2,364 research outputs found

    Putative HIV-1 reverse transcriptase inhibitors: design, synthesis, in vitro evaluation and in silico analysis.

    Get PDF
    Masters Degree. University of KwaZulu-Natal, Durban.One of the most significant treatments for HIV-1 infection has been the combination of drugs targeting the HIV life cycle with the aim of preventing further destruction of the host immune system. This study addresses the design, synthesis, in vitro evaluation, and in silico analysis of putative HIV-1 reverse transcriptase (RT) inhibitors. The inhibitors comprise two structurally diverse components which are intended to bind separately to the enzyme allosteric site and to a location at, or close to, the polymerase active site. Therefore, the hydrophobic N-tritylated phalo-DL-phenylalanine derivatives (fluoro, chloro, bromo, iodo) have been coupled to 8-(6- aminohexyl) amino-adenosine-3',5'-cyclic monophosphate through N-hydroxysuccinimidecarbodiimide chemistry. Compounds were characterized by thin layer chromatography, UV spectroscopy, MALDI-TOF mass spectrometry and proton NMR spectrometry. A reverse transcriptase colorimetric assay kit, which features a sandwich ELISA protocol, based on biotin-avidin and digoxygenin-anti DIG interactions, was used for quantitative determination of the inhibitory effect of synthesized compounds on recombinant HIV-1 reverse transcriptase activity in vitro. Molecular docking simulations of the chimeric inhibitors within the allosteric site of HIV-1 RT, were performed using AutoDock Vina. The predicted binding associations were compared with laboratory findings on HIV-1 RT inhibition. Two dimensional representations of protein-ligand interactions were generated using LigPlot. The non-halogenated N-trityl-L-phenylalanine-8-(6-aminohexyl)amino-adenosine-3',5'-cyclic monophosphate derivative (4a) inhibited RT activity down to 57 % at 10-4 M, while the Ntrityl-para-fluoro-DL-phenylalanine-8-(6-aminohexyl)aminoadenosine-3′,5′-cyclic monophosphate derivative (4b) was the strongest RT inhibitor reducing RT activity to 69 % at 10-7 M (IC50 = 29.2 μM). In the same assay, Nevirapine, a first-line anti-retroviral drug, showed a decline in RT activity down to 43% at 10-5 M (IC50 = 3.03 μM). Ranking of inhibitors according to estimated docking energies obtained from in silico docking was in excellent agreement with potencies calculated from experimental studies. The docking score of N-trityl-para-fluoro-DL-phenylalaline-8-(6-aminohexyl)amino-adenosine-3',5'-cyclic monophosphate was -8.8 kcal/mol, while that of Nevirapine was -9.9 kcal/mol. The benzene rings of the N-trityl-fluoro-DL-phenylalanine-8-(6-aminohexyl) amino-adenosine-3',5'-cyclic monophosphate derivative formed hydrophobic interactions with hydrophobic, non-aromatic amino acid residues Pro176 and Val179 in the allosteric site. Nevirapine, on the other hand showed strong van der Waals interactions with Val106 ,Val179 and Tyr188 due to the aromatic properties of the pyridine ring. Possible π-π stacking between phenyl rings of Nevirapine and Tyr 181/Tyr188 aromatic side chains may also be present. Other HIV-1 RT large subunit residues in the allosteric site common to the binding of Nevirapine and the active para-fluoro derivative include Lys101, Tyr318, Leu 100, Trp229 and Phe227. Apparent binding to the allosteric site suggests that compounds may be acting primarily as non-nucleoside reverse transcriptase inhibitors (NNRTIs)

    Hit optimization studies of 3-hydroxy-indolin-2-one analogs as potential anti-HIV-1 agents

    Get PDF
    International audienceIn the current study, twenty-two compounds based upon 3-hydroxy-3-(2-oxo-2-phenylethyl)indolin-2-one nucleus were designed, synthesized and in vitro evaluated for HIV-1 RT inhibition and anti-HIV-1 activity. Compounds 3d, 5c and 5e demonstrated encouraging potency against RT enzyme as well as HIV-1 in low micromolar to nanomolar concentration with good to excellent safety index. Structure activity relationship studies revealed that halogens such as bromo or chloro at 5th the position of oxindole ring remarkably enhanced the potency against RT. Moreover, methoxy or chloro groups at the ortho position of phenyl ring also significantly favored RT inhibition activity. Seven compounds (3b, 3c, 3d, 3e, 5b, 5c and 5e) with better anti-HIV-1 potency were tested against the mutant HIV-1 K103N strain. The putative binding mode, as well as interaction patterns of the best active compound 5c with wild HIV-1 RT were studied via docking studies

    Molecular modeling studies on HIV-1 Reverse Transcriptase (RT) and Heat shock protein (Hsp) 90 as a potential anti-HIV-1 target.

    Get PDF
    Masters Degree. University of KwaZulu-Natal, Durban.Human immunodeficiency virus (HIV) infection is the leading cause of death globally. This dissertation addresses two HIV-1 target proteins namely, HIV-1 Reverse Transcriptase (RT) and Heat shock protein (Hsp) 90. More specifically for HIV-1 RT, a case study for the identification of potential inhibitors as anti-HIV agents was carried out. A more refined virtual screening (VS) approach was implemented, which was an improvement on work previously published by our group- “target-bound pharmacophore modeling approach”. This study generated a pharmacophore library based only on highly contributing amino acid residues (HCAAR), instead of arbitrary pharmacophores, most commonly used in the conventional approaches in literature. HCAAR were distinguished based on free binding energy (FBE) contributions, obtained using calculation from molecular dynamics (MD) simulations. Previous approaches have relied on the docking score (DS) to generate energy-based pharmacophore models. However, DS are reportedly unreliable. Thus we present a model for a per-residue energy decomposition (PRED), constructed from MD simulation ensembles generating a more trustworthy pharmacophore model which can be applied in drug discovery workflow. This approach was employed in screening for potential HIV-1 RT inhibitors using the pharmacophoric features of the compound GSK952. The complex was subjected to docking and thereafter MD simulations confirmed the stability of the system. Experimentally determined inhibitors with known HIV-RT inhibitory activity were used to validate the proposed protocol. Two potential hits ZINC46849657 and ZINC54359621 showed a significant potential with regards to FBE. Reported results obtained from this work confirm that this new approach is favourable to the future of drug design process. Hsp90 was recently discovered to play a vital role in HIV-1 replication. Thus has emerged, as a promising target for anti-HIV-1 drugs. The molecular mechanism of Hsp90 is poorly understood, thus the second study was aimed to address this issue and provide a clear insight to the inhibition mechanism of Hsp90. Reasonable continuous MD simulations were employed for both unbound and bound Hsp90 conformations, to understand the dimerization and inhibition mechanisms. Results demonstrated that coumermycin A1 (C-A1), a newly discovered Hsp90 inhibitor, binds at the CTD dimer of Hsp90 and lead to a significant separation between orthogonally opposed residues, such as Arg591.B, Lys594.A, Ser663.A, Thr653.B, Ala665.A, Thr649.B, Leu646.B and Asn669A. A Large difference in magnitudes was observed in the radius of gyration (Rg), per-residue fluctuation, root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) confirming a completely more flexible state for the unbound conformation associated with dimerization. Whereas, a less globally correlated motion in the case of the bound conformer of Hsp90 approved a reduction of the dimeric process. This undoubtedly underlines the inhibition process due to ligand binding. The detailed dynamic analyses of Hsp90 presented herein are believed to give a greater insight and understanding to the function and mechanisms of inhibition of Hsp90. The report on the inhibitor-binding mode would also be of great assistance in the design of prospective inhibitors against Hsp90 as potential HIV target

    Adaptive HIV-1 evolutionary trajectories are constrained by protein stability

    Get PDF
    Despite the use of combination antiretroviral drugs for the treatment of HIV-1 infection, the emergence of drug resistance remains a problem. Resistance may be conferred either by a single mutation or a concerted set of mutations. The involvement of multiple mutations can arise due to interactions between sites in the amino acid sequence as a consequence of the need to maintain protein structure. To better understand the nature of such epistatic interactions, we reconstructed the ancestral sequences of HIV-1's Pol protein, and traced the evolutionary trajectories leading to mutations associated with drug resistance. Using contemporary and ancestral sequences we modelled the effects of mutations (i.e. amino acid replacements) on protein structure to understand the functional effects of residue changes. Although the majority of resistance-associated sequences tend to destabilise the protein structure, we find there is a general tendency for protein stability to decrease across HIV-1's evolutionary history. That a similar pattern is observed in the non-drug resistance lineages indicates that non-resistant mutations, for example, associated with escape from the immune response, also impacts on protein stability. Maintenance of optimal protein structure therefore represents a major constraining factor to the evolution of HIV-1

    A BATTLE AGAINST AIDS: NEW PYRAZOLE KEY TO AN OLDER LOCK-REVERSE TRANSCRIPTASE

    Get PDF
    Objective: The reason for the failure of most of the anti-HIV drugs are their poor pharmacokinetics, the poor risk to benefit ratio and the drug resistance. With the objective of developing newer pyrazole scaffolds for effective treatment of HIV, binding mode analysis of designing ligands with the HIV-1RT protein and prediction of key ADME and toxicity parameters of the compounds was in an area of interest.Methods: In this study, molecular docking studies and ADME-T studies were carried out in designing of some novel pyrazole analogs. The protein (PDB ID: 1RT2) was prepared using the Protein Preparation Wizard (Schrodinger Glide 5.0). ADME parameters calculated by QikProp 3.0v and toxicity of designed analogs checked by using two different online software's namely Lazar and protox.Results: Most of the designed pyrazole analogs have good oral absorption as well as good binding affinity towards HIV-1 reverse transcriptase.Conclusion: Finally total 5 analogs (SGS-2, 3, 12, 13 and 14) from the 14 designed leads were found to be best on the basis of molecular docking and ADME-T studies

    HIV-Reverse Transcriptase Inhibition: Inclusion of Ligand-Induced Fit by Cross-Docking Studies

    Get PDF
    Nonnucleoside reverse transcriptase inhibitors (NNRTIs) have, in addition to the nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs), a definitive role in the treatment of HIV-1 infections. Since the appearance of HEPT and TIBO, more than 30 structurally different classes of compounds have been reported as NNRTIs, which are specific inhibitors of HIV-1 replication, targeting the HIV-1 reverse transcriptase (RT). Nevirapine and delavirdine are the first formally licensed for clinical use, and others have been licensed afterward, while several are in preclinical or clinical development. The NNRTIs interact with a specific site of HIV-1 RT (nonnucleoside binding site, NNBS) that is close to, but distinct from, the NRTI binding site. In this work we report the application of the Autodock program assessing its usability through reproduction of 41 NNRTI experimental bound conformations. Moreover, cross-docking experiments on the wild-type and mutated RT forms were conducted to take into account the enzyme flexibility as a valuable tool for structure-based drug design (SBDD) studies and to gain insight on the mode of action of new anti-HIV agents active against both wild-type and resistant strains

    Synthesis, biological activity, pharmacokinetic properties and molecular modelling studies of novel 1H,3H-oxazolo[3,4-a]benzimidazoles: non-nucleoside HIV-1 reverse transcriptase inhibitors

    Get PDF
    New 1H,3H-oxazolo[3,4-a]benzimidazoles (OBZs) were synthesized as HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTI) to extend the structure-activity relationships observed for an early series of related 1H,3H-thiazolo[3,4-a]benzimidazole derivatives (TBZs). The new compounds showed inhibitory activity against the replication of various HIV-1 strains, including NNRTI-resistant strains. Testing of a representative OBZ derivative in an HPLC assay on biological fluids, indicated that the sulphur substitution appreciably improved the metabolic stability of the TBZ compound. In addition, molecular modelling studies demonstrated that OBZs, TBZs and other NNRTIs have similar structural properties, that is a butterfly-like conformation, which is a key structural requirement for reverse transcriptase inhibition

    Design and Synthesis of Novel Sultams: A Family of Non-nucleoside Reverse Transcriptase Inhibitors and Modeling Studies of a Rhodium Catalyst

    Get PDF
    3-Phenyl-2,3-dihydro-1,2-benzisothiazole 1,1 dioxide (NSC108406), identified as an HIV-1 reverse transcriptase inhibitor, is chosen for lead optimization. A series of analogues are docked using SYBYL FlexiDock into both wild-type (wt) reverse transcriptase (RT) and Tyr181 --\u3e Cys181 (Y181C) RT, from the dataset of efavirenz (Sustiva®) bound to the enzyme. Minimizations using genetic algorithms are performed, and the lowest energy conformations are evaluated. Five structures emerge as good fits either in both enzymes or only in Y181C RT. 3-(m-Cyclopropylphenyl)- and 3-(isopropylfuranyl)-2-methyl-2,3- dihydro-1,2-benzisothiazole 1,1-dioxides do not exhibit improved binding in wt RT over efavirenz. In the Y181C pocket, the furanyl ring oxygen is oriented towards Cys181, and the cyclopropyl group on the phenyl ring makes a strong contact with Tyr183. Three 3-(alkylethynyl)-2,3-dihydro-2-methyl-1,2-benzisothiazole 1,1-dioxides (ethynyl sultams) make very good contacts in both wt and Y181C RT. Synthesis of the ethynyl sultams is attempted using the appropriate alkylethynyllithium reagents with saccharin, but 3,3-bisalkylethynyl-2,3-dihydro- 1,2-benzisothiazole 1,1-dioxides are the principal products. These are methylated to give the bisalkylated sultams. When docked into wt RT, they are consistently placed outside the pocket. In Y181C RT they make similar contacts to nevirapine, a first-generation NNRTI. 3-Chloro-1,2-benzisothiazole 1,1-dioxide is then coupled to the alkylethynyllithium reagents to give the desired monosubstituted products. (R,R)-N-(p-tolunesulfonyl)-1,2-diphenylethylenediamine-rhodium- (pentamethycycopentadienyl)-Cl [(R,R)-TSDPEN-Rh-Cl], an enantioselective catalyst for the reduction of imines, is used in an attempt to produce optically active sultams; however, the products are not optically active. The cyclopropyland cyclobutylethynyl bonds are reduced to the corresponding alkanes. These new cycloalkylethyl sultams, when docked into RT, exhibit a better fit in Y181C than wt RT, similar to that of efavirenz. In a study on the mechanism of the enantioselective reduction of 3-alkylor aryl-imines by (R,R)-TSDPEN-Rh-Cl, a number of imines are docked into the catalyst cavity in two different approaches using the “original” approach that gives the observed enantioselectivity and the “reverse” approach, which is thought to give the opposite enantiomer. Molecular dynamic studies are carried out. In all 3-(aryl/alkyl)imine sultams, an average of at least 10 kcal/mol energy difference is observed between both approaches, showing probable structures for the intermediate complex in the catalytic cycle that accounts product stereochemistry
    • …
    corecore