinal chemistry research. The emergence of resistant variants and outbreaks of poorly studied viral diseases make this area constantly developing. The amount of antiviral activity data available in ChEMBL consistently grows, but virus taxonomy annotation of these data is not sufficient for thorough studies of antiviral chemical space. We developed a procedure for semi-automatic extraction of antiviral activity data from ChEMBL and mapped them to the virus taxonomy developed by the International Committee for Taxonomy of Viruses (ICTV). The procedure is based on the lists of virus-related values of ChEMBL annotation fields and a dictionary of virus names and acronyms mapped to ICTV taxa. Application of this data extraction procedure allows retrieving from ChEMBL 1.6 times more assays linked to 2.5 times more compounds and data points than ChEMBL web interface allows. Mapping of these data to ICTV taxa allows analyzing all the compounds tested against each viral species. Activity values and structures of the compounds were standardized, and the antiviral activity profile was created for each standard structure. Data set compiled using this algorithm was called ViralChEMBL. As case studies, we compared descriptor and scaffold distributions for the full ChEMBL and its `viral' and `non-viral' subsets, identified the most studied compounds and created a self-organizing map for ViralChEMBL. Our approach to data annotation appeared to be a very efficient tool for the study of antiviral chemical space.

Evaluation of novel N'-(3-hydroxybenzoyl)-2-oxo-2H-chromene-3-carbohydrazide derivatives as potential HIV-1 integrase inhibitors

In an attempt to identify potential new agents that are active against HIV-1 IN, a series of novel coumarin-3-carbohydrazide derivatives were designed and synthesised. The toxicity profiles of these compounds showed that they were non-toxic to human cells and they exhibited promising anti-HIV-1 IN activities with IC₅₀ values in nM range. Also, an accompanying molecular modeling study showed that the compounds bind to the active pocket of the enzyme.

Recent advances in the discovery of small-molecule inhibitors of HIV-1 integrase

AIDS caused by the infection of HIV is a prevalent problem today. Rapid development of drug resistance to existing drug classes has called for the discovery of new targets. Within the three major enzymes (i.e., HIV-1 protease, HIV-1 reverse transcriptase and HIV-1 integrase [IN]) of the viral replication cycle, HIV-1 IN has been of particular interest due to the absence of human cellular homolog. HIV-1 IN catalyzes the integration of viral genetic material with the host genome, a key step in the viral replication process. Several novel classes of HIV IN inhibitors have been explored by targeting different sites on the enzyme. This review strives to provide readers with updates on the recent developments of HIV-1 IN inhibitors.

AIDS is an epidemic disease that endangers the lives of millions of people across the world. The AIDS virus, also known as HIV, has developed resistance to the majority of available drugs on the market, thus requiring the need for new drugs. HIV integrase is one of the key viral enzymes required for viral cell proliferation. Since there is no similar enzyme in the human body, major emphasis is being made to develop therapeutics for this novel target. The drugs that are at various stages of development for this target are reviewed here.

A Short and Efficient Total Synthesis of Ficuseptamines A and B

A rapid and efficient total synthesis of ficuseptamines A and B by a cross metathesis strategy is described.

New Friedel–Crafts strategy for preparing 3-acylindoles

A new Friedel–Crafts acylation generates diverse high-biological value 3-acylindoles, and forms a new C–C bond under transition-metal-free conditions.

Synthesis, Characterization, and Biological Activities of Pendant Arm-Pyridyltetrazole Copper(II) Complexes: DNA Binding/Cleavage Activity and Cytotoxic Studies

2-(1H-Tetrazol-5-yl)pyridine (L) has been reacted separately with Me2NCH2CH2Cl⋅HCl and ClCH2CH2OH to yield two regioisomers in each case, N,N-dimethyl-2-[5-(pyridin-2-yl)-1H-tetrazol-1-yl]ethanamine (L1)/N,N-dimethyl-2-[5-(pyridin-2-yl)-2H-tetrazol-2-yl]ethanamine (L2) and 2-[5-(pyridin-2-yl)-1H-tetrazol-1-yl]ethanol (L3)/2-[5-(pyridin-2-yl)-2H-tetrazol-2-yl]ethanol (L4), respectively. These ligands, L1-L4, have been coordinated with CuCl2 ⋅H2O in 1 : 1 composition to furnish the corresponding complexes 1-4. EPR Spectra of Cu complexes 1 and 3 were characteristic of square planar geometry, with nuclear hyperfine spin 3/2. Single X-ray crystallographic studies of 3 revealed that the Cu center has a square planar structure. DNA binding studies were carried out by UV/VIS absorption; viscosity and thermal denaturation studies revealed that each of these complexes are avid binders of calf thymus DNA. Investigation of nucleolytic cleavage activities of the complexes was carried out on double-stranded pBR322 circular plasmid DNA by using a gel electrophoresis experiment under various conditions, where cleavage of DNA takes place by oxidative free-radical mechanism (OH(⋅)). In vitro anticancer activities of the complexes against MCF-7 (human breast adenocarcinoma) cells revealed that the complexes inhibit the growth of cancer cells. The IC50 values of the complexes showed that Cu complexes exhibit comparable cytotoxic activities compared to the standard drug cisplatin.

Homogeneous High-Throughput Screening Assays for HIV-1 Integrase 3β-Processing and Strand Transfer Activities

HIV-1 integrase (HIV-IN) is a well-validated antiviral drug target catalyzing a multistep reaction to incorporate the HIV-1 provirus into the genome of the host cell. Smallmolecule inhibitors of HIV-1 integrase that specifically target the strand transfer step have demonstrated efficacy in the suppression of virus propagation. However, only fewspecific strand transfer inhibitors have been identified to date, and the need to screen for novel compound scaffolds persists. Here, the authors describe 2 homogeneous time-resolved fluorescent resonance energy transfer-based assays for the measurement of HIV-1 integrase 3'-processing and strand transfer activities. Both assayswere optimized for high-throughput screening formats, and a diverse library containingmore than 1million compoundswas screened in 1536-well plates for HIV-IN strand transfer inhibitors. As a result, compounds were found that selectively affect the enzymatic strand transfer reaction over 3β processing. Moreover, several bioactivemoleculeswere identified that inhibited HIV-1 reporter virus infection in cellularmodel systems. In conclusion, the assays presented herein have proven their utility for the identification ofmechanistically interesting and biologically active inhibitors of HIV-1 integrase that hold potential for further development into potent antiviral drugs.

A targeted DNA substrate mechanism for the inhibition of HIV-1 integrase by inhibitors with antiretroviral activity

We recently reported that viral DNA could be the primary target of raltegravir (RAL), an efficient anti‐HIV‐1 drug, which acts by inhibiting integrase. To elucidate this mechanism, we conducted a comparative analysis of RAL and TB11, a diketoacid abandoned as an anti‐HIV‐1 drug for its weak efficiency and marked toxicity, and tested the effects of the catalytic cofactor Mg²⁺ (5 mm) on drug‐binding properties. We used circular dichroism and fluorescence to determine drug affinities for viral DNA long terminal repeats (LTRs) and peptides derived from the integrase active site and DNA retardation assays to assess drug intercalation into DNA base pairs. We found that RAL bound more tightly to LTR ends than did TB11 (a diketo acid bearing an azido group) and that Mg²⁺ significantly increased the affinity of both RAL and TB11. We also observed a good relationship between drug binding with processed LTR and strand transfer inhibition. This unusual type of inhibition was caused by Mg²⁺‐assisted binding of drugs to DNA substrate, rather than to enzyme. Notably, while RAL bound exclusively to the cleavable/cleaved site, TB11 further intercalated into DNA base pairs and interacted with the integrase‐derived peptides. These unwanted binding sites explain the weaker bioavailability and higher toxicity of TB11 compared with the more effective RAL.

A new methodology for functionalization at the 3-position of indoles by a combination of boron Lewis acid with nitriles

We discovered that a reagent comprising a combination of PhBCl2 and nitriles was useful for syntheses of both 3-acylindoles and 1-(1H-indol-3-yl)alkylamine from indoles. The reaction proceeded selectively at the 3-position of indoles providing 3-acylindoles in moderate to high yields on treatment with the above reagent. Furthermore, the reaction provided the corresponding amine products in moderate to high yields after the intermediate imine was reduced by NaBH3CN. These reactions proceeded under mild conditions and are applicable to the formation of indoles functionalized at the 3-position.

Exploring the role of the α-carboxyphosphonate moiety in the HIV-RT activity of α-carboxy nucleoside phosphonates

As α-carboxy nucleoside phosphonates (α-CNPs) have demonstrated a novel mode of action of HIV-1 reverse transcriptase inhibition, structurally related derivatives were synthesized, namely the malonate 2, the unsaturated and saturated bisphosphonates 3 and 4, respectively and the amide 5. These compounds were evaluated for inhibition of HIV-1 reverse transcriptase in cell-free assays. The importance of the α-carboxy phosphonoacetic acid moiety for achieving reverse transcriptase inhibition, without the need for prior phosphorylation, was confirmed. The malonate derivative 2 was less active by two orders of magnitude than the original α-CNPs, while displaying the same pattern of kinetic behavior; interestingly the activity resides in the “L”-enantiomer of 2, as seen with the earlier series of α-CNPs. A crystal structure with an RT/DNA complex at 2.95 Å resolution revealed the binding of the “L”-enantiomer of 2, at the polymerase active site with a weaker metal ion chelation environment compared to 1a (T-α-CNP) which may explain the lower inhibitory activity of 2.

Integrase Inhibitor Prodrugs: Approaches to Enhancing the Anti-HIV Activity of β-Diketo Acids

HIV integrase, encoded at the 3'-end of the HIV pol gene, is essential for HIV replication. This enzyme catalyzes the incorporation of HIV DNA into human DNA, which represents the point of "no-return" in HIV infection. Integrase is a significant target in anti-HIV drug discovery. This review article focuses largely on the design of integrase inhibitors that are β-diketo acids constructed on pyridinone scaffolds. Methodologies for synthesis of these compounds are discussed. Integrase inhibition data for the strand transfer (ST) step are compared with in vitro anti-HIV data. The review also examines the issue of the lack of correlation between the ST enzymology data and anti-HIV assay results. Because this disconnect appeared to be a problem associated with permeability, prodrugs of these inhibitors were designed and synthesized. Prodrugs dramatically improved the anti-HIV activity data. For example, for compound, 96, the anti-HIV activity (EC50) improved from 500 nM for this diketo acid to 9 nM for its prodrug 116. In addition, there was excellent correlation between the IC50 and IC90 ST enzymology data for 96 (6 nM and 97 nM, respectively) and the EC50 and EC90 anti-HIV data for its prodrug 116 (9 nM and 94 nM, respectively). Finally, it was confirmed that the prodrug 116 was rapidly hydrolyzed in cells to the active compound 96.

Mutagenesis of Lysines 156 and 159 in Human Immunodeficiency Virus Type 1 Integrase (IN) Reveals Differential Interactions between these Residues and Different IN Inhibitors

Human immunodeficiency virus (HIV) type 1 integrase (IN) active site, and viral DNA-binding residues K156 and K159 are predicted to interact both with strand transfer-selective IN inhibitors (STI), e.g. L-731,988, Elvitegravir (EVG), and the FDA-approved IN inhibitor, Raltegravir (RGV), and strand transfer non-selective inhibitors, e.g. dicaffeoyltartaric acids (DCTAs), e.g. L-chicoric acid (L-CA). To test posited roles for these two lysine residues in inhibitor action we assayed the potency of L-CA and several STI against a panel of K156 and K159 mutants. Mutagenesis of K156 conferred resistance to L-CA and mutagenesis of either K156 or K159 conferred resistance to STI indicating that the cationic charge at these two viral DNA-binding residues is important for inhibitor potency. IN K156N, a reported polymorphism associated with resistance to RGV, conferred resistance to L-CA and STI as well. To investigate the apparent preference L-CA exhibits for interactions with K156, we assayed the potency of several hybrid inhibitors containing combinations of DCTA and STI pharmacophores against recombinant IN K156A or K159A. Although K156A conferred resistance to diketo acid-branched bis-catechol hybrid inhibitors, neither K156A nor K159A conferred resistance to their monocatechol counterparts, suggesting that bis-catechol moieties direct DCTAs toward K156. In contrast, STI were more promiscuous in their interaction with K156 and K159. Taken together, the results of this study indicate that DCTAs interact with IN in a manner different than that of STI and suggest that DCTAs are an attractive candidate chemotype for development into drugs potent against STI-resistant IN.

Targeting HIV-1 integrase with strand transfer inhibitors

HIV-1 integrase (IN) is a retroviral enzyme essential for integration of genetic material into the DNA of the host cell and hence for viral replication. The absence of an equivalent enzyme in humans makes IN an interesting target for anti-HIV drug design. This review briefly overviews the structural and functional properties of HIV-1 IN. We analyze the binding modes of the established drugs, clinical candidates and a comprehensive library of leads based on innovative chemical scaffolds of HIV-1 IN strand transfer inhibitors (INSTIs). Computational clustering techniques are applied for identifying structural features relating to bioactivity. From bio- and chemo-informatics analyses, we provide novel insights into structure-activity relationships of INSTIs and elaborate new strategies for design of innovative inhibitors.

Theoretical study on the tautomerization of 1,5-diaminotetrazole (DAT)

The tautomerization pathways and kinetics of 1,5-diaminotetrazole (DAT) have been investigated by means of second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster theory, with single and double excitations including perturbative corrections for triple excitations (CCSD(T)). Five possible tautomers, namely 4-hydro-1-amino-5-imino-tetrazole (a), 2,5-diamino-tetrazole (b), 1,5-diamino-tetrazole (c), 2-hydro-1-imino-5-amino-tetrazole (d), and 2,4-dihydro-1,5-diimino-tetrazole (e) were identified. The structures of the reactants, transition states, and products along with the tautomerism pathways were optimized by the MP2 method using the 6-311G** basis set, and the energies were refined using CCSD(T)/6-311G**. The minimum-energy path (MEP) information for DAT was obtained at the CCSD(T)/6-311G**//MP2/6-311G** level of theory. Therein, reaction 2 (c → b) is an amino-shift reaction, while reaction 1 (c → a), reaction 3 (c → d), reaction 4 (a → e), and reaction 5 (d → e) are reactions of hydrogen-shift tautomerization. The calculated results show that 2,5-diaminotetrazole (b) with the minimum energy (taking c as a standard) among five tautomers, is the energetically preferred tautomer of DAT in the gas phase. In addition, the energy barrier of reaction 2 is 71.65 kcal · mol(-1) in the gas phase, while reaction 1 takes place more easily with an activation barrier of 61.53 kcal · mol(-1) also as compared to 63.71 kcal · mol(-1) in reaction 3. Moreover, the tautomerization of reaction 4 requires the largest energy barrier of 83.29 kcal · mol(-1), which is obviously bigger than reaction 5 with a value of 73.78 kcal · mol(-1). Thus, the hydrogen-shift of c to a is the easiest transformation, while the tautomerization of a to e is the hardest one. Again, the rate constants of tautomerization have been obtained by TST, TST/Eckart, CVT, CVT/SCT, and CVT/ZCT methods in the range 200-2500 K, and analysis indicated that variational effects are small over the whole temperature range, while tunneling effects are significant in the lower temperature range.

Computational models on quantitative prediction of bioactivity of HIV-1 integrase 3' processing inhibitors

In this study, four computational quantitative structure-activity relationship (QSAR) models were built to predict the bioactivity of 3' processing (3'P) inhibitors of HIV-1 integrase. Some 453 inhibitors whose bioactivity values were detected by the radiolabelling method were collected. The molecular structures were represented with MOE descriptors. In total, 21 descriptors were selected for modelling. All inhibitors were divided into a training set and a test set with two methods: (1) by a Kohonen's self-organizing map (SOM); (2) by a random selection. For every training set and test set, a multilinear regression (MLR) analysis and a support vector machine (SVM) were used to establish models, respectively. For the training/test set divided by SOM, the correlation coefficients (r) were over 0.84, and for the training/test set split randomly, the r values were over 0.86. Some molecular properties such as hydrogen bond donor capacity, atomic partial charge properties, molecular refractivity, the number of aromatic bonds and molecular surface area, volume and shape properties played important roles for inhibiting 3' processing step of HIV-1 integrase.

Inhibiting the HIV integration process: past, present, and the future

HIV integrase (IN) catalyzes the insertion into the genome of the infected human cell of viral DNA produced by the retrotranscription process. The discovery of raltegravir validated the existence of the IN, which is a new target in the field of anti-HIV drug research. The mechanism of catalysis of IN is depicted, and the characteristics of the inhibitors of the catalytic site of this viral enzyme are reported. The role played by the resistance is elucidated, as well as the possibility of bypassing this problem. New approaches to block the integration process are depicted as future perspectives, such as development of allosteric IN inhibitors, dual inhibitors targeting both IN and other enzymes, inhibitors of enzymes that activate IN, activators of IN activity, as well as a gene therapy approach.

Synthesis of 3-acyl-2-arylindole via palladium-catalyzed isocyanide insertion and oxypalladation of alkyne

The synthesis of 3-acyl-2-arylindole derivatives was performed through palladium-catalyzed isocyanide insertion and oxypalladation of an alkyne. As a result of the introduction of internal nucleophiles, domino cyclization was also achieved for the synthesis of several tetracyclic indole derivatives. Imidoylpalladium generated by isocyanide insertion is a key intermediate in these reactions.

Structure-guided discovery of phenyl-diketo acids as potent inhibitors of M. tuberculosis malate synthase

The glyoxylate shunt plays an important role in fatty acid metabolism and has been shown to be critical to survival of several pathogens involved in chronic infections. For Mycobacterium tuberculosis (Mtb), a strain with a defective glyoxylate shunt was previously shown to be unable to establish infection in a mouse model. We report the development of phenyl-diketo acid (PDKA) inhibitors of malate synthase (GlcB), one of two glyoxylate shunt enzymes, using structure-based methods. PDKA inhibitors were active against Mtb grown on acetate, and overexpression of GlcB ameliorated this inhibition. Crystal structures of complexes of GlcB with PDKA inhibitors guided optimization of potency. A selected PDKA compound demonstrated efficacy in a mouse model of tuberculosis. The discovery of these PDKA derivatives provides chemical validation of GlcB as an attractive target for tuberculosis therapeutics.