Indolylarylsulfones Bearing Natural and Unnatural Amino Acids. Discovery of Potent Inhibitors of HIV-1 Non-Nucleoside Wild Type and Resistant Mutant Strains Reverse Transcriptase and Coxsackie B4 Virus

2009 ◽  
Vol 52 (7) ◽  
pp. 1922-1934 ◽  
Author(s):  
Francesco Piscitelli ◽  
Antonio Coluccia ◽  
Andrea Brancale ◽  
Giuseppe La Regina ◽  
Anna Sansone ◽  
...  
Keyword(s):  
Amino Acids ◽  
Reverse Transcriptase ◽  
Unnatural Amino Acids ◽  
Resistant Mutant ◽  
Wild Type ◽  
Mutant Strains ◽  
Coxsackie B4 Virus ◽  
Hiv 1

scholarly journals Molecular modeling of HIV-1 reverse transcriptase drug-resistant mutant strains: implications for the mechanism of polymerase action

1997 ◽  
Vol 10 (12) ◽  
pp. 1379-1383 ◽  
Author(s):  
M. B. Kroeger Smith ◽  
C. J. Michejda ◽  
S. H. Hughes ◽  
P. L. Boyer ◽  
P. A. Janssen ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Reverse Transcriptase ◽  
Resistant Mutant ◽  
Drug Resistant ◽  
Mutant Strains ◽  
Drug Resistant Mutant ◽  
Hiv 1

scholarly journals Design of Biphenyl-Substituted Diarylpyrimidines with a Cyanomethyl Linker as HIV-1 NNRTIs via a Molecular Hybridization Strategy

Molecules ◽  
2020 ◽  
Vol 25 (5) ◽  
pp. 1050 ◽  
Author(s):  
Yuan Lei ◽  
Sheng Han ◽  
Yang Yang ◽  
Christophe Pannecouque ◽  
Erik De Clercq ◽  
...  
Keyword(s):  
Resistant Mutant ◽  
Molecular Hybridization ◽  
Binding Modes ◽  
Wild Type ◽  
Hiv Therapy ◽  
Mutant Strains ◽  
Drug Resistant Mutant ◽  
New Compounds ◽  
Anti Hiv ◽  
Hiv 1

The key problems of human immunodeficiency virus (HIV) therapy are the rapid emergence of drug-resistant mutant strains and significant cumulative drug toxicities. Therefore, there is an urgent demand for new anti-HIV agents with low toxicity and broad-spectrum antiviral potency. A series of biphenyl-substituted diarylpyrimidines with a cyanomethyl linker were designed using a molecular hybridization strategy. The cell-based anti-HIV assay showed that most of the compounds exhibited moderate to good activities against wild-type HIV-1 and clinically relevant mutant strains with a more favorable toxicity, and the enzymatic assay showed they had nanomolar activity against reverse transcriptase (RT). Compound 10p exhibited the best activity against wild-type HIV-1 with an EC50 (50% HIV-1 replication inhibitory concentration) value of 0.027 µM, an acceptable CC50 (50% cytotoxic concentration) value of 36.4 µM, and selectivity index of 1361, with moderate activities against the single mutants (EC50: E138K, 0.17 µM; Y181C, 0.87 µM; K103N, 0.9 µM; L100I, 1.21 µM, respectively), and an IC50 value of 0.059 µM against the RT enzyme, which was six-fold higher than nevirapine (NVP). The preliminary structure–activity relationship (SAR) of these new compounds was concluded. The molecular modeling predicted the binding modes of the new compounds with RT, providing molecular insight for further drug design.

Site- and subunit-specific incorporation of unnatural amino acids into HIV-1 reverse transcriptase

2004 ◽  
Vol 38 (1) ◽  
pp. 37-44 ◽  
Author(s):  
George J. Klarmann ◽  
Brian M. Eisenhauer ◽  
Yi Zhang ◽  
Kalavathy Sitaraman ◽  
Deb K. Chatterjee ◽  
...  
Keyword(s):  
Amino Acids ◽  
Reverse Transcriptase ◽  
Unnatural Amino Acids ◽  
Hiv 1

scholarly journals Switch to Unusual Amino Acids at Codon 215 of the Human Immunodeficiency Virus Type 1 Reverse Transcriptase Gene in Seroconvertors Infected with Zidovudine-Resistant Variants

1998 ◽  
Vol 72 (5) ◽  
pp. 3520-3523 ◽  
Author(s):  
Sabine Yerly ◽  
Abdelrahim Rakik ◽  
Sabine Kinloch De Loes ◽  
Bernard Hirschel ◽  
Diane Descamps ◽  
...  
Keyword(s):  
Amino Acids ◽  
Human Immunodeficiency Virus ◽  
Amino Acid ◽  
Reverse Transcriptase ◽  
Wild Type ◽  
Unusual Amino Acids ◽  
Immunodeficiency Virus ◽  
Hiv 1 ◽  
Over Time

ABSTRACT Sequences of the human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) domain were determined by direct sequencing of HIV-1 RNA in successive plasma samples from eight seroconverting patients infected with virus bearing the T215Y/F amino acid substitution associated with zidovudine (ZDV) resistance. At baseline, additional mutations associated with ZDV resistance were detected. Three patients had the M41L amino acid change, which persisted. Two patients had both the D67N and the K70R amino acid substitutions; reversion to the wild type was seen at both positions in one of these patients and at codon 70 in the other one. Reversion to the wild type at codon 215 was observed in only one of eight patients. Unusual amino acids, such as aspartic acid (D) and cysteine (C), appeared at position 215 in four patients during follow-up. These variants isolated by coculturing were sensitive to ZDV. Overgrowth of these variants suggests that they have better fitness than the original T215Y variant. Intraindividual nucleoside substitutions over time were 10 times more frequent in codons associated with ZDV resistance (41, 67, 70, 215, and 219) than in other codons of the RT domain. The predominance of nonsynonymous substitutions observed over time suggests that most changes reflect adaptation of the RT function. The variance in sequence evolution observed among patients, in particular at codon 215, supports a role for chance in the evolution of the RT domain.

Application of Molecular Docking for the Development of Improved HIV-1 Reverse Transcriptase Inhibitors

2020 ◽  
Vol 16 ◽  
Author(s):  
Arash Soltani ◽  
Seyed Isaac Hashemy ◽  
Farnaz Zahedi Avval ◽  
Houshang Rafatpanah ◽  
Seyed Abdolrahim Rezaee ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Binding Capacity ◽  
Binding Pocket ◽  
Ligand Docking ◽  
Binding Modes ◽  
Wild Type ◽  
Parent Molecule ◽  
Discovery Studio ◽  
Approved Drugs ◽  
Hiv 1

Introoduction: Inhibition of the reverse transcriptase (RT) enzyme of human immunodeficiency virus (HIV) by low molecular weight inhibitors is still an active area of research. Here, protein-ligand interactions and possible binding modes of novel compounds with the HIV-1 RT binding pocket (the wild-type as well as Y181C and K103N mutants) were obtained and discussed. Methods: A molecular fragment-based approach using FDA-approved drugs were followed to design novel chemical derivatives using delavirdine, efavirenz, etravirine and rilpivirine as the scaffolds. The drug-likeliness of the derivatives was evaluated using Swiss-ADME. Then the parent molecule and derivatives were docked into the binding pocket of related crystal structures (PDB ID: 4G1Q, 1IKW, 1KLM and 3MEC). Genetic Optimization for Ligand Docking (GOLD) Suite 5.2.2 software was used for docking and the results analyzed in the Discovery Studio Visualizer 4. A derivative was chosen for further analysis, if it passed drug-likeliness and the docked energy was more favorable than that of its parent molecule. Out of the fifty-seven derivatives, forty-eight failed in druglikeness screening by Swiss-ADME or in docking stage. Results: The final results showed that the selected compounds had higher predicted binding affinities than their parent scaffolds in both wild-type and the mutants. Binding energy improvement was higher for the structures designed based on second-generation NNRTIs (etravirine and rilpivirine) than the first-generation NNRTIs (delavirdine and efavirenz). For example, while the docked energy for rilpivirine was -51 KJ/mol, it was improved for its derivatives RPV01 and RPV15 up to -58.3 and -54.5 KJ/mol, respectively. Conclusion: In this study, we have identified and proposed some novel molecules with improved binding capacity for HIV RT using fragment-based approach.

scholarly journals Interactions of the HIV-1 reverse transcriptase ‘AZT-resistant’ mutant with substrates and AZT-TP

FEBS Letters ◽  
1993 ◽  
Vol 325 (3) ◽  
pp. 237-241 ◽  
Author(s):  
Dmitry K. Pokholok ◽  
Severin O. Gudima ◽  
Dmitry S. Yesipov ◽  
Vladimir N. Dobrynin ◽  
Vladimir O. Rechinsky ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Resistant Mutant ◽  
Hiv 1
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