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1.
Eur J Med Chem ; 186: 111900, 2020 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-31771827

RESUMO

Since dual inhibitors may yield lower toxicity and reduce the likelihood of drug resistance, as well as inhibitors of HIV-1 PR and RT constitute the core of chemotherapy for AIDS treatment, we herein designed and synthesized new coumarin derivatives characterized by various linkers that exhibited excellent potency against PR and a weak inhibition of RT. Among which, compounds 6f and 7c inhibited PR with IC50 values of 15.5 and 62.1 nM, respectively, and weakly affected also RT with IC50 values of 241.8 and 188.7 µM, respectively, showing the possibility in the future of developing dual HIV-1 PR/RT inhibitors. Creative stimulation for further research of more potent dual HIV-1 inhibitors was got according to the molecular docking studies.


Assuntos
Fármacos Anti-HIV/farmacologia , Cumarínicos/farmacologia , Inibidores da Protease de HIV/farmacologia , Protease de HIV/metabolismo , Transcriptase Reversa do HIV/antagonistas & inibidores , Inibidores da Transcriptase Reversa/farmacologia , Fármacos Anti-HIV/síntese química , Fármacos Anti-HIV/química , Linhagem Celular , Cumarínicos/síntese química , Cumarínicos/química , Relação Dose-Resposta a Droga , Desenho de Drogas , Infecções por HIV/tratamento farmacológico , Infecções por HIV/metabolismo , Inibidores da Protease de HIV/síntese química , Inibidores da Protease de HIV/química , Transcriptase Reversa do HIV/metabolismo , HIV-1/efeitos dos fármacos , HIV-1/enzimologia , Humanos , Simulação de Acoplamento Molecular , Estrutura Molecular , Inibidores da Transcriptase Reversa/síntese química , Inibidores da Transcriptase Reversa/química , Relação Estrutura-Atividade
2.
J Chem Theory Comput ; 16(2): 1284-1299, 2020 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-31877249

RESUMO

Over the past several decades, atomistic simulations of biomolecules, whether carried out using molecular dynamics or Monte Carlo techniques, have provided detailed insights into their function. Comparing the results of such simulations for a few closely related systems has guided our understanding of the mechanisms by which changes such as ligand binding or mutation can alter the function. The general problem of detecting and interpreting such mechanisms from simulations of many related systems, however, remains a challenge. This problem is addressed here by applying supervised and unsupervised machine learning techniques to a variety of thermodynamic observables extracted from molecular dynamics simulations of different systems. As an important test case, these methods are applied to understand the evasion by human immunodeficiency virus type-1 (HIV-1) protease of darunavir, a potent inhibitor to which resistance can develop via the simultaneous mutation of multiple amino acids. Complex mutational patterns have been observed among resistant strains, presenting a challenge to developing a mechanistic picture of resistance in the protease. In order to dissect these patterns and gain mechanistic insight into the role of specific mutations, molecular dynamics simulations were carried out on a collection of HIV-1 protease variants, chosen to include highly resistant strains and susceptible controls, in complex with darunavir. Using a machine learning approach that takes advantage of the hierarchical nature in the relationships among the sequence, structure, and function, an integrative analysis of these trajectories reveals key details of the resistance mechanism, including changes in the protein structure, hydrogen bonding, and protein-ligand contacts.


Assuntos
Farmacorresistência Viral , Protease de HIV/metabolismo , HIV-1/enzimologia , Ligantes , Aprendizado de Máquina , Protease de HIV/química , Protease de HIV/genética , Inibidores da Protease de HIV/química , Inibidores da Protease de HIV/metabolismo , Humanos , Ligações de Hidrogênio , Simulação de Dinâmica Molecular , Método de Monte Carlo , Mutação , Ligação Proteica , Eletricidade Estática
3.
BMC Complement Altern Med ; 19(1): 351, 2019 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-31805905

RESUMO

BACKGROUND: Acquired immunodeficiency syndrome (AIDS) is caused by the Human immunodeficiency virus type-1 (HIV-1). HIV-1 protease (HIV-1 PR) is an essential enzyme for the HIV replication, and therefore, it is an important target for antiretroviral drugs development, particularly from natural products. Auricularia polytricha (AP) is an edible mushroom with several important therapeutic properties. These properties will be investigated as HIV-1 PR inhibitors. METHODS: The sequential hexane (APH), ethanol (APE) and water (APW) extracts from AP were screened for inhibitory activity against HIV-1 PR. The extract that consistently showed the strong HIV-1 PR inhibition was further investigated for its phytochemical constituents. The compounds were purified by column chromatography. The isolated compounds were structurally elucidated using 1D and 2D NMR, HRMS, FTIR, and GC/MS techniques. Each compound was screened against HIV-1 PR to determine its inhibitory activity and to provide an explanation for the activity found in the extract. RESULTS: Hexane crude extract of AP (APH) exhibited significant inhibition on HIV-1 PR activity. Four major compounds isolated from APH fraction were identified to be two triacylglycerols, linoleic acid and ergosterol. Moreover, all four compounds showed significant inhibition of HIV-1 PR activity. CONCLUSION: The findings from this study suggest that AP is a good source of fatty esters, fatty acids and ergosterol. These natural products exhibit anti-HIV-1 properties by blocking HIV-1 PR. These important biological results warrant further development of AP as an alternative antiretroviral drug.


Assuntos
Agaricales/química , Produtos Biológicos/farmacologia , Inibidores da Protease de HIV/farmacologia , Protease de HIV/efeitos dos fármacos , Células 3T3-L1 , Animais , Produtos Biológicos/química , Produtos Biológicos/toxicidade , Sobrevivência Celular/efeitos dos fármacos , Ergosterol , Inibidores da Protease de HIV/química , Inibidores da Protease de HIV/toxicidade , HIV-1/efeitos dos fármacos , Ácido Linoleico , Camundongos , Triglicerídeos
4.
J Enzyme Inhib Med Chem ; 34(1): 1451-1456, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31409143

RESUMO

Herein, we report the effect of nine FDA approved protease inhibitor drugs against a new HIV-1 subtype C mutant protease, E35D↑G↑S. The mutant has five mutations, E35D, two insertions, position 36 (G and S), and D60E. Kinetics, inhibition constants, vitality, Gibbs free binding energies are reported. The variant showed a decreased affinity for substrate and low catalytic efficiency compared to the wild type. There was a significant decrease in the binding of seven FDA approved protease inhibitors against the mutant (p < .0001). Amprenavir and ritonavir showed the least decrease, but still significant reduced activity in comparison to the wildtype (4 and 5 folds, respectively, p = .0021 and .003, respectively). Nelfinavir and atazanavir were the worst inhibitors against the variant as seen from the IC50, with values of 1401 ± 3.0 and 685 ± 3.0 nM, respectively. Thermodynamics data showed less favourable Gibbs free binding energies for the protease inhibitors to the mutant.


Assuntos
Inibidores da Protease de HIV/farmacologia , Protease de HIV/efeitos dos fármacos , HIV-1/enzimologia , Termodinâmica , Protease de HIV/genética , Protease de HIV/metabolismo , Inibidores da Protease de HIV/química , Concentração Inibidora 50 , Cinética , Simulação de Acoplamento Molecular , Mutação
5.
Curr Top Med Chem ; 19(18): 1571-1598, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31237209

RESUMO

Acquired Immunodeficiency Syndrome (AIDS) is a chronic disease characterized by multiple life-threatening illnesses caused by a retro-virus, Human Immunodeficiency Virus (HIV). HIV infection slowly destroys the immune system and increases the risk of various other infections and diseases. Although, there is no immediate cure for HIV infection/AIDS, several drugs targeting various cruxes of HIV infection are used to slow down the progress of the disease and to boost the immune system. One of the key therapeutic strategies is Highly Active Antiretroviral Therapy (HAART) or ' AIDS cocktail' in a general sense, which is a customized combination of anti-retroviral drugs designed to combat the HIV infection. Since HAART's inception in 1995, this treatment was found to be effective in improving the life expectancy of HIV patients over two decades. Among various classes of HAART treatment regimen, Protease Inhibitors (PIs) are known to be widely used as a major component and found to be effective in treating HIV infection/AIDS. For the past several years, a variety of protease inhibitors have been reported. This review outlines the drug design strategies of PIs, chemical and pharmacological characteristics of some mechanism-based inhibitors, summarizes the recent developments in small molecule based drug discovery with HIV protease as a drug target. Further discussed are the pharmacology, PI drug resistance on HIV PR, adverse effects of HIV PIs and challenges/impediments in the successful application of HIV PIs as an important class of drugs in HAART regimen for the effective treatment of AIDS.


Assuntos
Síndrome de Imunodeficiência Adquirida/tratamento farmacológico , Fármacos Anti-HIV/farmacologia , Inibidores da Protease de HIV/farmacologia , Protease de HIV/metabolismo , HIV/efeitos dos fármacos , Fármacos Anti-HIV/química , Inibidores da Protease de HIV/química , Humanos
6.
J Biomol NMR ; 73(6-7): 365-374, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31243634

RESUMO

Over the last two decades, both the sensitivity of NMR and the time scale of molecular dynamics (MD) simulation have increased tremendously and have advanced the field of protein dynamics. HIV-1 protease has been extensively studied using these two methods, and has presented a framework for cross-evaluation of structural ensembles and internal dynamics by integrating the two methods. Here, we review studies from our laboratories over the last several years, to understand the mechanistic basis of protease drug-resistance mutations and inhibitor responses, using NMR and crystal structure-based parallel MD simulations. Our studies demonstrate that NMR relaxation experiments, together with crystal structures and MD simulations, significantly contributed to the current understanding of structural/dynamic changes due to HIV-1 protease drug resistance mutations.


Assuntos
Inibidores da Protease de HIV/química , Protease de HIV/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Ressonância Magnética Nuclear Biomolecular , Sítios de Ligação , Farmacorresistência Viral , Protease de HIV/genética , Protease de HIV/metabolismo , Inibidores da Protease de HIV/farmacologia , Humanos , Mutação , Ligação Proteica , Relação Estrutura-Atividade , Água/química
7.
Eur J Pharm Sci ; 131: 153-158, 2019 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-30790704

RESUMO

The main objective of this study was to evaluate the pharmacokinetics of ritonavir (RTV) nanosuspension in rats in both fed and fasted state in comparison with coarse powder, physical mixture and commercial product (Norvir®). The point to point relation model was generated between the results of in vitro dissolution and in vivo pharmacokinetic studies. The oral RTV nanosuspension was prepared with microfluidization method. Nanosuspension was obtained with 540-550 nm of particle size, 0.1-0.4 of particle size distribution and about -20 mV of zeta potential values. According to in vivo pharmacokinetic studies in rats, Cmax and AUC0-t values in nanosuspension displayed an 8.9- and 12.5-fold increase compared to the coarse powder, and a 1.9- and 2.1-fold increase compared to the commercial product, respectively in the fed group. The point to point relation model showed that the correlation model was significant. It is concluded that nanosuspension is a promising drug delivery system to enhance oral bioavailability of ritonavir.


Assuntos
Inibidores da Protease de HIV/farmacocinética , Nanopartículas/administração & dosagem , Ritonavir/farmacocinética , Administração Oral , Animais , Disponibilidade Biológica , Liberação Controlada de Fármacos , Jejum/metabolismo , Inibidores da Protease de HIV/sangue , Inibidores da Protease de HIV/química , Derivados da Hipromelose/química , Masculino , Nanopartículas/química , Ratos Wistar , Ritonavir/sangue , Ritonavir/química , Dodecilsulfato de Sódio/química , Suspensões
8.
Biol Pharm Bull ; 42(2): 261-267, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30713256

RESUMO

A series of tetraethyl 2,4,8,10-tetramethyl-6,12-diaryl-3,9-dioxahexacyclo[6.4.0.02,7.04,11.05,10]dodecane-1,5,7,11-tetracarboxylates (simplified as 3,9-dioxatetraasteranes) with C2-symmetric structural characteristics were synthesized through the [2 + 2] photocycloaddition of the diethyl 2,6-dimethyl-4-aryl-4H-pyran-3,5-dicarboxylates. Besides, their anti-human immunodeficiency virus (HIV)-1 activities were evaluated by enzyme-linked immunosorbent assay (ELISA) assay against HIV-1 (IIIB) replication in MT-4 cell culture. The result showed that the tested compounds exhibited potential activates with IC50 values less than 110 nM. Furthermore, docking study was carried out to study the binding mode of these compounds. The results indicated that the overall orientation of the inhibitors in the active site were similar to that of the cyclic urea AHA001 and a hydrogen bond with the protein residues might play a crucial role in their anti-HIV-1 activities. Such results will provide a theoretical foundation for further investigations on the biological activity of 3,9-dioxatetraasteranes.


Assuntos
Inibidores da Protease de HIV/química , Inibidores da Protease de HIV/farmacologia , Urease/química , Urease/farmacologia , Azepinas/química , Azepinas/farmacologia , Protease de HIV/metabolismo , Inibidores da Protease de HIV/síntese química , HIV-1/efeitos dos fármacos , HIV-1/enzimologia , Humanos , Concentração Inibidora 50 , Modelos Moleculares , Simulação de Acoplamento Molecular , Relação Estrutura-Atividade , Ureia/análogos & derivados , Ureia/química , Ureia/farmacologia , Urease/síntese química
9.
Arch Virol ; 164(4): 949-960, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30680529

RESUMO

HIV is one of the most lethal viral diseases in the human population. Patients often suffer from drug resistance, which hampers HIV therapy. Eleven different structural analogues of saquinavir (SQV), designed using ChemSketch™ and named S1 through S11, were compared with SQV with respect to their pharmacodynamic and pharmacokinetic properties. Pharmacokinetic predictions were carried out using AutoDock, and molecular docking between macromolecule HIV protease (PDB ID: 3IXO) and analogues S1 - S11 as ligands was performed. Analogues S1, S3, S4, S9 and S11 had lower binding scores when compared with saquinavir, whereas that of analogue S5 was similar. Pharmacokinetic predictions made using ACDilab2, including the Lipinski profile, general physical features, absorption, distribution, metabolism and excretion parameters, and toxicity values, for the eleven analogues and SQV suggested that S1 and S5 are pharmacodynamically and pharmacokinetically robust molecules that could be developed and established as lead molecules after in vitro and in vivo studies.


Assuntos
Infecções por HIV/tratamento farmacológico , Inibidores da Protease de HIV/química , Inibidores da Protease de HIV/farmacocinética , HIV-1/enzimologia , Saquinavir/análogos & derivados , Saquinavir/farmacocinética , Animais , Infecções por HIV/virologia , Protease de HIV/química , Protease de HIV/genética , Protease de HIV/metabolismo , Inibidores da Protease de HIV/administração & dosagem , HIV-1/efeitos dos fármacos , HIV-1/fisiologia , Humanos , Camundongos , Simulação de Acoplamento Molecular , Saquinavir/administração & dosagem
10.
Eur J Pharm Sci ; 127: 60-70, 2019 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-30343153

RESUMO

In this study, novel ritonavir solid dispersion (RTV SD) formulations were prepared with copovidone (PVPVA 64) and optimized plasticizers via hot-melt extrusion (HME) at different extrusion temperature to evaluate the effect of plasticizers on the process of HME. The optimized drug-loading content of RTV SD formulations was around 15% and RTV was converted to the amorphous state and integrated through physical interactions (possibly hydrogen bonding) with the polymeric carrier. Using Span 20 or HSPC as plasticizer, the HME extrusion temperature of RTV SD formulations suggested a decrease of 10 °C or 20 °C. Furthermore, the in vitro release and the in vivo pharmacokinetics analyses both showed that RTV SD formulations using Span 20 or HSPC as plasticizer possessed better release profiles and bioavailability over RTV bulk powder but showed equal physicochemical characteristics compared to RTV SD formulations without plasticizer. According to the increased drug solubility, enhanced dissolution profiles, superior bioavailability, but decreased extrusion temperature in HME process, the RTV SD formulation using HSPC as plasticizer could be potentially applied in the clinic as an efficient drug delivery system, and HSPC is recommended as an efficient plasticizer for manufacturing RTV SD formulations via HME.


Assuntos
Inibidores da Protease de HIV , Plastificantes , Pirrolidinas , Ritonavir , Compostos de Vinila , Animais , Composição de Medicamentos , Sistemas de Liberação de Medicamentos , Inibidores da Protease de HIV/administração & dosagem , Inibidores da Protease de HIV/química , Inibidores da Protease de HIV/farmacocinética , Masculino , Plastificantes/administração & dosagem , Plastificantes/química , Plastificantes/farmacocinética , Pirrolidinas/administração & dosagem , Pirrolidinas/química , Pirrolidinas/farmacocinética , Ratos Sprague-Dawley , Ritonavir/administração & dosagem , Ritonavir/química , Ritonavir/farmacocinética , Solubilidade , Compostos de Vinila/administração & dosagem , Compostos de Vinila/química , Compostos de Vinila/farmacocinética
11.
ACS Infect Dis ; 5(2): 316-325, 2019 02 08.
Artigo em Inglês | MEDLINE | ID: mdl-30543749

RESUMO

HIV-1 protease is one of the prime targets of agents used in antiretroviral therapy against HIV. However, under selective pressure of protease inhibitors, primary mutations at the active site weaken inhibitor binding to confer resistance. Darunavir (DRV) is the most potent HIV-1 protease inhibitor in clinic; resistance is limited, as DRV fits well within the substrate envelope. Nevertheless, resistance is observed due to hydrophobic changes at residues including I50, V82, and I84 that line the S1/S1' pocket within the active site. Through enzyme inhibition assays and a series of 12 crystal structures, we interrogated susceptibility of DRV and two potent analogues to primary S1' mutations. The analogues had modifications at the hydrophobic P1' moiety compared to DRV to better occupy the unexploited space in the S1' pocket where the primary mutations were located. Considerable losses of potency were observed against protease variants with I84V and I50V mutations for all three inhibitors. The crystal structures revealed an unexpected conformational change in the flap region of I50V protease bound to the analogue with the largest P1' moiety, indicating interdependency between the S1' subsite and the flap region. Collective analysis of protease-inhibitor interactions in the crystal structures using principle component analysis was able to distinguish inhibitor identity and relative potency solely based on van der Waals contacts. Our results reveal the complexity of the interplay between inhibitor P1' moiety and S1' mutations and validate principle component analyses as a useful tool for distinguishing resistance and inhibitor potency.


Assuntos
Darunavir/análogos & derivados , Inibidores da Protease de HIV/química , Inibidores da Protease de HIV/farmacologia , Protease de HIV/genética , HIV-1/efeitos dos fármacos , HIV-1/genética , Sítios de Ligação , Domínio Catalítico , Cristalografia por Raios X , Darunavir/química , HIV-1/enzimologia , Humanos , Cinética , Modelos Moleculares , Mutação , Conformação Proteica , Especificidade por Substrato
12.
J Chem Inf Model ; 59(1): 159-169, 2019 01 28.
Artigo em Inglês | MEDLINE | ID: mdl-30422654

RESUMO

Recent research has increasingly suggested that the crucial factors affecting drug potencies are related not only to the thermodynamic properties but also to the kinetic properties. Therefore, in silico prediction of ligand-binding kinetic properties, especially the dissociation rate constant ( koff), has aroused more and more attention. However, there are still a lot of challenges that need to be addressed. In this paper, steered molecular dynamics (SMD) combined with residue-based energy decomposition was employed to predict the dissociation rate constants of 37 HIV-1 protease inhibitors (HIV-1 PIs). For the first time, a predictive model of the dissociation rate constant was established by using the interaction-energy fingerprints sampled along the ligand dissociation pathway. On the basis of the key fingerprints extracted it can be inferred that the dissociation rates of 37 HIV-1 PIs are basically determined in the first half of the dissociation processes and that the H-bond interactions with active-site Asp25 and van der Waals interactions with flap-region Ile47 and Ile50 have important influences on the dissociation processes. In general, the strategy established in this paper can provide an efficient way for the prediction of dissociation rate constants as well as the unbinding mechanism research.


Assuntos
Inibidores da Protease de HIV/química , Simulação de Dinâmica Molecular , Domínio Catalítico , Protease de HIV/metabolismo , Inibidores da Protease de HIV/farmacologia , Ligações de Hidrogênio , Cinética , Termodinâmica
13.
Bioorg Med Chem Lett ; 29(3): 357-361, 2019 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-30580917

RESUMO

The design, synthesis and SAR study of a new series of HIV-1 protease inhibitors with pentacyclic triterpenoids as P2 ligands and phenylsulfonamide as P2' ligands were discussed. These compounds exhibited micromolar inhibitory potency, among which compound T1c displayed HIV-1 protease inhibition with IC50 values of 0.12 µM, which was 67 times the inhibitory activity of its raw material Ursolic acid (8.0 µM).


Assuntos
Fármacos Anti-HIV/farmacologia , Desenho de Drogas , Inibidores da Protease de HIV/farmacologia , Protease de HIV/metabolismo , Triterpenos Pentacíclicos/farmacologia , Sulfonamidas/farmacologia , Fármacos Anti-HIV/síntese química , Fármacos Anti-HIV/química , Relação Dose-Resposta a Droga , Inibidores da Protease de HIV/síntese química , Inibidores da Protease de HIV/química , HIV-1/efeitos dos fármacos , Humanos , Ligantes , Testes de Sensibilidade Microbiana , Estrutura Molecular , Triterpenos Pentacíclicos/síntese química , Triterpenos Pentacíclicos/química , Relação Estrutura-Atividade , Sulfonamidas/síntese química , Sulfonamidas/química
14.
J Comput Aided Mol Des ; 33(2): 287-294, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30564994

RESUMO

The COMBINE method was designed to study congeneric series of compounds including structural information of ligand-protein complexes. Although very successful, the method has not received the same level of attention than other alternatives to study Quantitative Structure Active Relationships (QSAR) mainly because lack of ways to measure the uncertainty of the predictions and the need for large datasets. Active learning, a semi-supervised learning approach that makes use of uncertainty to enhance models' performance while reducing the size of the training sets, has been used in this work to address both problems. We propose two estimators of uncertainty: the pool of regressors and the distance to the training set. The performance of the methods has been evaluated by testing the resulting active learning workflows in 3 diverse datasets: HIV-1 protease inhibitors, Taxol-derivatives and BRD4 inhibitors. The proposed strategies were successful in 80% of the cases for the taxol-derivatives and BRD4 inhibitors, while outperformed random selection in the case of the HIV-1 protease inhibitors time-split. Our results suggest that AL-COMBINE might be an effective way of producing consistently superior QSAR models with a limited number of samples.


Assuntos
Proteínas de Ciclo Celular/antagonistas & inibidores , Inibidores da Protease de HIV/química , Paclitaxel/análogos & derivados , Paclitaxel/química , Relação Quantitativa Estrutura-Atividade , Fatores de Transcrição/antagonistas & inibidores , Proteínas de Ciclo Celular/química , Bases de Dados de Compostos Químicos , Bases de Dados de Proteínas , Protease de HIV/química , Ligantes , Estrutura Molecular , Aprendizagem Baseada em Problemas , Termodinâmica , Fatores de Transcrição/química , Incerteza
15.
Biochem J ; 476(2): 375-384, 2019 01 31.
Artigo em Inglês | MEDLINE | ID: mdl-30573649

RESUMO

HIV protease is essential for processing the Gag polyprotein to produce infectious virions and is a major target in antiretroviral therapy. We have identified an unusual HIV-1 subtype C variant that contains insertions of leucine and asparagine (L38↑N↑L) in the hinge region of protease at position 38. This was isolated from a protease inhibitor naïve infant. Isothermal titration calorimetry showed that 10% less of L38↑N↑L protease was in the active conformation as compared with a reference strain. L38↑N↑L protease displayed a ±50% reduction in K M and k cat The catalytic efficiency (k cat/K M) of L38↑N↑L protease was not significantly different from that of wild type although there was a 42% reduction in specific activity for the variant. An in vitro phenotypic assay showed the L38↑N↑L protease to be susceptible to lopinavir (LPV), atazanavir (ATV) and darunavir in the context of an unrelated Gag. However, in the presence of the related Gag, L38↑N↑L showed reduced susceptibility to darunavir while remaining susceptible to LPV and ATV. Furthermore, a reduction in viral replication capacity (RC) was observed in combination with the related Gag. The reduced susceptibility to darunavir and decrease in RC may be due to PTAPP duplication in the related Gag. The present study shows the importance of considering the Gag region when looking at drug susceptibility of HIV-1 protease variants.


Assuntos
Darunavir/química , Inibidores da Protease de HIV/química , Protease de HIV/química , Protease de HIV/genética , HIV-1 , Lopinavir/química , Mutagênese Insercional , Produtos do Gene gag do Vírus da Imunodeficiência Humana/química , Produtos do Gene gag do Vírus da Imunodeficiência Humana/genética , Darunavir/farmacologia , Infecções por HIV/tratamento farmacológico , Infecções por HIV/enzimologia , Infecções por HIV/genética , Protease de HIV/metabolismo , HIV-1/enzimologia , HIV-1/genética , Humanos , Lopinavir/farmacologia , Produtos do Gene gag do Vírus da Imunodeficiência Humana/antagonistas & inibidores , Produtos do Gene gag do Vírus da Imunodeficiência Humana/metabolismo
16.
Colloids Surf B Biointerfaces ; 175: 143-149, 2019 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-30529999

RESUMO

The present work aimed to formulate Darunavir loaded lipid nanoemulsion to increase its oral bioavailability and enhance brain uptake. Various batches of lipid nanoemulsion of Darunavir were prepared by high pressure homogenization using soya bean oil, egg lecithin and Tween 80. The optimized batch DNE-3 had globule size of 109.5 nm, zeta potential of -41.1 mV, entrapment efficiency 93% and creaming volume 98%. The batch remained stable at 4 °C for 1 month with an insignificant change in globule size and zeta potential (P > 0.05). In-vivo pharmacokinetics male wistar rats indicated 223% bioavailability of Darunavir relative to drug suspension. Cmax of DNE-3 was twofold higher than suspension form. The organ biodistribution study indicated 2.65 fold higher brain uptake for DNE-3 than that for suspension. The higher bioavailability of Darunavir from nanoemulsion could lessen the dose related side effects. Moreover, high organ distribution results in passive uptake of Darunavir to HIV reservoir organs.


Assuntos
Encéfalo/metabolismo , Darunavir/farmacocinética , Emulsões/química , Lipídeos/química , Nanopartículas/química , Administração Oral , Animais , Disponibilidade Biológica , Darunavir/administração & dosagem , Darunavir/química , Liberação Controlada de Fármacos , Inibidores da Protease de HIV/administração & dosagem , Inibidores da Protease de HIV/química , Inibidores da Protease de HIV/farmacocinética , Masculino , Microscopia Eletrônica de Transmissão , Nanopartículas/ultraestrutura , Ratos Wistar , Distribuição Tecidual
17.
Sci Rep ; 8(1): 17938, 2018 12 18.
Artigo em Inglês | MEDLINE | ID: mdl-30560871

RESUMO

The use of antiretrovirals (ARVs) has drastically improved the life quality and expectancy of HIV patients since their introduction in health care. Several millions are still afflicted worldwide by HIV and ARV resistance is a constant concern for both healthcare practitioners and patients, as while treatment options are finite, the virus constantly adapts via complex mutation patterns to select for resistant strains under the pressure of drug treatment. The HIV protease is a crucial enzyme for viral maturation and has been a game changing drug target since the first application. Due to similarities in protease inhibitor designs, drug cross-resistance is not uncommon across ARVs of the same class. It is known that resistance against protease inhibitors is associated with a wider active site, but results from our large scale molecular dynamics simulations combined with statistical tests and network analysis further show, for the first time, that there are regions of local expansions and compactions associated with high levels of resistance conserved across eight different protease inhibitors visible in their complexed form within closed receptor conformations. The observed conserved expansion sites may provide an alternative drug-targeting site. Further, the method developed here is novel, supplementary to methods of variation analysis at sequence level, and should be applicable in analysing the structural consequences of mutations in other contexts using molecular ensembles.


Assuntos
Farmacorresistência Viral , Inibidores da Protease de HIV/química , Protease de HIV/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Sítios de Ligação , Desenho de Drogas , Protease de HIV/genética , Inibidores da Protease de HIV/farmacologia , Humanos , Conformação Molecular , Mutação , Ligação Proteica , Relação Estrutura-Atividade , Fluxo de Trabalho
18.
J Am Chem Soc ; 140(43): 14015-14018, 2018 10 31.
Artigo em Inglês | MEDLINE | ID: mdl-30346745

RESUMO

Boronic acids have been typecast as moieties for covalent complexation and are employed only rarely as agents for non-covalent recognition. By exploiting the profuse ability of a boronic acid group to form hydrogen bonds, we have developed an inhibitor of HIV-1 protease with extraordinary affinity. Specifically, we find that replacing an aniline moiety in darunavir with a phenylboronic acid leads to 20-fold greater affinity for the protease. X-ray crystallography demonstrates that the boronic acid group participates in three hydrogen bonds, more than the amino group of darunavir or any other analog. Importantly, the boronic acid maintains its hydrogen bonds and its affinity for the drug-resistant D30N variant of HIV-1 protease. The BOH···OC hydrogen bonds between the boronic acid hydroxy group and Asp30 (or Asn30) of the protease are short ( rO···O = 2.2 Å), and density functional theory analysis reveals a high degree of covalency. These data highlight the utility of boronic acids as versatile functional groups in the design of small-molecule ligands.


Assuntos
Ácidos Borônicos/farmacologia , Inibidores da Protease de HIV/farmacologia , Protease de HIV/metabolismo , Ácidos Borônicos/química , Relação Dose-Resposta a Droga , Inibidores da Protease de HIV/química , Estrutura Molecular , Relação Estrutura-Atividade
19.
J Med Chem ; 61(21): 9722-9737, 2018 11 08.
Artigo em Inglês | MEDLINE | ID: mdl-30354121

RESUMO

We have designed, synthesized, and evaluated a new class of potent HIV-1 protease inhibitors with novel bicyclic oxazolidinone derivatives as the P2 ligand. We have developed an enantioselective synthesis of these bicyclic oxazolidinones utilizing a key o-iodoxybenzoic acid mediated cyclization. Several inhibitors displayed good to excellent activity toward HIV-1 protease and significant antiviral activity in MT-4 cells. Compound 4k has shown an enzyme Ki of 40 pM and antiviral IC50 of 31 nM. Inhibitors 4k and 4l were evaluated against a panel of highly resistant multidrug-resistant HIV-1 variants, and their fold-changes in antiviral activity were similar to those observed with darunavir. Additionally, two X-ray crystal structures of the related inhibitors 4a and 4e bound to HIV-1 protease were determined at 1.22 and 1.30 Å resolution, respectively, and revealed important interactions in the active site that have not yet been explored.


Assuntos
Desenho de Drogas , Inibidores da Protease de HIV/síntese química , Inibidores da Protease de HIV/farmacologia , Protease de HIV/metabolismo , HIV-1/enzimologia , Oxazolidinonas/síntese química , Oxazolidinonas/farmacologia , Domínio Catalítico , Técnicas de Química Sintética , Protease de HIV/química , Inibidores da Protease de HIV/química , Inibidores da Protease de HIV/metabolismo , HIV-1/efeitos dos fármacos , Ligantes , Modelos Moleculares , Oxazolidinonas/química , Oxazolidinonas/metabolismo , Estereoisomerismo , Relação Estrutura-Atividade
20.
BMC Bioinformatics ; 19(Suppl 11): 362, 2018 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-30343664

RESUMO

BACKGROUND: Drug resistance in HIV is the major problem limiting effective antiviral therapy. Computational techniques for predicting drug resistance profiles from genomic data can accelerate the appropriate choice of therapy. These techniques can also be used to select protease mutants for experimental studies of resistance and thereby assist in the development of next-generation therapies. RESULTS: The machine learning produced highly accurate and robust classification of HIV protease resistance. Genotype data were mapped to the enzyme structure and encoded using Delaunay triangulation. Generative machine learning models trained on one inhibitor could classify resistance from other inhibitors with varying levels of accuracy. Generally, the accuracy was best when the inhibitors were chemically similar. CONCLUSIONS: Restricted Boltzmann Machines are an effective machine learning tool for classification of genomic and structural data. They can also be used to compare resistance profiles of different protease inhibitors.


Assuntos
Farmacorresistência Viral/genética , Protease de HIV/genética , Algoritmos , Bases de Dados como Assunto , Farmacorresistência Viral/efeitos dos fármacos , Genótipo , Infecções por HIV/tratamento farmacológico , Inibidores da Protease de HIV/química , Inibidores da Protease de HIV/farmacologia , Humanos , Aprendizado de Máquina , Análise de Componente Principal
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