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Zhang X, Mei LC, Gao YY, Hao GF, Song BA. Web tools support predicting protein-nucleic acid complexes stability with affinity changes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1781. [PMID: 36693636 DOI: 10.1002/wrna.1781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/10/2022] [Accepted: 11/28/2022] [Indexed: 01/26/2023]
Abstract
Numerous biological processes, such as transcription, replication, and translation, rely on protein-nucleic acid interactions (PNIs). Demonstrating the binding stability of protein-nucleic acid complexes is vital to deciphering the code for PNIs. Numerous web-based tools have been developed to attach importance to protein-nucleic acid stability, facilitating the prediction of PNIs characteristics rapidly. However, the data and tools are dispersed and lack comprehensive integration to understand the stability of PNIs better. In this review, we first summarize existing databases for evaluating the stability of protein-nucleic acid binding. Then, we compare and evaluate the pros and cons of web tools for forecasting the interaction energies of protein-nucleic acid complexes. Finally, we discuss the application of combining models and capabilities of PNIs. We may hope these web-based tools will facilitate the discovery of recognition mechanisms for protein-nucleic acid binding stability. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Xiao Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Long-Can Mei
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan, China
| | - Yang-Yang Gao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan, China
| | - Bao-An Song
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
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Lehman A, Ellis J, Nalintya E, Bahr NC, Loyse A, Rajasingham R. Advanced HIV disease: A review of diagnostic and prophylactic strategies. HIV Med 2023; 24:859-876. [PMID: 37041113 PMCID: PMC10642371 DOI: 10.1111/hiv.13487] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/13/2023] [Indexed: 04/13/2023]
Abstract
BACKGROUND Despite expanded access to antiretroviral therapy (ART) and the rollout of the World Health Organization's (WHO) 'test-and-treat' strategy, the proportion of people with HIV (PWH) presenting with advanced HIV disease (AHD) remains unchanged at approximately 30%. Fifty percent of persons with AHD report prior engagement to care. ART failure and insufficient retention in HIV care are major causes of AHD. People living with AHD are at high risk for opportunistic infections and death. In 2017, the WHO published guidelines for the management of AHD that included a comprehensive package of care for screening and prophylaxis of major opportunistic infections (OIs). In the interim, ART regimens have evolved: integrase inhibitors are first-line therapy globally, and the diagnostic landscape is evolving. The objective of this review is to highlight novel point-of-care (POC) diagnostics and treatment strategies that can facilitate OI screening and prophylaxis for persons with AHD. METHODS We reviewed the WHO guidelines for recommendations for persons with AHD. We summarized the scientific literature on current and emerging diagnostics, along with emerging treatment strategies for persons with AHD. We also highlight the key research and implementation gaps together with potential solutions. RESULTS While POC CD4 testing is being rolled out in order to identify persons with AHD, this alone is insufficient; implementation of the Visitect CD4 platform has been challenging given operational and test interpretation issues. Numerous non-sputum POC TB diagnostics are being evaluated, many with limited sensitivity. Though imperfect, these tests are designed to provide rapid results (within hours) and are relatively affordable for resource-poor settings. While novel POC diagnostics are being developed for cryptococcal infection, histoplasmosis and talaromycosis, implementation science studies are urgently needed to understand the clinical benefit of these tests in the routine care. CONCLUSIONS Despite progress with HIV treatment and prevention, a persistent 20%-30% of PWH present to care with AHD. Unfortunately, these persons with AHD continue to carry the burden of HIV-related morbidity and mortality. Investment in the development of additional POC or near-bedside CD4 platforms is urgently needed. Implementation of POC diagnostics theoretically could improve HIV retention in care and thereby reduce mortality by overcoming delays in laboratory testing and providing patients and healthcare workers with timely same-day results. However, in real-world scenarios, people with AHD have multiple comorbidities and imperfect follow-up. Pragmatic clinical trials are needed to understand whether these POC diagnostics can facilitate timely diagnosis and treatment, thereby improving clinical outcomes such as HIV retention in care.
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Affiliation(s)
- Alice Lehman
- Division of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jayne Ellis
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Nathan C. Bahr
- Division of Infectious Diseases, University of Kansas, Kansas City, Kansas, USA
| | - Angela Loyse
- Division of Infection and Immunity Research Institute, St George’s University of London, London, UK
| | - Radha Rajasingham
- Division of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, Minnesota, USA
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Gupta A, Sun X, Krishnan S, Matoga M, Pierre S, Mcintire K, Koech L, Faesen S, Kityo C, Dadabhai SS, Naidoo K, Samaneka WP, Lama JR, Veloso VG, Mave V, Lalloo U, Langat D, Hogg E, Bisson GP, Kumwenda J, Hosseinipour MC. Isoniazid adherence reduces mortality and incident tuberculosis at 96 weeks among adults initiating antiretroviral therapy with advanced HIV in multiple high burden settings. Open Forum Infect Dis 2022; 9:ofac325. [PMID: 35899273 PMCID: PMC9314898 DOI: 10.1093/ofid/ofac325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/01/2022] [Indexed: 12/01/2022] Open
Abstract
Background People with human immunodeficiency virus (HIV) and advanced immunosuppression initiating antiretroviral therapy (ART) remain vulnerable to tuberculosis (TB) and early mortality. To improve early survival, isoniazid preventive therapy (IPT) or empiric TB treatment have been evaluated; however, their benefit on longer-term outcomes warrants investigation. Methods We present a 96-week preplanned secondary analysis among 850 ART-naive outpatients (≥13 years) enrolled in a multicountry, randomized trial of efavirenz-containing ART plus either 6-month IPT (n = 426) or empiric 4-drug TB treatment (n = 424). Inclusion criteria were CD4 count <50 cells/mm3 and no confirmed or probable TB. Death and incident TB were compared by strategy arm using the Kaplan-Meier method. The impact of self-reported adherence (calculated as the proportion of 100% adherence) was assessed using Cox-proportional hazards models. Results By 96 weeks, 85 deaths and 63 TB events occurred. Kaplan-Meier estimated mortality (10.1% vs 10.5%; P = .86) and time-to-death (P = .77) did not differ by arm. Empiric had higher TB risk (6.1% vs 2.7%; risk difference, −3.4% [95% confidence interval, −6.2% to −0.6%]; P = .02) and shorter time to TB (P = .02) than IPT. Tuberculosis medication adherence lowered the hazards of death by ≥23% (P < .0001) in empiric and ≥20% (P < .035) in IPT and incident TB by ≥17% (P ≤ .0324) only in IPT. Conclusions Empiric TB treatment offered no longer-term advantage over IPT in our population with advanced immunosuppression initiating ART. High IPT adherence significantly lowered death and TB incidence through 96 weeks, emphasizing the benefit of ART plus IPT initiation and completion, in persons with advanced HIV living in high TB-burden, resource-limited settings.
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Affiliation(s)
- Amita Gupta
- Johns Hopkins University , Baltimore, MD , USA
| | - Xim Sun
- Harvard T.H. Chan School of Public Health , Boston, MA , USA
| | | | | | | | | | - Lucy Koech
- Kenya Medical Research Institute (KEMRI)/Walter Reed Project , Kericho , Kenya
| | - Sharlaa Faesen
- Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand , Johannesburg , South Africa
| | - Cissy Kityo
- Joint Clinical Research Centre , Kampala , Uganda
| | - Sufia S Dadabhai
- Johns Hopkins University , Baltimore, MD , USA
- College of Medicine-Johns Hopkins Research Project , Blantyre , Malawi
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA) , Durban , South Africa
- Medical Research Council (MRC)-CAPRISA-HIV-TB Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal Nelson R Mandela School of Medicine , Durban , South Africa
| | | | - Javier R Lama
- Asociacion Civil Impacta Salud y Educacion , Lima , Peru
| | - Valdilea G Veloso
- Instituto Nacional de Infectologia Evandro Chagas/FIOCRUZ , Rio de Janeiro , Brazil
| | - Vidya Mave
- Johns Hopkins University , Baltimore, MD , USA
| | - Umesh Lalloo
- Enhancing Care Foundation, Durban University of Technology , Durban , South Africa
| | - Deborah Langat
- Kenya Medical Research Institute (KEMRI)/Walter Reed Project , Kericho , Kenya
| | - Evelyn Hogg
- Social & Scientific Systems, Inc., a DLH Holdings Company , Silver Spring, MD , USA
| | - Gregory P Bisson
- University of Pennsylvania Perelman School of Medicine , Philadelphia, PA , USA
| | | | - Mina C Hosseinipour
- 3UNC Project , Lilongwe , Malawi
- University of North Carolina at Chapel Hill School of Medicine , Chapel Hill, NC , USA
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