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1.
Antimicrob Agents Chemother ; 67(7): e0046223, 2023 07 18.
Article in English | MEDLINE | ID: mdl-37310224

ABSTRACT

HIV-1 integrase-LEDGF allosteric inhibitors (INLAIs) share the binding site on the viral protein with the host factor LEDGF/p75. These small molecules act as molecular glues promoting hyper-multimerization of HIV-1 IN protein to severely perturb maturation of viral particles. Herein, we describe a new series of INLAIs based on a benzene scaffold that display antiviral activity in the single digit nanomolar range. Akin to other compounds of this class, the INLAIs predominantly inhibit the late stages of HIV-1 replication. A series of high-resolution crystal structures revealed how these small molecules engage the catalytic core and the C-terminal domains of HIV-1 IN. No antagonism was observed between our lead INLAI compound BDM-2 and a panel of 16 clinical antiretrovirals. Moreover, we show that compounds retained high antiviral activity against HIV-1 variants resistant to IN strand transfer inhibitors and other classes of antiretroviral drugs. The virologic profile of BDM-2 and the recently completed single ascending dose phase I trial (ClinicalTrials.gov identifier: NCT03634085) warrant further clinical investigation for use in combination with other antiretroviral drugs. Moreover, our results suggest routes for further improvement of this emerging drug class.


Subject(s)
HIV Infections , HIV Integrase Inhibitors , HIV Integrase , Humans , Virus Replication , HIV Integrase Inhibitors/pharmacology , HIV Integrase Inhibitors/therapeutic use , Antiviral Agents/pharmacology , HIV Integrase/metabolism , HIV Infections/drug therapy , Allosteric Regulation
2.
J Med Chem ; 62(9): 4742-4754, 2019 05 09.
Article in English | MEDLINE | ID: mdl-30995398

ABSTRACT

Penicillin-binding proteins (PBPs) are the targets of the ß-lactams, the most successful class of antibiotics ever developed against bacterial infections. Unfortunately, the worldwide and rapid spread of large spectrum ß-lactam resistance genes such as carbapenemases is detrimental to the use of antibiotics in this class. New potent PBP inhibitors are needed, especially compounds that resist ß-lactamase hydrolysis. Here we describe the structure of the E. coli PBP2 in its Apo form and upon its reaction with 2 diazabicyclo derivatives, avibactam and CPD4, a new potent PBP2 inhibitor. Examination of these structures shows that unlike avibactam, CPD4 can perform a hydrophobic stacking on Trp370 in the active site of E. coli PBP2. This result, together with sequence analysis, homology modeling, and SAR, allows us to propose CPD4 as potential starting scaffold to develop molecules active against a broad range of bacterial species at the top of the WHO priority list.


Subject(s)
Anti-Bacterial Agents/pharmacology , Azabicyclo Compounds/pharmacology , Escherichia coli Proteins/antagonists & inhibitors , Escherichia coli/drug effects , Penicillin-Binding Proteins/antagonists & inhibitors , Amino Acid Sequence , Anti-Bacterial Agents/chemical synthesis , Anti-Bacterial Agents/metabolism , Azabicyclo Compounds/chemical synthesis , Azabicyclo Compounds/metabolism , Catalytic Domain , Drug Design , Escherichia coli/chemistry , Escherichia coli Proteins/isolation & purification , Escherichia coli Proteins/metabolism , Ligands , Microbial Sensitivity Tests , Molecular Structure , Penicillin-Binding Proteins/isolation & purification , Penicillin-Binding Proteins/metabolism , Protein Binding , Pseudomonas aeruginosa/drug effects , Sequence Alignment , Structure-Activity Relationship
3.
J Biol Chem ; 293(16): 6172-6186, 2018 04 20.
Article in English | MEDLINE | ID: mdl-29507092

ABSTRACT

Recently, a new class of HIV-1 integrase (IN) inhibitors with a dual mode of action, called IN-LEDGF/p75 allosteric inhibitors (INLAIs), was described. Designed to interfere with the IN-LEDGF/p75 interaction during viral integration, unexpectedly, their major impact was on virus maturation. This activity has been linked to induction of aberrant IN multimerization, whereas inhibition of the IN-LEDGF/p75 interaction accounts for weaker antiretroviral effect at integration. Because these dual activities result from INLAI binding to IN at a single binding site, we expected that these activities co-evolved together, driven by the affinity for IN. Using an original INLAI, MUT-A, and its activity on an Ala-125 (A125) IN variant, we found that these two activities on A125-IN can be fully dissociated: MUT-A-induced IN multimerization and the formation of eccentric condensates in viral particles, which are responsible for inhibition of virus maturation, were lost, whereas inhibition of the IN-LEDGF/p75 interaction and consequently integration was fully retained. Hence, the mere binding of INLAI to A125 IN is insufficient to promote the conformational changes of IN required for aberrant multimerization. By analyzing the X-ray structures of MUT-A bound to the IN catalytic core domain (CCD) with or without the Ala-125 polymorphism, we discovered that the loss of IN multimerization is due to stabilization of the A125-IN variant CCD dimer, highlighting the importance of the CCD dimerization energy for IN multimerization. Our study reveals that affinity for the LEDGF/p75-binding pocket is not sufficient to induce INLAI-dependent IN multimerization and the associated inhibition of viral maturation.


Subject(s)
HIV Integrase Inhibitors/pharmacology , HIV Integrase/drug effects , HIV-1/physiology , Virus Assembly/drug effects , Virus Integration/drug effects , Allosteric Regulation , Binding Sites , Cell Line , HIV Integrase Inhibitors/chemistry , Humans , Molecular Structure , Pyridines/chemistry , Pyridines/pharmacology , Structure-Activity Relationship , Thiophenes/chemistry , Thiophenes/pharmacology
4.
Retrovirology ; 14(1): 50, 2017 11 09.
Article in English | MEDLINE | ID: mdl-29121950

ABSTRACT

BACKGROUND: HIV-1 Integrase (IN) interacts with the cellular co-factor LEDGF/p75 and tethers the HIV preintegration complex to the host genome enabling integration. Recently a new class of IN inhibitors was described, the IN-LEDGF allosteric inhibitors (INLAIs). Designed to interfere with the IN-LEDGF interaction during integration, the major impact of these inhibitors was surprisingly found on virus maturation, causing a reverse transcription defect in target cells. RESULTS: Here we describe the MUT-A compound as a genuine INLAI with an original chemical structure based on a new type of scaffold, a thiophene ring. MUT-A has all characteristics of INLAI compounds such as inhibition of IN-LEDGF/p75 interaction, IN multimerization, dual antiretroviral (ARV) activities, normal packaging of genomic viral RNA and complete Gag protein maturation. MUT-A has more potent ARV activity compared to other INLAIs previously reported, but similar profile of resistance mutations and absence of ARV activity on SIV. HIV-1 virions produced in the presence of MUT-A were non-infectious with the formation of eccentric condensates outside of the core. In studying the immunoreactivity of these non-infectious virions, we found that inactivated HIV-1 particles were captured by anti-HIV-specific neutralizing and non-neutralizing antibodies (b12, 2G12, PGT121, 4D4, 10-1074, 10E8, VRC01) with efficiencies comparable to non-treated virus. Autologous CD4+ T lymphocyte proliferation and cytokine induction by monocyte-derived dendritic cells (MDDC) pulsed either with MUT-A-inactivated HIV or non-treated HIV were also comparable. CONCLUSIONS: Although strongly defective in infectivity, HIV-1 virions produced in the presence of the MUT-A INLAI have a normal protein and genomic RNA content as well as B and T cell immunoreactivities comparable to non-treated HIV-1. These inactivated viruses might form an attractive new approach in vaccine research in an attempt to study if this new type of immunogen could elicit an immune response against HIV-1 in animal models.


Subject(s)
HIV Integrase Inhibitors/pharmacology , HIV Integrase/metabolism , HIV-1/drug effects , HIV-1/enzymology , Intercellular Signaling Peptides and Proteins/metabolism , Pyridines/pharmacology , Thiophenes/pharmacology , Cell Line , HIV Antibodies/immunology , HIV Integrase Inhibitors/chemistry , HIV-1/immunology , Humans , Pyridines/chemistry , Thiophenes/chemistry , Virus Assembly/drug effects , Virus Integration/drug effects , Virus Replication/drug effects
5.
Retrovirology ; 10: 144, 2013 Nov 21.
Article in English | MEDLINE | ID: mdl-24261564

ABSTRACT

BACKGROUND: LEDGF/p75 (LEDGF) is the main cellular cofactor of HIV-1 integrase (IN). It acts as a tethering factor for IN, and targets the integration of HIV in actively transcribed gene regions of chromatin. A recently developed class of IN allosteric inhibitors can inhibit the LEDGF-IN interaction. RESULTS: We describe a new series of IN-LEDGF allosteric inhibitors, the most active of which is Mut101. We determined the crystal structure of Mut101 in complex with IN and showed that the compound binds to the LEDGF-binding pocket, promoting conformational changes of IN which explain at the atomic level the allosteric effect of the IN/LEDGF interaction inhibitor on IN functions. In vitro, Mut101 inhibited both IN-LEDGF interaction and IN strand transfer activity while enhancing IN-IN interaction. Time of addition experiments indicated that Mut101 behaved as an integration inhibitor. Mut101 was fully active on HIV-1 mutants resistant to INSTIs and other classes of anti-HIV drugs, indicative that this compound has a new mode of action. However, we found that Mut101 also displayed a more potent antiretroviral activity at a post-integration step. Infectivity of viral particles produced in presence of Mut101 was severely decreased. This latter effect also required the binding of the compound to the LEDGF-binding pocket. CONCLUSION: Mut101 has dual anti-HIV-1 activity, at integration and post-integration steps of the viral replication cycle, by binding to a unique target on IN (the LEDGF-binding pocket). The post-integration block of HIV-1 replication in virus-producer cells is the mechanism by which Mut101 is most active as an antiretroviral. To explain this difference between Mut101 antiretroviral activity at integration and post-integration stages, we propose the following model: LEDGF is a nuclear, chromatin-bound protein that is absent in the cytoplasm. Therefore, LEDGF can outcompete compound binding to IN in the nucleus of target cells lowering its antiretroviral activity at integration, but not in the cytoplasm where post-integration production of infectious viral particles takes place.


Subject(s)
HIV Integrase Inhibitors/pharmacology , HIV Integrase/metabolism , HIV-1/drug effects , HIV-1/physiology , Intercellular Signaling Peptides and Proteins/metabolism , Virus Integration/drug effects , Virus Replication/drug effects , Cell Line , Crystallography, X-Ray , HIV Integrase/chemistry , HIV Integrase Inhibitors/chemistry , Humans , Intercellular Signaling Peptides and Proteins/chemistry , Protein Binding , Protein Conformation
6.
J Med Chem ; 56(5): 1908-21, 2013 Mar 14.
Article in English | MEDLINE | ID: mdl-23445125

ABSTRACT

In this paper, we present different strategies to vectorize HldE kinase inhibitors with the goal to improve their gram-negative intracellular concentration. Syntheses and biological effects of siderophoric, aminoglycosidic, amphoteric, and polycationic vectors are discussed. While siderophoric and amphoteric vectorization efforts proved to be disappointing in this series, aminoglycosidic and polycationic vectors were able for the first time to achieve synergistic effects of our inhibitors with erythromycin. Although these effects proved to be nonspecific, this study provides information about the required stereoelectronic arrangement of the polycationic amines and their basicity requirements to fulfill outer membrane destabilization resulting in better erythromycin synergies.


Subject(s)
Erythromycin/metabolism , Escherichia coli/metabolism , Multienzyme Complexes/antagonists & inhibitors , Nucleotidyltransferases/antagonists & inhibitors , Phosphotransferases (Alcohol Group Acceptor)/antagonists & inhibitors , Aminoglycosides/pharmacology , Anti-Bacterial Agents/metabolism , Erythromycin/chemistry , Erythromycin/pharmacology , Escherichia coli/drug effects , Lipopolysaccharides/biosynthesis , Microbial Sensitivity Tests , Multienzyme Complexes/drug effects , Nucleotidyltransferases/drug effects , Phosphotransferases (Alcohol Group Acceptor)/drug effects , Polyamines/pharmacology , Polyelectrolytes
7.
J Med Chem ; 46(17): 3655-61, 2003 Aug 14.
Article in English | MEDLINE | ID: mdl-12904069

ABSTRACT

Novel quinolone antibacterial agents bearing (3S)-amino-(4R)-ethylpiperidines were designed by using low energy conformation analysis and synthesized by applying a conventional coupling reaction of the quinolone nuclei with new piperidine side chains. These compounds were tested in MIC assays and found to be highly potent against Gram-positive and Gram-negative organisms. In particular, the new compounds exhibited high activity against the resistant pathogens Staphylococcus aureus (MRCR) and Streptococcus pneumoniae (PR). Importantly, when the (3S)-amino-(4R)-ethylpiperidinyl quinolones were compared with marketed quinolones sharing the same quinolone nuclei but different side chains at the C-7 position, the new quinolones showed superior activity against Gram-positive organisms, including resistant pathogens.


Subject(s)
Anti-Bacterial Agents/chemical synthesis , Bacteria/drug effects , Drug Resistance, Bacterial , Piperidines/chemical synthesis , Quinolones/chemical synthesis , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , DNA Gyrase/chemistry , DNA Gyrase/drug effects , DNA, Superhelical/chemistry , DNA, Superhelical/drug effects , Escherichia coli/enzymology , Gram-Negative Bacteria/drug effects , Gram-Positive Bacteria/drug effects , Microbial Sensitivity Tests , Models, Molecular , Molecular Conformation , Piperidines/chemistry , Piperidines/pharmacology , Quinolones/chemistry , Quinolones/pharmacology , Stereoisomerism , Structure-Activity Relationship
8.
Antimicrob Agents Chemother ; 47(8): 2526-37, 2003 Aug.
Article in English | MEDLINE | ID: mdl-12878515

ABSTRACT

We have characterized an early series of 5,6-bridged dioxinoquinolones which behaved strikingly different from typical quinolones. The 5,6-bridged dioxinoquinolones inhibited Escherichia coli DNA gyrase supercoiling activity but, unlike typical quinolones, failed to stimulate gyrase-dependent cleavable complex formation. Analogous unsubstituted compounds stimulated cleavable complex formation but were considerably less potent than the corresponding 5,6-bridged compounds. Consistent with a previous report (M. Antoine et al., Chim. Ther. 7:434-443, 1972) and contrary to established quinolone SAR trends, a compound with an N-1 methyl substitution (PGE-8367769) was more potent than its analog with an N-1 ethyl substitution (PGE-6596491). PGE-8367769 was shown to antagonize ciprofloxacin-mediated cleavable complex formation in a dose-dependent manner, suggesting an interaction with the gyrase-DNA complex that overlaps that of ciprofloxacin. Resistance to PGE-8367769 in E. coli was found to arise through missense mutations in gyrA, implicating DNA gyrase as the primary antibacterial target. Notably, only 1 of 15 distinct mutations selected on PGE-8367769 (D87G) has previously been implicated in quinolone resistance in E. coli. The remaining 14 mutations (E16V, G31V, R38L, G40A, Y50D, V70A, A84V, I89L, M135T, G173S, T180I, F217C, P218T, and F513C) have not been previously reported, and most were located outside of the traditional quinolone resistance-determining region. These novel GyrA mutations decreased sensitivity to 5,6-bridged dioxinoquinolones by four- to eightfold, whereas they did not confer resistance to other quinolones such as ciprofloxacin, clinafloxacin, or nalidixic acid. These results demonstrate that the 5,6-bridged quinolones act via a mechanism that is related to but qualitatively different from that of typical quinolones.


Subject(s)
Anti-Infective Agents/pharmacology , Bridged-Ring Compounds/pharmacology , 4-Quinolones , Anti-Infective Agents/chemistry , Bacterial Outer Membrane Proteins/metabolism , Bridged-Ring Compounds/chemistry , DNA Gyrase/genetics , DNA, Superhelical/drug effects , Enzyme Inhibitors/pharmacology , Escherichia coli/drug effects , Escherichia coli/enzymology , Genotype , Kinetics , Microbial Sensitivity Tests , Mutation/genetics , Oligonucleotides/pharmacology , Phenotype , Structure-Activity Relationship , Topoisomerase II Inhibitors , Topoisomerase Inhibitors
10.
Curr Drug Targets Infect Disord ; 2(1): 51-65, 2002 Mar.
Article in English | MEDLINE | ID: mdl-12462153

ABSTRACT

Wide variations in the antibacterial potency and spectrum of quinolones are presumably attributable, in part, to their variable potency against the molecular targets, DNA gyrase and topoisomerase i.v. In addition, susceptibility of quinolones to resistance development via known point mutations in the target genes gyrA and parC/grlA varies depending on the effective affinities of the compounds toward the mutated targets. Using a medicinal chemistry approach, a series of 8-methoxy, Non-Fluorinated Quinolones (NFQs), with fluorine in the R6 position of the traditional fluoroquinolones replaced with hydrogen, were designed to retain potency against DNA gyrase and/or topoisomerase i.v. with point mutations in the serine-aspartate/glutamate hotspots. This resulted in compounds with antibacterial activity against a broad-spectrum of bacterial species, including multidrug-resistant gram-positive pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA) and penicillin-resistant Streptococcus pneumoniae (PRSP). The efficacy of the NFQs was also demonstrated in a murine septicemia model. Furthermore, the design of the NFQs resulted in lower acute intravenous (i.v.) toxicity and clastogenicity relative to their 6-fluorinated counterparts. Use of the non-fluorinated quinolone nucleus allowed exploration of new structure-activity space and generation of a series of NFQs with unique combinations of affinities toward the wild type and mutated forms of the molecular targets.


Subject(s)
Anti-Infective Agents/pharmacology , Gram-Positive Bacteria/drug effects , 4-Quinolones , Amino Acid Sequence , Anti-Infective Agents/chemical synthesis , Anti-Infective Agents/chemistry , Drug Resistance, Microbial , Genes, Bacterial/genetics , Gram-Positive Bacteria/genetics , Gram-Positive Bacteria/metabolism , Humans , Molecular Sequence Data , Structure-Activity Relationship
11.
Org Lett ; 4(25): 4499-502, 2002 Dec 12.
Article in English | MEDLINE | ID: mdl-12465922

ABSTRACT

[reaction: see text] trans-(3S)-Amino piperidines bearing various alkyl and aryl substituents at the C-4 position were synthesized via a ring-closing metathesis reaction. The absolute stereochemistry was controlled using a protected D-serine as a starting material. Stereoselective hydrogenation of allylamines provided trans-(3S)-amino-(4R)-alkyl- and -(4S)-aryl-piperidines. This procedure presents the first method for the asymmetric synthesis of 4-substituted 3-amino piperidines.

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