Application of Structure-based Methods to Analyze Resistance Mutations for Chemically Diverse Non-Nucleoside Reverse Transcriptase Inhibitors

2020 ◽  
Vol 18 (4) ◽  
pp. 283-291
Author(s):  
Tasnim Tabassum ◽  
Syeda M. Azeem ◽  
Alecia N. Muwonge ◽  
Kathleen M. Frey
Keyword(s):  
Reverse Transcriptase ◽  
Resistance Mutations ◽  
Allosteric Site ◽  
Reverse Transcriptase Inhibitors ◽  
Hiv Patients ◽  
Nucleoside Reverse Transcriptase Inhibitors ◽  
Nnrti Resistance ◽  
Ic50 Values ◽  
Modeling Strategy ◽  
High Level

Background: Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are used in combination antiretroviral therapy to suppress viral loads in HIV patients. The chemical design of NNRTIs has changed in recent years in response to resistance associated mutations (RAMs) and resistance. NNRTIs are chemically diverse compounds that bind an allosteric site of HIV RT. Resistance-associated mutations (RAMs) identified in HIV patients are associated with NNRTI resistance. RAMs confer amino acid changes that alter both structural and physiochemical properties of the allosteric site. Ultimately these changes reduce NNRTI affinity. Previously, we used a combination of computational and experimental methods to analyze and validate RAMs for 3 diarylpyrimidine (DAPY) NNRTIs. Objective: The objective of this study is to apply these methods to other chemically diverse, non-DAPY NNRTIs. Materials and Methods: We selected MIV-150 (experimental microbicide) and doravirine for this study. A computational and molecular modeling strategy was used to evaluate the effects of RAMs. Calculated changes in drug affinity and stability (ΔS + ΔA) were used to determine overall resistance levels: susceptible, low, intermediate, and high. The ΔS + ΔA values for K101P suggest that this mutation confers intermediate/high-level resistance to MIV-150, but remains susceptible to doravirine. Based on the determined resistance levels, we analyzed the models and used Molecular Dynamics (MD) to compare the interactions of MIV-150/doravirine with RT wild-type (WT) and RT (K101P). From MD, we found key interactions were lost with RT (K101P), but are retained with doravirine. To experimentally validate our findings, we conducted a fluorescence-based reverse transcription assay for MIV-150 with RT (WT) and RT (K101P). IC50 values determined in assays show a 101-fold change in potency for MIV-150, but essentially no change for doravirine. Results: Our computational and experimental results are also consistent with antiviral data reported in the literature. Conclusion: We believe that this approach is effective for analyzing mutations to determine resistance profiles for chemically diverse NNRTIs in development.

scholarly journals Study of antiretroviral mutants in HIV patients with treatment failures and the effect of risk factors in the virological failures

2005 ◽  
Vol 47 (6) ◽  
pp. 327-331 ◽  
Author(s):  
Lizeth Taylor-Castillo ◽  
Gisela Herrera-Martínez ◽  
María Paz León-Bratti ◽  
Ricardo Boza ◽  
Bernal León-Rodríguez ◽  
...  
Keyword(s):  
Risk Factors ◽  
Reverse Transcriptase ◽  
Relevant Information ◽  
Treatment Schedule ◽  
Resistance Mutations ◽  
Reverse Transcriptase Inhibitors ◽  
Hiv Patients ◽  
Nucleoside Reverse Transcriptase Inhibitors ◽  
Primary Resistance ◽  
Selection Of

INTRODUCTION: Information about HIV phenotypes of resistant to available ART and the influence of different risk factors on virological failures (VF) in Costa Rican HIV positive patients prior or during HAART is unknown. MATERIALS AND METHODS: Eighty nine samples, 72 VF and 17 basal (before treatment) were analyzed by examining resistant mutants in reverse transcriptase (RT) and protease (PT) regions using Trugene or LIPA genotyping kits. Sixty eight control patients were selected and relevant information was collected in a questionnaire. RESULTS: Poor adherence, presence of resistant mutations and number of treatment's changes were the only significant factors found (p = 0.006, 0.04 and 0.01 respectively). From 66 sequenced samples, 78%, 50% and 50% showed resistance to NRTI (nucleoside reverse transcriptase inhibitors), NNRT (non-nucleoside reverse transcriptase inhibitors) and PI (protease inhibitors), respectively. The most frequent mutations were M41L, M184V, and T215FY in RT and L62PI, L10FIRV and M36I in PT. DISCUSSION: The most important factor related to treatment response in this study was adherence to treatment. Mutations in RT were related to the treatment failure while the ones found in PT were secondary mutations which have been previously described to influence the selection of primary resistance mutations in these regions. The study reveals the urgency to detect resistant mutations in VF to be considered by physicians for selection of treatment schedule, to analyze basal HIV patients for monitoring of the spread of resistant mutations and the importance to reinforce the adherence in the patients for overall treatment outcome.

scholarly journals HIV Drug Resistance Mutations in Patients with HIV and HIV-TB Coinfection After Failure of First-Line Therapy: A Prevalence Study in a Resource-Limited Setting

2019 ◽  
Vol 18 ◽  
pp. 232595821984906
Author(s):  
Nawaid Hussain Khan ◽  
Mikashmi Kohli ◽  
Kartik Gupta ◽  
Bimal Kumar Das ◽  
Ravindra Mohan Pandey ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Drug Resistant ◽  
Resistance Mutations ◽  
Reverse Transcriptase Inhibitors ◽  
Nucleoside Reverse Transcriptase Inhibitors ◽  
First Line Therapy ◽  
Resource Limited ◽  
High Prevalence ◽  
Hiv 1 ◽  
Limited Setting

Introduction: The present study aimed to report the prevalent HIV-1 drug-resistant mutations in patients with HIV-1 alone and tuberculosis (TB) coinfection alone to improve our understanding of the mutation patterns and aid treatment decisions. Methods: Patients with HIV-1 and HIV-TB on treatment for more than 1 year with suspected failure were recruited. Sequencing of protease and two-thirds of the region of reverse transcriptase gene was done for drug-resistant mutations. Results: In the HIV-TB group (n = 25), 88%, 92%, and 12% had mutations to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), and protease inhibitors (PIs), respectively. In the HIV-alone group (n = 25), 84%, 100%, and 4% had mutations to NRTIs, NNRTIs, and PIs, respectively. M184V, M41L, D67N, G190A, A98G, and K103N were the most common mutations seen. Conclusion: There is a high prevalence of drug-resistant mutations in HIV and HIV-TB coinfected patients.

New resistance mutations to nucleoside reverse transcriptase inhibitors at codon 184 of HIV-1 reverse transcriptase (M184L and M184T)

2018 ◽  
Vol 93 (1) ◽  
pp. 50-59 ◽  
Author(s):  
Lydia Pouga ◽  
Maria Mercedes Santoro ◽  
Charlotte Charpentier ◽  
Domenico Di Carlo ◽  
Isabella Romeo ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Resistance Mutations ◽  
Reverse Transcriptase Inhibitors ◽  
Nucleoside Reverse Transcriptase Inhibitors ◽  
Hiv 1

scholarly journals Diabetes and HIV

2019 ◽  
Vol 7 (02) ◽  
pp. 45-49
Author(s):  
Ranabir Salam ◽  
Sarita Bajaj ◽  
Nitin Kapoor ◽  
Banshi Saboo ◽  
Arundhati Dasgupta
Keyword(s):  
Diabetes Mellitus ◽  
Reverse Transcriptase ◽  
People Living With Hiv ◽  
Reverse Transcriptase Inhibitors ◽  
First Line ◽  
Hiv Patients ◽  
Nucleoside Reverse Transcriptase Inhibitors ◽  
Family History Of Diabetes ◽  
Drug Of Choice ◽  
History Of

AbstractIn India, the prevalence of HIV infection among adults (15–49 years) is estimated at 0.26%. The total number of people living with HIV (PLHIV) in India was estimated at 21.17 lakhs in 2015. There has been a declining trend in the mortality rate of HIV-infected patients on antiretroviral therapy (ART). With HIV becoming a chronic manageable disease, metabolic complications like diabetes mellitus (DM) and dyslipidemia are coming to the forefront. Generally, protease inhibitors (PI) are implicated in metabolic derangement; however, nucleoside reverse transcriptase inhibitors (NRTI) like stavudine can also cause diabetes. Among HIV-infected patients, the prevalence of diabetes is reported to range from 2 to 19%, so there is strong case for screening of diabetes among HIV-infected cases. The South Asian Consensus Guidelines recommend that both fasting and postprandial glucose values should be checked at screening and during monitoring of therapy. National AIDS Control Organization (NACO) recommends fasting plasma glucose with value ≥ 126 mg% diagnostic of diabetes mellitus. HbA1c may underestimate the degree of hyperglycemia in HIV-infected individuals and may not be a good diagnostic tool. Lifestyle modification is recommended as part of treatment. Metformin should be used with caution in HIV patients. Concomitant use of metformin with non-nucleoside reverse transcriptase inhibitors (NNRTI) can cause lactic acidosis. Thiazolidinediones should be the drug of choice in HIV, particularly in patients with lipodystrophy. Insulin secretagogues (meglitinides and sulfonylureas) are safe but may not be effective in the presence of severe insulin resistance. There are concerns regarding the use of gliptins in HIV-infected patients as they have molecular targets on immune cells. Insulin should be the drug of choice for HIV-infected patients with marked hyperglycemia (HbA1c > 9%), ketonuria, severe liver disease, or severe kidney disease. SGLT2 inhibitor may increase the risk of urinary tract infection and genital mycotic infections in HIV-infected diabetics. Regarding the use of ART among HIV patients with diabetes, NACO guidelines recommend that Tenofovir, lamivudine, and efavirenz should be used as first-line ART for all new patients, except known cases of severe diabetes, severe hypertension, or renal disease. Tenofovir, lamivudine, and lopinavir/ritonavir should be used as first line in women ever exposed to single dose Nevirapine in the past and also for all confirmed HIV-2 or HIV-1 & 2 coinfected patients. HIV infected with diabetes mellitus and microalbuminuria or proteinuria need Abacavir-based regimen (Abacavir + Lamivudine + Efavirenz). There is some suggestion that PI-based regimes should be avoided in patients at high risk of developing diabetes, for example, those with a history of gestational diabetes, positive family history of diabetes, or impaired glucose tolerance on screening.

scholarly journals Barcoding analysis of HIV drug resistance mutations using Oxford Nanopore MinION (ONT) sequencing

2017 ◽  
Author(s):  
Claudia Gonzalez ◽  
Jessica Gondola ◽  
Alma Y Ortiz ◽  
Juan M Castillo ◽  
Juan M Pascale ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Reverse Transcriptase ◽  
Treatment Resistance ◽  
Resistance Mutations ◽  
Reverse Transcriptase Inhibitors ◽  
Nucleoside Reverse Transcriptase Inhibitors ◽  
Hiv Drug Resistance ◽  
Drug Resistance Mutations ◽  
Oxford Nanopore ◽  
Pre Treatment

ABSTRACTDetermination of HIV drug resistance (HIVDR) is becoming an integral baseline HIV evaluation for newly infected subjects, as the level of pre-treatment resistance is increasing worldwide. Until now, the gold standard for monitoring ART mutations is the Sanger sequencing method, however, next-generation sequencing technologies (NGS) because high-throughput capability, are gaining attention as a method for detection of HIVDR. In the present work, we evaluated the use of the Oxford Nanopore Technologies (ONT) MinION as an alternative method for detection of drug resistance mutations in pre-treatment HIV positive subjects.We evaluate 36 samples taken during November 2016 from treatment naïve subjects with age greater than 18 years old, who went to the lab for their first HIV monitoring. To evaluate the agreement between Sanger and MinION generated sequences, we aligned the sequences (∼1200bp) with muscle v. 3.8.31. Then we counted the differences and calculated the p-distance of the obtained sequences, comparing paired sequences and grouping Sanger and MinION obtained sequences. The percentage of similarity among each sequence was also evaluated.All samples were submitted to the Standford University HIV drug resistance database (HIVdb version 8.4). Then we compared the resistance predictions obtained from the sequences generated by Sanger and MinION methods.Results: The median of available pores was 1314 for the first run, 1215 for the second run, and 536 for the third run. After 3 hours with SQK-NSK007 a total of 18803 2D reads were base-called and in 16577 reads (88%) a barcode was detected.Comparing the nucleotide differences of each sample, we observed that 23 (74%) samples had identical sequence, for the other samples the percentage of identity among each analyzed sequence was greater than 95%. A good positive predictive value (100%) in the estimation of drug resistance mutations in the groups of protease inhibitors (PI), nucleoside reverse transcriptase inhibitors (NRTIs), and non-nucleoside reverse transcriptase inhibitors (NNRTIs).We present an approach for the analysis of HIV reads generated with MinION ONT, further studies are guaranteed before the application of this methodology in clinical settings to assess its suitability for HIVDR testing.

scholarly journals PREVALENCE OF DRUG RESISTANT HIV STRAINS IN HIV-INFECTED PATIENTS OF REPRODUCTIVE AGE

2016 ◽  
Vol 72 (2) ◽  
pp. 8-13
Author(s):  
N. Babii
Keyword(s):  
Reverse Transcriptase ◽  
Reproductive Age ◽  
Drug Resistant ◽  
Resistance Mutations ◽  
Reverse Transcriptase Inhibitors ◽  
Nonnucleoside Reverse Transcriptase Inhibitors ◽  
High Prevalence ◽  
High Level ◽  
Drug Resistant Strains ◽  
Level Resistance

The prevalence of drug resistant HIV strains among HIV-positive reproductive aged persons with ineffective antiretroviral therapy (ART) was assessed. The prevalence of drug resistant strains of HIV was 73.8% in the group of women and 89.29% in the group of men (totally in 80.0% of patients). In the spectrum of drug resistance mutations (DRMs) the most prevalent mutation associated with high-level resistance to nucleoside reverse transcriptase inhibitors was substitution M184V (80.36%); in addition, the high prevalence of K65R (26.79%) was indicated. The most common mutations causing a high-level resistance to nonnucleoside reverse transcriptase inhibitors were G190S/A (57.14%), Y181C (37.50%), K101E (33.93%). The DRMs to protease inhibitors were indicated with significantly less frequent (5.36%).

Evaluation of a novel in-house HIV-1 genotype drug resistance assay using clinical samples in China

2021 ◽  
Vol 19 ◽  
Author(s):  
Peijie Gao ◽  
Fengting Yu ◽  
Xiaozhen Yang ◽  
Dan Li ◽  
Yalun Shi ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Reverse Transcriptase ◽  
High Efficiency ◽  
Clinical Samples ◽  
Genotype Distribution ◽  
Resistance Mutations ◽  
Reverse Transcriptase Inhibitors ◽  
Nucleoside Reverse Transcriptase Inhibitors ◽  
Subtype B ◽  
Hiv 1

Background: HIV drug resistance poses a major challenge for anti-retroviral treatment (ART) and the prevention and control of HIV epidemic. Objective: The study aims to establish a novel in-house assay with high efficiency, named AP in-house method, that would be suitable for HIV-1 drug resistance detection in China. Methods: An in-house HIV-1 genotyping method was used to sequence the partial pol gene from 60 clinical plasma samples; the results of our test were compared with a commercial ViroSeq HIV-1 genotyping system. Results : Among sixty samples, 58(96.7%) were successfully amplified by AP in-house method, five of them harbored viral load below 1,000 copies/ml. The genotype distribution was 43.1% CRF07_BC (25/58), 39.7% CRF01_AE (23/58), 6.9% CRF55_01B (4/58), 5.2% subtype B (3/58) and 5.2% CRF08_BC (3/58). Compared with that of the ViroSeq system, the consistent rate of these nucleotides and amino acids obtained by AP in-house method was up to 99.5 ± 0.4% and 99.5 ± 0.4%, respectively. A total of 290 HIV-1 drug resistance mutations were identified by two methods, including 126 nucleoside reverse transcriptase inhibitors (NRTIs), 145 non-nucleoside reverse transcriptase inhibitors (NNRTIs) and 19 protease inhibitors (PIs) resistance mutations. Out of them, 94.1% (273/290) were completely concordant between the AP in-house method and the ViroSeq system. Conclusion: Overall, the evaluation of AP in-house method provided comparable results to those of the ViroSeq system on diversified HIV-1 subtypes in China.

scholarly journals Non-Nucleoside Reverse Transcriptase Inhibitors Join Forces with Integrase Inhibitors to Combat HIV

2020 ◽  
Vol 13 (6) ◽  
pp. 122
Author(s):  
Daniel M. Himmel ◽  
Eddy Arnold
Keyword(s):  
Reverse Transcriptase ◽  
Immune Deficiency Syndrome ◽  
Deficiency Syndrome ◽  
Strand Transfer ◽  
Hiv Integrase ◽  
Resistance Mutations ◽  
Reverse Transcriptase Inhibitors ◽  
Nucleoside Reverse Transcriptase Inhibitors ◽  
Novel Treatments ◽  
Wide Range

In the treatment of acquired immune deficiency syndrome (AIDS), the diarylpyrimidine (DAPY) analogs etravirine (ETR) and rilpivirine (RPV) have been widely effective against human immunodeficiency virus (HIV) variants that are resistant to other non-nucleoside reverse transcriptase inhibitors (NNRTIs). With non-inferior or improved efficacy, better safety profiles, and lower doses or pill burdens than other NNRTIs in the clinic, combination therapies including either of these two drugs have led to higher adherence than other NNRTI-containing treatments. In a separate development, HIV integrase strand transfer inhibitors (INSTIs) have shown efficacy in treating AIDS, including raltegravir (RAL), elvitegravir (EVG), cabotegravir (CAB), bictegravir (BIC), and dolutegravir (DTG). Of these, DTG and BIC perform better against a wide range of resistance mutations than other INSTIs. Nevertheless, drug-resistant combinations of mutations have begun to emerge against all DAPYs and INSTIs, attributable in part to non-adherence. New dual therapies that may promote better adherence combine ETR or RPV with an INSTI and have been safer and non-inferior to more traditional triple-drug treatments. Long-acting dual- and triple-therapies combining ETR or RPV with INSTIs are under study and may further improve adherence. Here, highly resistant emergent mutations and efficacy data on these novel treatments are reviewed. Overall, ETR or RPV, in combination with INSTIs, may be treatments of choice as long-term maintenance therapies that optimize efficacy, adherence, and safety.

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