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Agrawal K, Kumar S. Wavelet Collocation Method for HIV-1/HTLV-I Co-Infection Model Using Hermite Polynomial. Adv Biol (Weinh) 2024:e2300629. [PMID: 39123297 DOI: 10.1002/adbi.202300629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/17/2024] [Indexed: 08/12/2024]
Abstract
In this study, the dynamic behavior of fractional order co-infection model with human immunodeficiency virus type 1 (HIV-1) and human T-lymphotropic virus type I (HTLV-I) is analyzed using operational matrix of Hermite wavelet collocation method. Also, the uniqueness and existence of solutions are calculated based on the fixed point hypothesis. For the fractional order co-infection model, its positivity and boundedness are demonstrated. Furthermore, different types of Ulam-Hyres stability are also discussed. The numerical solution of the model are obtained by using the operational matrix of the Hermite wavelet approach. This scheme is used to solve the system of nonlinear equations that are very fruitful and easy to implement. Additionally, the stability analysis of the numerical scheme is explained. The mathematical model taken in this work incorporates the biological characteristics of both HIV-1 and HTLV-I. After that all the equilibrium points of the fractional order co-infection model are found and their existence conditions are explored with the help of the Caputo derivative. The global stability of all equilibrium points of this model are determined with the help of Lyapunov functions and the LaSalle invariance principle. Convergence analysis is also discussed. Hermite wavelet operational matrix methods are more accurate and convergent than other numerical methods. Lastly, variations in model dynamics are found when examining different fractional order values. These findings will be valuable to biologists in the treatment of HIV-1/HTLV-I.
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Affiliation(s)
- Khushbu Agrawal
- Department of Mathematics, National Institute of Technology, Jamshedpur, Jharkhand, 831014, India
| | - Sunil Kumar
- Department of Mathematics, National Institute of Technology, Jamshedpur, Jharkhand, 831014, India
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2
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Umumararungu T, Nyandwi JB, Katandula J, Twizeyimana E, Claude Tomani J, Gahamanyi N, Ishimwe N, Olawode EO, Habarurema G, Mpenda M, Uyisenga JP, Saeed SI. Current status of the small molecule anti-HIV drugs in the pipeline or recently approved. Bioorg Med Chem 2024; 111:117860. [PMID: 39094527 DOI: 10.1016/j.bmc.2024.117860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
Human Immunodeficiency Virus (HIV) is the causative agent of Acquired Immunodeficiency Syndrome (AIDS) with high morbidity and mortality rates. Treatment of AIDS/HIV is being complicated by increasing resistance to currently used antiretroviral (ARV) drugs, mainly in low- and middle-income countries (LMICs) due to drug misuse, poor drug supply and poor treatment monitoring. However, progress has been made in the development of new ARV drugs, targeting different HIV components (Fig. 1). This review aims at presenting and discussing the progress made towards the discovery of new ARVs that are at different stages of clinical trials as of July 2024. For each compound, the mechanism of action, target biomolecule, genes associated with resistance, efficacy and safety, class, and phase of clinical trial are discussed. These compounds include analogues of nucleoside reverse transcriptase inhibitors (NRTIs) - islatravir and censavudine; non-nucleoside reverse transcriptase inhibitors (NNRTIs) - Rilpivirine, elsulfavirine and doravirine; integrase inhibitors namely cabotegravir and dolutegravir and chemokine coreceptors 5 and 2 (CC5/CCR2) antagonists for example cenicriviroc. Also, fostemsavir is being developed as an attachment inhibitor while lenacapavir, VH4004280 and VH4011499 are capsid inhibitors. Others are maturation inhibitors such as GSK-254, GSK3532795, GSK3739937, GSK2838232, and other compounds labelled as miscellaneous (do not belong to the classical groups of anti-HIV drugs or to the newer classes) such as obefazimod and BIT225. There is a considerable progress in the development of new anti-HIV drugs and the effort will continue since HIV infections has no cure or vaccine till now. Efforts are needed to reduce the toxicity of available drugs or discover new drugs with new classes which can delay the development of resistance.
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Affiliation(s)
- Théoneste Umumararungu
- Department of Industrial Pharmacy, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda.
| | - Jean Baptiste Nyandwi
- Department of Pharmacology and Toxicology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda; East African Community Regional Centre of Excellence for Vaccines, Immunization and Health Supply Chain Management, Kigali, Rwanda
| | - Jonathan Katandula
- Department of Pharmacology and Toxicology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda
| | - Eric Twizeyimana
- Department of Physiology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda
| | - Jean Claude Tomani
- Department of Chemistry, School of Science, College of Science and Technology, University of Rwanda, Rwanda
| | - Noël Gahamanyi
- Department of Biology, School of Science, College of Science and Technology, University of Rwanda, Rwanda
| | - Nestor Ishimwe
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Emmanuel Oladayo Olawode
- Department of Pharmaceutical Sciences, College of Pharmacy, Larkin University, 18301 N Miami Ave #1, Miami, FL 33169, USA
| | - Gratien Habarurema
- Department of Chemistry, School of Science, College of Science and Technology, University of Rwanda, Rwanda
| | - Matabishi Mpenda
- Department of Pharmacology and Toxicology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda
| | - Jeanne Primitive Uyisenga
- Department of Biology, School of Science, College of Science and Technology, University of Rwanda, Rwanda
| | - Shamsaldeen Ibrahim Saeed
- Faculty of Veterinary Science, University of Nyala, P.O. Box: 155, Nyala, Sudan; Nanotechnology in Veterinary Medicine (NanoVet) Research Group, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kelantan 16100, Pengkalan Chepa, Malaysia
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3
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Garduño-Juárez R, Tovar-Anaya DO, Perez-Aguilar JM, Lozano-Aguirre Beltran LF, Zubillaga RA, Alvarez-Perez MA, Villarreal-Ramirez E. Molecular Dynamic Simulations for Biopolymers with Biomedical Applications. Polymers (Basel) 2024; 16:1864. [PMID: 39000719 PMCID: PMC11244511 DOI: 10.3390/polym16131864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/13/2024] [Accepted: 04/13/2024] [Indexed: 07/17/2024] Open
Abstract
Computational modeling (CM) is a versatile scientific methodology used to examine the properties and behavior of complex systems, such as polymeric materials for biomedical bioengineering. CM has emerged as a primary tool for predicting, setting up, and interpreting experimental results. Integrating in silico and in vitro experiments accelerates scientific advancements, yielding quicker results at a reduced cost. While CM is a mature discipline, its use in biomedical engineering for biopolymer materials has only recently gained prominence. In biopolymer biomedical engineering, CM focuses on three key research areas: (A) Computer-aided design (CAD/CAM) utilizes specialized software to design and model biopolymers for various biomedical applications. This technology allows researchers to create precise three-dimensional models of biopolymers, taking into account their chemical, structural, and functional properties. These models can be used to enhance the structure of biopolymers and improve their effectiveness in specific medical applications. (B) Finite element analysis, a computational technique used to analyze and solve problems in engineering and physics. This approach divides the physical domain into small finite elements with simple geometric shapes. This computational technique enables the study and understanding of the mechanical and structural behavior of biopolymers in biomedical environments. (C) Molecular dynamics (MD) simulations involve using advanced computational techniques to study the behavior of biopolymers at the molecular and atomic levels. These simulations are fundamental for better understanding biological processes at the molecular level. Studying the wide-ranging uses of MD simulations in biopolymers involves examining the structural, functional, and evolutionary aspects of biomolecular systems over time. MD simulations solve Newton's equations of motion for all-atom systems, producing spatial trajectories for each atom. This provides valuable insights into properties such as water absorption on biopolymer surfaces and interactions with solid surfaces, which are crucial for assessing biomaterials. This review provides a comprehensive overview of the various applications of MD simulations in biopolymers. Additionally, it highlights the flexibility, robustness, and synergistic relationship between in silico and experimental techniques.
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Affiliation(s)
- Ramón Garduño-Juárez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - David O Tovar-Anaya
- Laboratorio de Bioingeniería de Tejidos, División de Estudios de Posgrado e Investigación, Coyoacán 04510, Mexico
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | | | - Rafael A Zubillaga
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City 09340, Mexico
| | - Marco Antonio Alvarez-Perez
- Laboratorio de Bioingeniería de Tejidos, División de Estudios de Posgrado e Investigación, Coyoacán 04510, Mexico
| | - Eduardo Villarreal-Ramirez
- Laboratorio de Bioingeniería de Tejidos, División de Estudios de Posgrado e Investigación, Coyoacán 04510, Mexico
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Ferreiro D, Khalil R, Sousa SF, Arenas M. Substitution Models of Protein Evolution with Selection on Enzymatic Activity. Mol Biol Evol 2024; 41:msae026. [PMID: 38314876 PMCID: PMC10873502 DOI: 10.1093/molbev/msae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024] Open
Abstract
Substitution models of evolution are necessary for diverse evolutionary analyses including phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical substitution models are traditionally used due to their simplicity, but they ignore the variability of substitution patterns among protein sites. Next, in order to improve the realism of the modeling of protein evolution, a series of structurally constrained substitution models were presented, but still they usually ignore constraints on the protein activity. Here, we present a substitution model of protein evolution with selection on both protein structure and enzymatic activity, and that can be applied to phylogenetics. In particular, the model considers the binding affinity of the enzyme-substrate complex as well as structural constraints that include the flexibility of structural flaps, hydrogen bonds, amino acids backbone radius of gyration, and solvent-accessible surface area that are quantified through molecular dynamics simulations. We applied the model to the HIV-1 protease and evaluated it by phylogenetic likelihood in comparison with the best-fitting empirical substitution model and a structurally constrained substitution model that ignores the enzymatic activity. We found that accounting for selection on the protein activity improves the fitting of the modeled functional regions with the real observations, especially in data with high molecular identity, which recommends considering constraints on the protein activity in the development of substitution models of evolution.
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Affiliation(s)
- David Ferreiro
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, 36310 Vigo, Spain
| | - Ruqaiya Khalil
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, 36310 Vigo, Spain
| | - Sergio F Sousa
- UCIBIO/REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal
| | - Miguel Arenas
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, 36310 Vigo, Spain
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5
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Rajendran M, Ferran MC, Mouli L, Babbitt GA, Lynch ML. Evolution of drug resistance drives destabilization of flap region dynamics in HIV-1 protease. BIOPHYSICAL REPORTS 2023; 3:100121. [PMID: 37662576 PMCID: PMC10469570 DOI: 10.1016/j.bpr.2023.100121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023]
Abstract
The HIV-1 protease is one of several common key targets of combination drug therapies for human immunodeficiency virus infection and acquired immunodeficiency syndrome. During the progression of the disease, some individual patients acquire drug resistance due to mutational hotspots on the viral proteins targeted by combination drug therapies. It has recently been discovered that drug-resistant mutations accumulate on the "flap region" of the HIV-1 protease, which is a critical dynamic region involved in nonspecific polypeptide binding during invasion and infection of the host cell. In this study, we utilize machine learning-assisted comparative molecular dynamics, conducted at single amino acid site resolution, to investigate the dynamic changes that occur during functional dimerization and drug binding of wild-type and common drug-resistant versions of the main protease. We also use a multiagent machine learning model to identify conserved dynamics of the HIV-1 main protease that are preserved across simian and feline protease orthologs. We find that a key conserved functional site in the flap region, a solvent-exposed isoleucine (Ile50) that controls flap dynamics is functionally targeted by drug resistance mutations, leading to amplified molecular dynamics affecting the functional ability of the flap region to hold the drugs. We conclude that better long-term patient outcomes may be achieved by designing drugs that target protease regions that are less dependent upon single sites with large functional binding effects.
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Affiliation(s)
- Madhusudan Rajendran
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Maureen C. Ferran
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Leora Mouli
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Gregory A. Babbitt
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
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Kramer L, Sarkar A, Foderaro T, Markley AL, Lee J, Edstrom H, Sharma S, Gill E, Traylor MJ, Fox JM. Genetically Encoded Detection of Biosynthetic Protease Inhibitors. ACS Synth Biol 2023; 12:83-94. [PMID: 36574400 PMCID: PMC10072156 DOI: 10.1021/acssynbio.2c00384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Proteases are an important class of drug targets that continue to drive inhibitor discovery. These enzymes are prone to resistance mutations, yet their promise for treating viral diseases and other disorders continues to grow. This study develops a general approach for detecting microbially synthesized protease inhibitors and uses it to screen terpenoid pathways for inhibitory compounds. The detection scheme relies on a bacterial two-hybrid (B2H) system that links protease inactivation to the transcription of a swappable reporter gene. This system, which can accomodate multiple biochemical outputs (i.e., luminescence and antibiotic resistance), permitted the facile incorporation of four disease-relevant proteases. A B2H designed to detect the inactivation of the main protease of severe acute respiratory syndrome coronavirus 2 enabled the identification of a terpenoid inhibitor of modest potency. An analysis of multiple pathways that make this terpenoid, however, suggested that its production was necessary but not sufficient to confer a survival advantage in growth-coupled assays. This finding highlights an important challenge associated with the use of genetic selection to search for inhibitors─notably, the influence of pathway toxicity─and underlines the value of including multiple pathways with overlapping product profiles in pathway screens. This study provides a detailed experimental framework for using microbes to screen libraries of biosynthetic pathways for targeted protease inhibitors.
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Affiliation(s)
- Levi Kramer
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
| | - Ankur Sarkar
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
| | - Tom Foderaro
- Think Bioscience, Inc., 1945 Colorado Avenue, Boulder, Colorado80309, United States
| | - Andrew L Markley
- Think Bioscience, Inc., 1945 Colorado Avenue, Boulder, Colorado80309, United States
| | - Jessica Lee
- Think Bioscience, Inc., 1945 Colorado Avenue, Boulder, Colorado80309, United States
| | - Hannah Edstrom
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
| | - Shajesh Sharma
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
| | - Eden Gill
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
| | - Matthew J Traylor
- Think Bioscience, Inc., 1945 Colorado Avenue, Boulder, Colorado80309, United States
| | - Jerome M Fox
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
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7
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Sreedharan V, Rao KB. Protease inhibitors as a potential agent against visceral Leishmaniasis: A review to inspire future study. Braz J Infect Dis 2023; 27:102739. [PMID: 36603827 PMCID: PMC9871078 DOI: 10.1016/j.bjid.2022.102739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/21/2022] [Accepted: 12/16/2022] [Indexed: 01/04/2023] Open
Abstract
Leishmaniasis is transmitted by sandfly which carries the intracellular protozoa in their midgut. Among visceral, cutaneous and mucocutaneous leishmaniasis, visceral type that is caused by Leishmania donovani is the most lethal one. Findings of leishmanial structure and species took place in 19th century and was initiated by Donovan. Leishmaniasis is still a major concern of health issues in many endemic countries in Asia, Africa, the Americas, and the Mediterranean region. Worldwide1.5-2 million new cases of cutaneous leishmaniasis and 500,000 cases of visceral leishmaniasis are reported each year. Leishmaniasis is endemic in nearly 90 countries worldwide and close to 12 million new cases of leishmaniasis are reported worldwide annually. Studies on antileishmanial drug development is of major concern as leishmaniasis are the second largest parasitic killer in the world and the available drugs are either toxic or costly. The major surface GP63 protease, also known as Zinc- metalloproteases present on the surface of leishmanial promastigotes, can be targeted for drug development. Protease inhibitors targeting such surface proteases show promising results. Different protease inhibitors have been isolated from marine actinobacteria against many infectious diseases. Metabolites produced by these actinobacteria may have greater importance for the discovery and development of new antileishmanial drugs. Hence, this review discusses the background, current situation, treatment, and protease inhibitors from marine actinobacteria for drug development against GP63 molecules.
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Affiliation(s)
| | - K.V. Bhaskara Rao
- Corresponding author at: Department of Biomedical Sciences, School of BioSciences and Technology, VIT University, Vellore, Tamil Nadu, 632 014, India.
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Hu L, Li Z, Tang Z, Zhao C, Zhou X, Hu P. Effectively predicting HIV-1 protease cleavage sites by using an ensemble learning approach. BMC Bioinformatics 2022; 23:447. [PMID: 36303135 PMCID: PMC9608884 DOI: 10.1186/s12859-022-04999-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background The site information of substrates that can be cleaved by human immunodeficiency virus 1 proteases (HIV-1 PRs) is of great significance for designing effective inhibitors against HIV-1 viruses. A variety of machine learning-based algorithms have been developed to predict HIV-1 PR cleavage sites by extracting relevant features from substrate sequences. However, only relying on the sequence information is not sufficient to ensure a promising performance due to the uncertainty in the way of separating the datasets used for training and testing. Moreover, the existence of noisy data, i.e., false positive and false negative cleavage sites, could negatively influence the accuracy performance. Results In this work, an ensemble learning algorithm for predicting HIV-1 PR cleavage sites, namely EM-HIV, is proposed by training a set of weak learners, i.e., biased support vector machine classifiers, with the asymmetric bagging strategy. By doing so, the impact of data imbalance and noisy data can thus be alleviated. Besides, in order to make full use of substrate sequences, the features used by EM-HIV are collected from three different coding schemes, including amino acid identities, chemical properties and variable-length coevolutionary patterns, for the purpose of constructing more relevant feature vectors of octamers. Experiment results on three independent benchmark datasets demonstrate that EM-HIV outperforms state-of-the-art prediction algorithm in terms of several evaluation metrics. Hence, EM-HIV can be regarded as a useful tool to accurately predict HIV-1 PR cleavage sites.
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Affiliation(s)
- Lun Hu
- grid.9227.e0000000119573309Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Ürümqi, China
| | - Zhenfeng Li
- grid.162110.50000 0000 9291 3229School of Computer Science and Artificial Intelligence, Wuhan University of Technology, Wuhan, China
| | - Zehai Tang
- grid.162110.50000 0000 9291 3229School of Computer Science and Artificial Intelligence, Wuhan University of Technology, Wuhan, China
| | - Cheng Zhao
- grid.162110.50000 0000 9291 3229School of Computer Science and Artificial Intelligence, Wuhan University of Technology, Wuhan, China
| | - Xi Zhou
- grid.9227.e0000000119573309Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Ürümqi, China
| | - Pengwei Hu
- grid.9227.e0000000119573309Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Ürümqi, China
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Xu PY, Li XQ, Chen WG, Deng LL, Tan YZ, Zhang Q, Xie SY, Zheng LS. Progress in Antiviral Fullerene Research. NANOMATERIALS 2022; 12:nano12152547. [PMID: 35893515 PMCID: PMC9330071 DOI: 10.3390/nano12152547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022]
Abstract
Unlike traditional small molecule drugs, fullerene is an all-carbon nanomolecule with a spherical cage structure. Fullerene exhibits high levels of antiviral activity, inhibiting virus replication in vitro and in vivo. In this review, we systematically summarize the latest research regarding the different types of fullerenes investigated in antiviral studies. We discuss the unique structural advantage of fullerenes, present diverse modification strategies based on the addition of various functional groups, assess the effect of structural differences on antiviral activity, and describe the possible antiviral mechanism. Finally, we discuss the prospective development of fullerenes as antiviral drugs.
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Affiliation(s)
- Piao-Yang Xu
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; (P.-Y.X.); (Y.-Z.T.); (S.-Y.X.); (L.-S.Z.)
| | - Xiao-Qing Li
- Funano New Material Technology Company Ltd., Xiamen 361110, China; (X.-Q.L.); (W.-G.C.)
| | - Wei-Guang Chen
- Funano New Material Technology Company Ltd., Xiamen 361110, China; (X.-Q.L.); (W.-G.C.)
| | - Lin-Long Deng
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China;
| | - Yuan-Zhi Tan
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; (P.-Y.X.); (Y.-Z.T.); (S.-Y.X.); (L.-S.Z.)
| | - Qianyan Zhang
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; (P.-Y.X.); (Y.-Z.T.); (S.-Y.X.); (L.-S.Z.)
- Correspondence:
| | - Su-Yuan Xie
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; (P.-Y.X.); (Y.-Z.T.); (S.-Y.X.); (L.-S.Z.)
| | - Lan-Sun Zheng
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; (P.-Y.X.); (Y.-Z.T.); (S.-Y.X.); (L.-S.Z.)
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Wang C, Chen L, Wang R, Tang W, Zhao B. Effects of the G48M mutant on the dynamics properties and binding mechanism of PR with SQV and ATV. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2055013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Chao Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, People’s Republic of China
| | - Lin Chen
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, People’s Republic of China
| | - Ruige Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, People’s Republic of China
| | - Wanxia Tang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, People’s Republic of China
| | - Bing Zhao
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, People’s Republic of China
- Heilongjiang Provincial Key Laboratory of Surface Active Agent and Auxiliary, Qiqihar, People’s Republic of China
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The role of pharmacogenetics in Efficacy and safety of protease inhibitor based therapy in human immunodeficiency virus type (HIV) infection. ACTA BIOMEDICA SCIENTIFICA 2021. [DOI: 10.29413/abs.2021-6.6-2.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Antiretroviral therapy has markedly reduced morbidity and mortality for persons living with human immunodeficiency virus (HIV). HIV can now be classified as a chronic disease; until a cure is found, patients are likely to require life-long therapy. However, despite these undoubted advances, there are many issues that need to be resolved, including the problems associated with long-term efficacy and toxicity. Moreover, pharmacotherapy of patients infected with HIV is challenging because a great number of comorbidities increase polypharmacy and the risk for drug-drug interactions. There is considerable interindividual variability in patient outcomes in terms of drug disposition, drug efficacy and adverse events. The basis of these differences is multifactorial, but host genetics are believed to play a significant part. HIV-infected population consists of ethnically diverse individuals on complex and potentially toxic antiretroviral regimens on a long-term basis. These individuals would benefit greatly from predictive tests that identify the most durable regimens. Pharmacogenetics holds that promise. Thus, detailed understanding of the metabolism and transport of antiretrovirals and the influence of genetics on these pathways is important. To this end, this review provides an up-to-date overview of the metabolism of antiHIV therapeutics of the protease inhibitors Lopinavir and Ritonavir and the impact of genetic variation in drug metabolism and transport on the treatment of HIV.
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12
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Nanopore detects γ-radiation inhibited HIV-1 protease activity. Biosens Bioelectron 2021; 194:113602. [PMID: 34481241 DOI: 10.1016/j.bios.2021.113602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/16/2021] [Accepted: 08/28/2021] [Indexed: 12/28/2022]
Abstract
Inhibition of HIV-1 protease (PR) activity is realized by exposure to 60Co γ-radiation. The radiation effects on enzyme kinetics of HIV-1 PR are subsequently monitored using nanopore sensor. Substantial loss of proteolytic efficiency towards GagPol polypeptide is observed due to the radiation treatment. Results shows ~50% of GagPol polypeptide was not involved in HIV-1 PR proteolysis by exposure to ultra-low intensity of γ-radiation (0.1K Gy), and the values reach to over 90% with high γ-ray treatment. Besides, the inactivation effect is also verified in blood samples which contain the virus protease. Our finding provides the potential benefits of γ-radiation to inactivate viral proteinic function, and might be a complementary to the designation of HIV-1 PR inhibitors.
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Bauso LV, Imbesi C, Irene G, Calì G, Bitto A. New Approaches and Repurposed Antiviral Drugs for the Treatment of the SARS-CoV-2 Infection. Pharmaceuticals (Basel) 2021; 14:503. [PMID: 34070359 PMCID: PMC8228036 DOI: 10.3390/ph14060503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/02/2021] [Accepted: 05/08/2021] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes coronavirus disease 2019 (COVID-19). The outbreak of this coronavirus was first identified in Wuhan (Hubei, China) in December 2019, and it was declared as pandemic by the World Health Organization (WHO) in March 2020. Today, several vaccines against SARS-CoV-2 have been approved, and some neutralizing monoclonal antibodies are being tested as therapeutic approaches for COVID-19 but, one of the key questions is whether both vaccines and monoclonal antibodies could be effective against infections by new SARS-CoV-2 variants. Nevertheless, there are currently more than 1000 ongoing clinical trials focusing on the use and effectiveness of antiviral drugs as a possible therapeutic treatment. Among the classes of antiviral drugs are included 3CL protein inhibitors, RNA synthesis inhibitors and other small molecule drugs which target the ability of SARS-COV-2 to interact with host cells. Considering the need to find specific treatment to prevent the emergent outbreak, the aim of this review is to explain how some repurposed antiviral drugs, indicated for the treatment of other viral infections, could be potential candidates for the treatment of COVID-19.
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Affiliation(s)
- Luana Vittoria Bauso
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (L.V.B.); (C.I.); (G.I.); (G.C.)
| | - Chiara Imbesi
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (L.V.B.); (C.I.); (G.I.); (G.C.)
- Laboratori Campisi, Corso Vittorio Emanuele 231, 96012 Avola, Italy
| | - Gasparo Irene
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (L.V.B.); (C.I.); (G.I.); (G.C.)
| | - Gabriella Calì
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (L.V.B.); (C.I.); (G.I.); (G.C.)
| | - Alessandra Bitto
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (L.V.B.); (C.I.); (G.I.); (G.C.)
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14
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Velozo CT, Cabral LM, Pinto EC, de Sousa VP. Lopinavir/Ritonavir: A Review of Analytical Methodologies for the Drug Substances, Pharmaceutical Formulations and Biological Matrices. Crit Rev Anal Chem 2021; 52:1846-1862. [PMID: 34024199 DOI: 10.1080/10408347.2021.1920364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Lopinavir/ritonavir is a potent coformulation of protease inhibitors used against HIV infection. Lopinavir is the main responsible for viral load suppression, whereas ritonavir is a pharmacokinetic enhancer. Both of them have recently gained relevance as candidate drugs against severe coronavirus disease (COVID-19). However, significant beneficial effects were not observed in randomized clinical trials. This review summarizes the main physical-chemical, pharmacodynamic, and pharmacokinetic properties of ritonavir and lopinavir, along with the analytical methodologies applied for biological matrices, pharmaceutical formulations, and stability studies. The work also aimed to provide a comprehensive impurity profile for the combined formulation. Several analytical methods in four different pharmacopeias and 37 articles in literature were evaluated and summarized. Chromatographic methods for these drugs frequently use C8 or C18 stationary phases with acetonitrile and phosphate buffer (with ultraviolet detection) or acetate buffer (with tandem mass spectrometry detection) as the mobile phase. Official compendia methods show disadvantages as extended total run time and complex mobile phases. HPLC tandem-mass spectrometry provided high sensitivity in methodologies applied for human plasma and serum samples, supporting the therapeutic drug monitoring in HIV patients. Ritonavir and lopinavir major degradation products arise in alkaline and acidic environments, respectively. Other non-chromatographic methods were also summarized. Establishing the impurity profile for the combined formulation is challenging due to a large number of impurities reported. Easier and faster analytical methods for impurity assessment are still needed.
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Affiliation(s)
- Carolina Trajano Velozo
- Department of Drugs and Pharmaceutics, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucio Mendes Cabral
- Department of Drugs and Pharmaceutics, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eduardo Costa Pinto
- Department of Drugs and Pharmaceutics, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Valéria Pereira de Sousa
- Department of Drugs and Pharmaceutics, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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15
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The Anti-Cancer Properties of the HIV Protease Inhibitor Nelfinavir. Cancers (Basel) 2020; 12:cancers12113437. [PMID: 33228205 PMCID: PMC7699465 DOI: 10.3390/cancers12113437] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary To this day, cancer remains a medical challenge despite the development of cutting-edge diagnostic methods and therapeutics. Thus, there is a continual demand for improved therapeutic options for managing cancer patients. However, novel drug development requires decade-long time commitment and financial investments. Repurposing approved and market-available drugs for cancer therapy is a way to reduce cost and the timeframe for developing new therapies. Nelfinavir is an anti-infective agent that has extensively been used to treat acquired immunodeficiency syndrome (AIDS) in adult and pediatric patients. In addition to its anti-infective properties, nelfinavir has demonstrated potent off-target anti-cancer effects, suggesting that it could be a suitable candidate for drug repurposing for cancer. In this review, we systematically compiled the therapeutic benefits of nelfinavir against cancer as a single drug or in combination with chemoradiotherapy, and outlined the possible underlying mechanistic pathways contributing to the anti-cancer effects. Abstract Traditional cancer treatments may lose efficacy following the emergence of novel mutations or the development of chemoradiotherapy resistance. Late diagnosis, high-cost of treatment, and the requirement of highly efficient infrastructure to dispense cancer therapies hinder the availability of adequate treatment in low-income and resource-limited settings. Repositioning approved drugs as cancer therapeutics may reduce the cost and timeline for novel drug development and expedite the availability of newer, efficacious options for patients in need. Nelfinavir is a human immunodeficiency virus (HIV) protease inhibitor that has been approved and is extensively used as an anti-infective agent to treat acquired immunodeficiency syndrome (AIDS). Yet nelfinavir has also shown anti-cancer effects in in vitro and in vivo studies. The anti-cancer mechanism of nelfinavir includes modulation of different cellular conditions, such as unfolded protein response, cell cycle, apoptosis, autophagy, the proteasome pathway, oxidative stress, the tumor microenvironment, and multidrug efflux pumps. Multiple clinical trials indicated tolerable and reversible toxicities during nelfinavir treatment in cancer patients, either as a monotherapy or in combination with chemo- or radiotherapy. Since orally available nelfinavir has been a safe drug of choice for both adult and pediatric HIV-infected patients for over two decades, exploiting its anti-cancer off-target effects will enable fast-tracking this newer option into the existing repertoire of cancer chemotherapeutics.
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16
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Lawal MM, Sanusi ZK, Govender T, Maguire GE, Honarparvar B, Kruger HG. From Recognition to Reaction Mechanism: An Overview on the Interactions between HIV-1 Protease and its Natural Targets. Curr Med Chem 2020; 27:2514-2549. [DOI: 10.2174/0929867325666181113122900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 11/04/2018] [Accepted: 11/07/2018] [Indexed: 12/28/2022]
Abstract
Current investigations on the Human Immunodeficiency Virus Protease (HIV-1
PR) as a druggable target towards the treatment of AIDS require an update to facilitate further
development of promising inhibitors with improved inhibitory activities. For the past two
decades, up to 100 scholarly reports appeared annually on the inhibition and catalytic mechanism
of HIV-1 PR. A fundamental literature review on the prerequisite of HIV-1 PR action
leading to the release of the infectious virion is absent. Herein, recent advances (both computationally
and experimentally) on the recognition mode and reaction mechanism of HIV-1 PR
involving its natural targets are provided. This review features more than 80 articles from
reputable journals. Recognition of the natural Gag and Gag-Pol cleavage junctions by this
enzyme and its mutant analogs was first addressed. Thereafter, a comprehensive dissect of
the enzymatic mechanism of HIV-1 PR on its natural polypeptide sequences from literature
was put together. In addition, we highlighted ongoing research topics in which in silico
methods could be harnessed to provide deeper insights into the catalytic mechanism of the
HIV-1 protease in the presence of its natural substrates at the molecular level. Understanding
the recognition and catalytic mechanism of HIV-1 PR leading to the release of an infective
virion, which advertently affects the immune system, will assist in designing mechanismbased
inhibitors with improved bioactivity.
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Affiliation(s)
- Monsurat M. Lawal
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Zainab K. Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Glenn E.M. Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
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17
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Cuesta SA, Mora JR, Zambrano CH, Torres FJ, Rincón L. Comparative study of the nucleophilic attack step in the proteases catalytic activity: A theoretical study. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1705412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Sebastián A. Cuesta
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - José R. Mora
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Cesar H. Zambrano
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - F. Javier Torres
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Luis Rincón
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
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18
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Voshavar C. Protease Inhibitors for the Treatment of HIV/AIDS: Recent Advances and Future Challenges. Curr Top Med Chem 2019; 19:1571-1598. [PMID: 31237209 DOI: 10.2174/1568026619666190619115243] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 02/07/2023]
Abstract
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.
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Affiliation(s)
- Chandrashekhar Voshavar
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, United States
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19
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Mobaraki N, Hemmateenejad B, Weikl TR, Sakhteman A. On the relationship between docking scores and protein conformational changes in HIV-1 protease. J Mol Graph Model 2019; 91:186-193. [DOI: 10.1016/j.jmgm.2019.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/10/2019] [Accepted: 06/14/2019] [Indexed: 11/25/2022]
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20
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Agnello S, Brand M, Chellat MF, Gazzola S, Riedl R. A Structural View on Medicinal Chemistry Strategies against Drug Resistance. Angew Chem Int Ed Engl 2019; 58:3300-3345. [PMID: 29846032 DOI: 10.1002/anie.201802416] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/24/2018] [Indexed: 12/31/2022]
Abstract
The natural phenomenon of drug resistance is a widespread issue that hampers the performance of drugs in many major clinical indications. Antibacterial and antifungal drugs are affected, as well as compounds for the treatment of cancer, viral infections, or parasitic diseases. Despite the very diverse set of biological targets and organisms involved in the development of drug resistance, the underlying molecular mechanisms have been identified to understand the emergence of resistance and to overcome this detrimental process. Detailed structural information on the root causes for drug resistance is nowadays frequently available, so next-generation drugs can be designed that are anticipated to suffer less from resistance. This knowledge-based approach is essential for fighting the inevitable occurrence of drug resistance.
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Affiliation(s)
- Stefano Agnello
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Michael Brand
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Mathieu F Chellat
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Silvia Gazzola
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
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21
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Agnello S, Brand M, Chellat MF, Gazzola S, Riedl R. Eine strukturelle Evaluierung medizinalchemischer Strategien gegen Wirkstoffresistenzen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201802416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Stefano Agnello
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Michael Brand
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Mathieu F. Chellat
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Silvia Gazzola
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Rainer Riedl
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
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22
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Ganotra GK, Wade RC. Prediction of Drug-Target Binding Kinetics by Comparative Binding Energy Analysis. ACS Med Chem Lett 2018; 9:1134-1139. [PMID: 30429958 PMCID: PMC6231175 DOI: 10.1021/acsmedchemlett.8b00397] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/04/2018] [Indexed: 12/02/2022] Open
Abstract
![]()
A growing
consensus is emerging that optimizing the drug–target
affinity alone under equilibrium conditions does not necessarily translate
into higher potency in vivo and that instead binding kinetic parameters
should be optimized to ensure better efficacy. Therefore, in silico
methods are needed to predict the kinetic parameters and the mechanistic
determinants of drug–protein binding. Here we demonstrate the
application of COMparative BINding Energy (COMBINE) analysis to derive
quantitative structure–kinetics relationships (QSKRs) for the
dissociation rate constants (koff) of
inhibitors of heat shock protein 90 (HSP90) and HIV-1 protease. We
derived protein-specific scoring functions by correlating koff rate constants with a subset of weighted
interaction energy components determined from the energy-minimized
structures of drug–protein complexes. As the QSKRs derived
for these sets of chemically diverse compounds have good predictive
ability and provide insights into important drug–protein interactions
for optimizing koff, COMBINE analysis
offers a promising approach for binding kinetics-guided lead optimization.
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Affiliation(s)
- Gaurav K. Ganotra
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Rebecca C. Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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23
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Hassan S, Srikakulam SK, Chandramohan Y, Thangam M, Muthukumar S, Gayathri Devi PK, Hanna LE. Exploring the conformational landscapes of HIV protease structural ensembles using principal component analysis. Proteins 2018; 86:990-1000. [PMID: 30051500 DOI: 10.1002/prot.25534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 05/15/2018] [Accepted: 06/02/2018] [Indexed: 12/14/2022]
Abstract
HIV protease, an essential enzyme for viral particle maturation, is an important drug target of HIV. Its structural conformation is a key determinant of both biological function as well as efficient binding of protease inhibitor molecules. In the present study we analyzed 471 crystal structures of HIV-1 protease to understand the conformational changes induced by mutations or binding of various ligands and substrates. We performed principal component analysis on the ensembles of the HIV-1 protease structures to explore the conformational landscapes. The study identified structural differences between drug resistant and drug sensitive protease structures. Conformational changes were identified in the A and B chains of homo-dimeric HIV protease structures having different combinations of mutations, and also rigidity in the binding conformation of HIV drugs within the active site of the protein.© 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Sameer Hassan
- Department of Biomedical Informatics, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | | | - Yuvaraj Chandramohan
- Department of Immunology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600031, India
| | - Manonanthini Thangam
- Bioinformatics Lab, AU-KBC Research Centre, MIT Campus, Anna University, Chromepet, Chennai, India
| | - Soundharrya Muthukumar
- Department of Biomedical Informatics, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - P K Gayathri Devi
- Department of Biomedical Informatics, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Luke Elizabeth Hanna
- Department of Biomedical Informatics, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India.,Department of Clinical Research, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
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24
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Cong Y, Li Y, Jin K, Zhong S, Zhang JZH, Li H, Duan L. Exploring the Reasons for Decrease in Binding Affinity of HIV-2 Against HIV-1 Protease Complex Using Interaction Entropy Under Polarized Force Field. Front Chem 2018; 6:380. [PMID: 30197882 PMCID: PMC6117221 DOI: 10.3389/fchem.2018.00380] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/03/2018] [Indexed: 12/28/2022] Open
Abstract
In this study, the differences of binding patterns between two type HIV (HIV-1 and HIV-2) protease and two inhibitors (darunavir and amprenavir) are analyzed and compared using the newly developed interaction entropy (IE) method for the entropy change calculation combined with the polarized force field. The functional role of protonation states in the two HIV-2 complexes is investigated and our study finds that the protonated OD1 atom of Asp25' in B chain is the optimal choice. Those calculated binding free energies obtained from the polarized force field combined with IE method are significantly consistent with the experimental observed. The bridging water W301 is favorable to the binding of HIV-1 complexes; however, it is unfavorable to the HIV-2 complexes in current study. The volume of pocket, B-factor of Cα atoms and the distance of flap tip in HIV-2 complexes are smaller than that of HIV-1 consistently. These changes may cause localized rearrangement of residues lining their surface and finally result in the different binding mode for the two types HIV. Predicated hot-spot residues (Ala28/Ala28', Ile50/Ile50', and Ile84/Ile84') are nearly same in the four systems. However, the contribution to the free energy of Asp30 residue is more favorable in HIV-1 system than in HIV-2 system. Current study, to some extent, reveals the origin for the decrease in binding affinity of inhibitors against HIV-2 compared with HIV-1 and will provides theoretical guidance for future design of potent dual inhibitors targeting two type HIV protease.
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Affiliation(s)
- Yalong Cong
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Yuchen Li
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Kun Jin
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Susu Zhong
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
- Department of Chemistry, New York University, New York, NY, United States
| | - Hao Li
- School of Physics and Electronics, Shandong Normal University, Jinan, China
- Department of Science and Technology, Shandong Normal University, Jinan, China
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, China
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25
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Madgulkar AR, Bhalekar MR, Kadam AA. Improvement of Oral Bioavailability of Lopinavir Without Co-administration of Ritonavir Using Microspheres of Thiolated Xyloglucan. AAPS PharmSciTech 2018; 19:293-302. [PMID: 28717974 DOI: 10.1208/s12249-017-0834-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 06/11/2017] [Indexed: 11/30/2022] Open
Abstract
Lopinavir is a BCS Class IV drug exhibiting poor bioavailability due to P-gp efflux and limited permeation. The aim of this research was to formulate and characterize microspheres of lopinavir using thiolated xyloglucan (TH-MPs) as carrier to improve its oral bioavailability without co-administration of ritonavir. Thiomeric microspheres were prepared by ionotropic gelation between alginic acid and calcium ions. Interaction studies were performed using Fourier transform infrared spectroscopy (FT-IR). The thiomeric microspheres were characterized for its entrapment efficiency, T80, surface morphology, and mucoadhesion employing in vitro wash off test. The microspheres were optimized by 32 factorial design. The optimized thiomeric microsphere formulation revealed 93.12% entrapment efficiency, time for 80% drug release (T80) of 358.1 min, and 88% mucoadhesion after 1 h. The permeation of lopinavir from microspheres was enhanced 3.15 times as determined by ex vivo study using everted chick intestine and increased relative bioavailability over 3.22-fold over combination of lopinavir and ritonavir as determined by in vivo study in rat model.
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26
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Lv Y, Li J, Fang J, Jiao X, Yan L, Shan B. Systematic profiling of substrate binding response to multidrug-resistant mutations in HIV-1 protease: Implication for combating drug resistance. J Mol Graph Model 2017; 74:83-88. [PMID: 28371730 DOI: 10.1016/j.jmgm.2017.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 11/30/2022]
Abstract
Human immunodeficiency virus 1 (HIV-1) protease (PR) represents one of the primary targets for developing antiviral agents for the treatment of HIV-infected patients. However, a number of multidrug-resistant mutations in the enzyme have been observed over the past decades, largely limiting the application of PR inhibitors in antiviral therapy. A systematic investigation of the intermolecular interaction between the multidrug-resistant mutants of HIV-1 PR and its substrates would help to establish a complete profile of substrate response to PR mutations and to design new antiviral agents combating drug resistance. Here, we describe an integrative method to profile 6 clinical multidrug-resistant PR mutants against a panel of 16 substrate octapeptides that flank 12 distinct PR cleavage sites in viral precursor polyproteins. It is found that most multidrug-resistant mutations have only a modest or moderate effect on substrate peptide binding, although these mutations would cause a large free energy loss in PR inhibitor binding. Structural analysis reveals that the substrate peptides are loosely bound within PR active pocket to form a wide contact interface between them, and thus mutation of just single or few residues seems not to influence PR-substrate binding considerably. In addition, peptides derived from variable cleavage sites are generally more sensitive to the mutations as compared to those derived from conserved sites, supporting the co-evaluation mechanism of HIV-1 PR and its substrates under drug suppression. We also identify 12 functionally conserved key residues around the enzyme's active site, which play crucial role in substrate recognition. In vitro fluorescence anisotropy assays confirm that wild-type PR can bind substrate peptides ARVL/AEAM and NLAF/PQGE with a moderately high affinity (KD=2 and 16μM, respectively). In contrast, the key residue mutations N25D/D29N can completely eliminate (KD=n.d.) or largely reduce (KD=32 and 120μM, respectively) the binding capability of the two peptides, suggesting that these PR residues could be the potential target sites for developing resistance-free anti-HIV agents.
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Affiliation(s)
- Yonglei Lv
- Henan Red Cross Blood Center, Zhengzhou 450053, PR China
| | - Jianbing Li
- Henan Red Cross Blood Center, Zhengzhou 450053, PR China
| | - Jianhua Fang
- Henan Red Cross Blood Center, Zhengzhou 450053, PR China
| | - Xiufeng Jiao
- Henan Red Cross Blood Center, Zhengzhou 450053, PR China.
| | - Lumin Yan
- Henan Red Cross Blood Center, Zhengzhou 450053, PR China
| | - Baifeng Shan
- Shanxi Provincial Blood Center, Xi'an 710061, PR China
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27
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Matrix Metalloproteinases in the Interstitial Space. Protein Sci 2016. [DOI: 10.1201/9781315374307-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Jain P, Wadhwa PK, Jadhav HR. Design, synthesis and evaluation of acridin-9-yl hydrazide derivatives as BACE-1 inhibitors. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1581-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Humber DC, Bamford MJ, Bethell RC, Cammack N, Orr DC, Storer R, Weingarten GG, Wyatt PG. Synthesis and Structure Activity Relationships of a Series of Penicillin-Derived Pseudosymmetric Inhibitors of HIV-1 Proteinase. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029400500311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The synthesis from penicillin G of a series of potent pseudosymmetric inhibitors 11 a-k of HIV-1 proteinase is described. The 2-pyridyl substituted compounds 11a and 11j showed improved antiviral activity compared to their C2-symmetric counterparts 3 and 4.
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Affiliation(s)
- D. C. Humber
- Departments of Medicinal Chemistry II, Glaxo Group Research Limited, Greenford, Middlesex, UB6 0HE, UK
| | - M. J. Bamford
- Departments of Medicinal Chemistry II, Glaxo Group Research Limited, Greenford, Middlesex, UB6 0HE, UK
| | - R. C. Bethell
- Departments of Virology, Glaxo Group Research Limited, Greenford, Middlesex, UB6 0HE, UK
| | - N. Cammack
- Departments of Virology, Glaxo Group Research Limited, Greenford, Middlesex, UB6 0HE, UK
| | - D. C. Orr
- Departments of Virology, Glaxo Group Research Limited, Greenford, Middlesex, UB6 0HE, UK
| | - R. Storer
- Departments of Medicinal Chemistry II, Glaxo Group Research Limited, Greenford, Middlesex, UB6 0HE, UK
| | - G. G. Weingarten
- Departments of Medicinal Chemistry II, Glaxo Group Research Limited, Greenford, Middlesex, UB6 0HE, UK
| | - P. G. Wyatt
- Departments of Medicinal Chemistry II, Glaxo Group Research Limited, Greenford, Middlesex, UB6 0HE, UK
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30
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Nitschko H, Lindhofer H, Schätzl H, Eberle J, Deby G, Kranz B, von der Helm K. Long-Term Treatment of HIV-Infected MT-4 Cells in Culture with HIV Proteinase Inhibitor RO 31-8959 Leads to Complete Cure of Infection. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029400500405] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
An HIV-infected cell culture was treated with the specific HIV proteinase inhibitor Ro 31-8959 for three months to analyse the antiviral effect and possible cytotoxicity of the drug in long-term treatment. The drug was added 1 h after HIV infection with 0.002 m.o.i. and maintained for 87 days in the cell culture. There was no detectable cell death nor any evidence of HIV production in this time. Cells were proven to be initially infected, since premature drug removal led to a re-emergence of infectious HIV and cell death. However, after 87 days of treatment the drug could be removed safely and HIV was cleared demonstrably from the culture. These data suggest that long-term dosage may be advantageous to the clinical treatment of HIV infection by HIV proteinase inhibitors.
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Affiliation(s)
- H. Nitschko
- Max-von-Pattenkofer Institut, University of Munich, D-80336-Munich, Germany
| | - H. Lindhofer
- Max-von-Pattenkofer Institut, University of Munich, D-80336-Munich, Germany
| | - H. Schätzl
- Max-von-Pattenkofer Institut, University of Munich, D-80336-Munich, Germany
| | - J. Eberle
- Max-von-Pattenkofer Institut, University of Munich, D-80336-Munich, Germany
| | - G. Deby
- Max-von-Pattenkofer Institut, University of Munich, D-80336-Munich, Germany
| | - B. Kranz
- Institut für Immunologie, GSF, Munich, Germany
| | - K. von der Helm
- Max-von-Pattenkofer Institut, University of Munich, D-80336-Munich, Germany
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31
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Hodge CN, Aldrich PE, Fernandez CH, Otto MJ, Rayner MM, Wong YN, Erickson-Viitanen S. Studies on Orally Available Inhibitors of HIV Protease. Peptidyl Aldehydes and Trifluoromethyl Ketones. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029400500407] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Low-molecular-weight peptidyl aldehyde inhibitors of HIV protease that reach in vivo plasma concentrations after oral administration substantiailly in excess of the antiviral IC90 are described. We also report efforts to improve the potency and stability of these compounds that culminated in a series of peptidyl trifluoromethyl ketones with increased potency but decreased bioavailability.
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Affiliation(s)
- C. N. Hodge
- Department of Chemical and Physical Sciences, The DuPont Merck Pharmaceutical Co., Wilmington, DE, 19880, USA
| | - P. E. Aldrich
- Department of Chemical and Physical Sciences, The DuPont Merck Pharmaceutical Co., Wilmington, DE, 19880, USA
| | - C. H. Fernandez
- Department of Chemical and Physical Sciences, The DuPont Merck Pharmaceutical Co., Wilmington, DE, 19880, USA
| | - M. J. Otto
- Department of Virology Research, The DuPont Merck Pharmaceutical Co., Wilmington, DE, 19880, USA
| | - M. M. Rayner
- Department of Virology Research, The DuPont Merck Pharmaceutical Co., Wilmington, DE, 19880, USA
| | - Y. N. Wong
- Department of Drug Metabolism, The DuPont Merck Pharmaceutical Co., Wilmington, DE, 19880, USA
| | - S. Erickson-Viitanen
- Department of Virology Research, The DuPont Merck Pharmaceutical Co., Wilmington, DE, 19880, USA
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32
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Taylor DL, Ahmed PS, Brennan TM, Bridges CG, Tyms AS, Van Dorsselaer V, Tarnus C, Hornsperger JM, Schirlin D. Anti-Human Immunodeficiency Virus Activity, Bioavailability and Drug Resistance Profile of the Novel Proteinase Inhibitor MDL 74,695. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029700800304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
MDL 74,695, a novel dipeptide-like compound containing the ‘difluorostatone type’ transition state mimic and a potent inhibitor of the human immunodeficiency virus (HIV) proteinase, was investigated for anti-HIV activity in vitro. The compound showed selective inhibition of both HIV-1 and HIV-2 in MT-4 cells. A potent antiviral effect against a range of clinical isolates of HIV-1 cultured in human peripheral blood mononuclear cells and primary monocytes was also demonstrated. The antiviral activity of MDL 74,695 against viruses resistant to a range of reverse transcriptase inhibitors was equivalent to the wild-type. In rats MDL 74,695 (30 mg kg−1) was 4.9% orally bioavailable and maintained levels above the in vitro 50% inhibitory concentration (IC50) for approximately 3 h. Viruses with reduced sensitivity to MDL 74,695 and saquinavir were selected in cell culture by continuous passage in increasing drug concentrations, and first appeared after 20 and 17 passages, respectively. Amino acid changes were identified at positions 48 (glycine to valine), 50 (isoleucine to valine) and 82 (valine to either isoleucine or alanine) in various combinations for MDL 74,695-resistant viruses. For saquinavir-resistant viruses changes were identified at positions 48 (glycine to valine) and 90 (leucine to methionine). Studies using MDL 74,695, saquinavir and a third proteinase inhibitor indinavir, indicated that virus selected in the presence of MDL 74,695, with amino acid exchanges at positions 48 and 82 showed cross-resistance to saquinavir. However, viruses selected in the presence of MDL 74,695 with amino acid exchanges at positions 50 and 82 showed no significant change in sensitivity to saquinavir. Likewise, viruses selected in the presence of saquinavir with amino acid exchanges at positions 48 and 90 remained sensitive to MDL 74,695. All viruses selected after growth in the presence of either MDL 74,695 or saquinavir showed little or no resistance to indinavir.
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Affiliation(s)
- DL Taylor
- MRC Collaborative Centre, 1–3 Burtonhole Lane, Mill Hill, London, UK
| | - PS Ahmed
- MRC Collaborative Centre, 1–3 Burtonhole Lane, Mill Hill, London, UK
| | - TM Brennan
- MRC Collaborative Centre, 1–3 Burtonhole Lane, Mill Hill, London, UK
| | - CG Bridges
- MRC Collaborative Centre, 1–3 Burtonhole Lane, Mill Hill, London, UK
| | - AS Tyms
- MRC Collaborative Centre, 1–3 Burtonhole Lane, Mill Hill, London, UK
| | - V Van Dorsselaer
- Marion Merrell Dow Research Institute, 16 rue d'Ankara, 67080 Strasbourg Cedex, France
| | - C Tarnus
- Marion Merrell Dow Research Institute, 16 rue d'Ankara, 67080 Strasbourg Cedex, France
| | - J-M Hornsperger
- Marion Merrell Dow Research Institute, 16 rue d'Ankara, 67080 Strasbourg Cedex, France
| | - D Schirlin
- Marion Merrell Dow Research Institute, 16 rue d'Ankara, 67080 Strasbourg Cedex, France
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33
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Frogier PRT, Tran TT, Viani S, Condom R, Guedj R. Fluorinated Analogues of the p17/p24 Sequence Incorporating 3-fluoro and 3,3-difluoro Phenylalanines as Potential Inhibitors of HIV Protease. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029400500604] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The synthesis and activity of a series of fluorinated peptide analogues of the p17/p24 sequence incorporating 3-fluoro and 3,3-difluoro phenylananines at the P1 position of the scissile bond are described. It was hoped that these might act as potent inhibitors of HIV protease. In fact, none of the compounds studied displayed any anti-HIV activity in vitro. This may be attributed to poor cell penetration of the compounds and metabolic cleavage of their peptide bonds.
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Affiliation(s)
- P. R. T. Frogier
- Laboratoire de Chimie Bio-Organique, Faculté des Sciences, UNSA, BP 71, 06108 Nice, Cedex-2, France
| | - T. T. Tran
- Laboratoire de Chimie Bio-Organique, Faculté des Sciences, UNSA, BP 71, 06108 Nice, Cedex-2, France
| | - S. Viani
- Laboratoire de Chimie Bio-Organique, Faculté des Sciences, UNSA, BP 71, 06108 Nice, Cedex-2, France
| | - R. Condom
- Laboratoire de Chimie Bio-Organique, Faculté des Sciences, UNSA, BP 71, 06108 Nice, Cedex-2, France
| | - R. Guedj
- Laboratoire de Chimie Bio-Organique, Faculté des Sciences, UNSA, BP 71, 06108 Nice, Cedex-2, France
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34
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Interactions of HIV-1 proteins as targets for developing anti-HIV-1 peptides. Future Med Chem 2015; 7:1055-77. [DOI: 10.4155/fmc.15.46] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Protein–protein interactions (PPI) are essential in every step of the HIV replication cycle. Mapping the interactions between viral and host proteins is a fundamental target for the design and development of new therapeutics. In this review, we focus on rational development of anti-HIV-1 peptides based on mapping viral–host and viral–viral protein interactions all across the HIV-1 replication cycle. We also discuss the mechanism of action, specificity and stability of these peptides, which are designed to inhibit PPI. Some of these peptides are excellent tools to study the mechanisms of PPI in HIV-1 replication cycle and for the development of anti-HIV-1 drug leads that modulate PPI.
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35
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Fatemi MH, Heidari A, Gharaghani S. QSAR prediction of HIV-1 protease inhibitory activities using docking derived molecular descriptors. J Theor Biol 2015; 369:13-22. [PMID: 25600056 DOI: 10.1016/j.jtbi.2015.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 01/10/2015] [Accepted: 01/12/2015] [Indexed: 01/30/2023]
Abstract
In this study, application of a new hybrid docking-quantitative structure activity relationship (QSAR) methodology to model and predict the HIV-1 protease inhibitory activities of a series of newly synthesized chemicals is reported. This hybrid docking-QSAR approach can provide valuable information about the most important chemical and structural features of the ligands that affect their inhibitory activities. Docking studies were used to find the actual conformations of chemicals in active site of HIV-1 protease. Then the molecular descriptors were calculated from these conformations. Multiple linear regression (MLR) and least square support vector machine (LS-SVM) were used as QSAR models, respectively. The obtained results reveal that statistical parameters of the LS-SVM model are better than the MLR model, which indicate that there are some non-linear relations between selected molecular descriptors and anti-HIV activities of interested chemicals. The correlation coefficient (R), root mean square error (RMSE) and average absolute error (AAE) for LS-SVM are: R=0.988, RMSE=0.207 and AAE=0.145 for the training set, and R=0.965, RMSE=0.403 and AAE=0.338 for the test set. Leave one out cross validation test was used for assessment of the predictive power and validity of models which led to cross-validation correlation coefficient QUOTE of 0.864 and 0.850 and standardized predicted relative error sum of squares (SPRESS) of 0.553 and 0.581 for LS-SVM and MLR models, respectively.
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Affiliation(s)
- Mohammad H Fatemi
- Chemometrics Laboratory, Faculty of Chemistry, University of Mazandaran, Babolsar 47416-95447, Iran.
| | - Afsane Heidari
- Chemometrics Laboratory, Faculty of Chemistry, University of Mazandaran, Babolsar 47416-95447, Iran
| | - Sajjad Gharaghani
- Department of Bioinformatics, Laboratory of Chemoinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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36
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Liu Q, Wang J, Boyd BJ. Peptide-based biosensors. Talanta 2015; 136:114-27. [PMID: 25702993 DOI: 10.1016/j.talanta.2014.12.020] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 11/26/2014] [Accepted: 12/18/2014] [Indexed: 12/24/2022]
Abstract
Peptides have been used as components in biological analysis and fabrication of novel biosensors for a number of reasons, including mature synthesis protocols, diverse structures and as highly selective substrates for enzymes. Bio-conjugation strategies can provide an efficient way to convert interaction information between peptides and analytes into a measurable signal, which can be used for fabrication of novel peptide-based biosensors. Many sensitive fluorophores can respond rapidly to environmental changes and stimuli manifest as a change in spectral characteristics, hence environmentally-sensitive fluorophores have been widely used as signal markers to conjugate to peptides to construct peptide-based molecular sensors. Additionally, nanoparticles, fluorescent polymers, graphene and near infrared dyes are also used as peptide-conjugated signal markers. On the other hand, peptides may play a generalist role in peptide-based biosensors. Peptides have been utilized as bio-recognition elements to bind various analytes including proteins, nucleic acid, bacteria, metal ions, enzymes and antibodies in biosensors. The selectivity of peptides as an enzymatic substrate has thus been utilized to construct enzyme sensors or enzyme-activity sensors. In addition, progress on immobilization and microarray techniques of peptides has facilitated the progress and commercial application of chip-based peptide biosensors in clinical diagnosis.
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Affiliation(s)
- Qingtao Liu
- Drug Delivery Disposition and Dynamics-Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville 3052, VIC, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville 3052, VIC, Australia
| | - Jinfeng Wang
- Australian Future Fibres Research and Innovation Centre, Institute for Frontier Materials, Deakin University, Geelong 3217, VIC, Australia
| | - Ben J Boyd
- Drug Delivery Disposition and Dynamics-Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville 3052, VIC, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville 3052, VIC, Australia.
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37
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Goldfarb NE, Ohanessian M, Biswas S, McGee TD, Mahon BP, Ostrov DA, Garcia J, Tang Y, McKenna R, Roitberg A, Dunn BM. Defective hydrophobic sliding mechanism and active site expansion in HIV-1 protease drug resistant variant Gly48Thr/Leu89Met: mechanisms for the loss of saquinavir binding potency. Biochemistry 2015; 54:422-33. [PMID: 25513833 PMCID: PMC4303317 DOI: 10.1021/bi501088e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
HIV drug resistance continues to
emerge; consequently, there is
an urgent need to develop next generation antiretroviral therapeutics.1 Here we report on the structural and kinetic
effects of an HIV protease drug resistant variant with the double
mutations Gly48Thr and Leu89Met (PRG48T/L89M), without
the stabilizing mutations Gln7Lys, Leu33Ile, and Leu63Ile. Kinetic
analyses reveal that PRG48T/L89M and PRWT share
nearly identical Michaelis–Menten parameters; however, PRG48T/L89M exhibits weaker binding for IDV (41-fold), SQV (18-fold),
APV (15-fold), and NFV (9-fold) relative to PRWT. A 1.9
Å resolution crystal structure was solved for PRG48T/L89M bound with saquinavir (PRG48T/L89M-SQV) and compared
to the crystal structure of PRWT bound with saquinavir
(PRWT-SQV). PRG48T/L89M-SQV has
an enlarged active site resulting in the loss of a hydrogen bond in
the S3 subsite from Gly48 to P3 of SQV, as well as less favorable
hydrophobic packing interactions between P1 Phe of SQV and the S1
subsite. PRG48T/L89M-SQV assumes a more open conformation
relative to PRWT-SQV, as illustrated by the downward
displacement of the fulcrum and elbows and weaker interatomic flap
interactions. We also show that the Leu89Met mutation disrupts the
hydrophobic sliding mechanism by causing a redistribution of van der
Waals interactions in the hydrophobic core in PRG48T/L89M-SQV. Our mechanism for PRG48T/L89M-SQV drug resistance
proposes that a defective hydrophobic sliding mechanism results in
modified conformational dynamics of the protease. As a consequence,
the protease is unable to achieve a fully closed conformation that
results in an expanded active site and weaker inhibitor binding.
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Affiliation(s)
- Nathan E Goldfarb
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §Departments of Pathology, Immunology, and Laboratory Medicine, University of Florida , Gainesville, Florida 32601-0245, United States
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38
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Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease. Proc Natl Acad Sci U S A 2014; 111:15993-8. [PMID: 25355911 DOI: 10.1073/pnas.1414063111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Drug resistance mutations in response to HIV-1 protease inhibitors are selected not only in the drug target but elsewhere in the viral genome, especially at the protease cleavage sites in the precursor protein Gag. To understand the molecular basis of this protease-substrate coevolution, we solved the crystal structures of drug resistant I50V/A71V HIV-1 protease with p1-p6 substrates bearing coevolved mutations. Analyses of the protease-substrate interactions reveal that compensatory coevolved mutations in the substrate do not restore interactions lost due to protease mutations, but instead establish other interactions that are not restricted to the site of mutation. Mutation of a substrate residue has distal effects on other residues' interactions as well, including through the induction of a conformational change in the protease. Additionally, molecular dynamics simulations suggest that restoration of active site dynamics is an additional constraint in the selection of coevolved mutations. Hence, protease-substrate coevolution permits mutational, structural, and dynamic changes via molecular mechanisms that involve distal effects contributing to drug resistance.
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39
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Yedidi RS, Proteasa G, Martin PD, Liu Z, Vickrey JF, Kovari IA, Kovari LC. A multi-drug resistant HIV-1 protease is resistant to the dimerization inhibitory activity of TLF-PafF. J Mol Graph Model 2014; 53:105-111. [PMID: 25108107 DOI: 10.1016/j.jmgm.2014.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/23/2014] [Accepted: 06/26/2014] [Indexed: 11/25/2022]
Abstract
Human immunodeficiency virus type-1 (HIV-1) protease, a homodimeric aspartyl protease, is a critical drug target in designing anti-retroviral drugs to treat HIV/AIDS. Multidrug-resistant (MDR) clinical isolate-769 HIV-1 protease (PDB ID: 3PJ6) has been shown to exhibit expanded active site cavity with wide-open conformation of flaps (Gly48-Gly52) due to the accumulation of multiple mutations. In this study, an HIV-1 protease dimerization inhibitor (PDI)-TLF-PafF, was evaluated against MDR769 HIV-1 protease using X-ray crystallography. It was hypothesized that co-crystallization of MDR769 HIV-1 protease in complex with TLF-PafF would yield either a monomeric or a disrupted dimeric structure. However, crystal structure of MDR769 I10V HIV-1 protease co-crystallized with TLF-PafF revealed an undisrupted dimeric protease structure (PDB ID: 4NKK) that is comparable to the crystal structure of its corresponding apo-protease (PDB ID: 3PJ6). In order to understand the binding profile of TLF-PafF as a PDI, docking analysis was performed using monomeric protease (prepared from the dimeric crystal structure, PDB ID: 4NKK) as docking receptor. Docking analysis revealed that TLF-PafF binds at the N and C termini (dimerization domain) in a clamp shape for the monomeric wild type receptor but not the MDR769 monomeric receptor. TLF-PafF preferentially showed higher binding affinity to the expanded active site cavity of MDR769 HIV-1 protease than to the termini. Irrespective of binding location, the binding affinity of TLF-PafF against wild type receptor (-6.7kcal/mol) was found to be higher compared to its corresponding binding affinity against MDR receptor (-4.6kcal/mol) suggesting that the MDR769 HIV-1 protease could be resistant to the PDI-activity of TLF-PafF, thus supporting the dimeric crystal structure (PDB ID: 4NKK).
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Affiliation(s)
- Ravikiran S Yedidi
- Queensborough Community College-City University of New York, Bayside, NY 11364, USA
| | - Gheorghe Proteasa
- Queensborough Community College-City University of New York, Bayside, NY 11364, USA
| | - Philip D Martin
- Queensborough Community College-City University of New York, Bayside, NY 11364, USA
| | - Zhigang Liu
- Queensborough Community College-City University of New York, Bayside, NY 11364, USA
| | - John F Vickrey
- Queensborough Community College-City University of New York, Bayside, NY 11364, USA
| | - Iulia A Kovari
- Queensborough Community College-City University of New York, Bayside, NY 11364, USA
| | - Ladislau C Kovari
- Queensborough Community College-City University of New York, Bayside, NY 11364, USA.
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40
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Affiliation(s)
- Mathilde Krim
- The Foundation for AIDS Research, New York, New York
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41
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Reyskens KMSE, Essop MF. HIV protease inhibitors and onset of cardiovascular diseases: a central role for oxidative stress and dysregulation of the ubiquitin-proteasome system. Biochim Biophys Acta Mol Basis Dis 2013; 1842:256-68. [PMID: 24275553 DOI: 10.1016/j.bbadis.2013.11.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/09/2013] [Accepted: 11/18/2013] [Indexed: 12/18/2022]
Abstract
The successful roll-out of highly active antiretroviral therapy (HAART) has extended life expectancy and enhanced the overall well-being of HIV-positive individuals. There are, however, increased concerns regarding HAART-mediated metabolic derangements and its potential risk for cardiovascular diseases (CVD) in the long-term. Here certain classes of antiretroviral drugs such as the HIV protease inhibitors (PIs) are strongly implicated in this process. This article largely focuses on the direct PI-linked development of cardio-metabolic complications, and reviews the inter-linked roles of oxidative stress and the ubiquitin-proteasome system (UPS) as key mediators driving this process. It is proposed that PIs trigger reactive oxygen species (ROS) production that leads to serious downstream consequences such as cell death, impaired mitochondrial function, and UPS dysregulation. Moreover, we advocate that HIV PIs may also directly lower myocardial UPS function. The attenuation of cardiac UPS can initiate transcriptional changes that contribute to perturbed lipid metabolism, thereby fueling a pro-atherogenic milieu. It may also directly alter ionic channels and interfere with electrical signaling in the myocardium. Therefore HIV PI-induced ROS together with a dysfunctional UPS elicit detrimental effects on the cardiovascular system that will eventually result in the onset of heart diseases. Thus while HIV PIs substantially improve life expectancy and quality of life in HIV-positive patients, its longer-term side-effects on the cardiovascular system should lead to a) greater clinical awareness regarding its benefit-harm paradigm, and b) the development and evaluation of novel co-treatment strategies.
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Affiliation(s)
- Kathleen M S E Reyskens
- Cardio-Metabolic Research Group (CMRG), Department of Physiological Sciences, Stellenbosch University, Stellenbosch 7600, South Africa
| | - M Faadiel Essop
- Cardio-Metabolic Research Group (CMRG), Department of Physiological Sciences, Stellenbosch University, Stellenbosch 7600, South Africa.
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42
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Yedidi RS, Muhuhi JM, Liu Z, Bencze KZ, Koupparis K, O'Connor CE, Kovari IA, Spaller MR, Kovari LC. Design, synthesis and evaluation of a potent substrate analog inhibitor identified by scanning Ala/Phe mutagenesis, mimicking substrate co-evolution, against multidrug-resistant HIV-1 protease. Biochem Biophys Res Commun 2013; 438:703-8. [PMID: 23921229 DOI: 10.1016/j.bbrc.2013.07.117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 07/28/2013] [Indexed: 10/26/2022]
Abstract
Multidrug-resistant (MDR) clinical isolate-769, human immunodeficiency virus type-1 (HIV-1) protease (PDB ID: 1TW7), was shown to exhibit wide-open flaps and an expanded active site cavity, causing loss of contacts with protease inhibitors. In the current study, the expanded active site cavity of MDR769 HIV-1 protease was screened with a series of peptide-inhibitors that were designed to mimic the natural substrate cleavage site, capsid/p2. Scanning Ala/Phe chemical mutagenesis approach was incorporated into the design of the peptide series to mimic the substrate co-evolution. Among the peptides synthesized and evaluated, a lead peptide (6a) with potent activity (IC50: 4.4nM) was identified against the MDR769 HIV-1 protease. Isothermal titration calorimetry data showed favorable binding profile for 6a against both wild type and MDR769 HIV-1 protease variants. Nuclear magnetic resonance spectrum of (15)N-labeled MDR769 HIV-1 protease in complex with 6a showed some major perturbations in chemical shift, supporting the peptide induced conformational changes in protease. Modeling analysis revealed multiple contacts between 6a and MDR769 HIV-1 protease. The lead peptide-inhibitor, 6a, with high potency and good binding profile can be used as the basis for developing potent small molecule inhibitors against MDR variants of HIV.
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Affiliation(s)
- Ravikiran S Yedidi
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
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43
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Structural and thermodynamic basis of amprenavir/darunavir and atazanavir resistance in HIV-1 protease with mutations at residue 50. J Virol 2013; 87:4176-84. [PMID: 23365446 DOI: 10.1128/jvi.03486-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Drug resistance occurs through a series of subtle changes that maintain substrate recognition but no longer permit inhibitor binding. In HIV-1 protease, mutations at I50 are associated with such subtle changes that confer differential resistance to specific inhibitors. Residue I50 is located at the protease flap tips, closing the active site upon ligand binding. Under selective drug pressure, I50V/L substitutions emerge in patients, compromising drug susceptibility and leading to treatment failure. The I50V substitution is often associated with amprenavir (APV) and darunavir (DRV) resistance, while the I50L substitution is observed in patients failing atazanavir (ATV) therapy. To explain how APV, DRV, and ATV susceptibility are influenced by mutations at residue 50 in HIV-1 protease, structural and binding thermodynamics studies were carried out on I50V/L-substituted protease variants in the compensatory mutation A71V background. Reduced affinity to both I50V/A71V and I50L/A71V double mutants is largely due to decreased binding entropy, which is compensated for by enhanced enthalpy for ATV binding to I50V variants and APV binding to I50L variants, leading to hypersusceptibility in these two cases. Analysis of the crystal structures showed that the substitutions at residue 50 affect how APV, DRV, and ATV bind the protease with altered van der Waals interactions and that the selection of I50V versus I50L is greatly influenced by the chemical moieties at the P1 position for APV/DRV and the P2 position for ATV. Thus, the varied inhibitor susceptibilities of I50V/L protease variants are largely a direct consequence of the interdependent changes in protease inhibitor interactions.
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44
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Towards tricking a pathogen's protease into fighting infection: the 3D structure of a stable circularly permuted onconase variant cleavedby HIV-1 protease. PLoS One 2013; 8:e54568. [PMID: 23349931 PMCID: PMC3548804 DOI: 10.1371/journal.pone.0054568] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 12/12/2012] [Indexed: 11/19/2022] Open
Abstract
Onconase® is a highly cytotoxic amphibian homolog of Ribonuclease A. Here, we describe the construction of circularly permuted Onconase® variants by connecting the N- and C-termini of this enzyme with amino acid residues that are recognized and cleaved by the human immunodeficiency virus protease. Uncleaved circularly permuted Onconase® variants are unusually stable, non-cytotoxic and can internalize in human T-lymphocyte Jurkat cells. The structure, stability and dynamics of an intact and a cleaved circularly permuted Onconase® variant were determined by Nuclear Magnetic Resonance spectroscopy and provide valuable insight into the changes in catalytic efficiency caused by the cleavage. The understanding of the structural environment and the dynamics of the activation process represents a first step toward the development of more effective drugs for the treatment of diseases related to pathogens expressing a specific protease. By taking advantage of the protease’s activity to initiate a cytotoxic cascade, this approach is thought to be less susceptible to known resistance mechanisms.
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45
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Toshima K. Chemical biology based on target-selective degradation of proteins and carbohydrates using light-activatable organic molecules. ACTA ACUST UNITED AC 2013; 9:834-54. [DOI: 10.1039/c2mb25416f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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46
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Braz ASK, Tufanetto P, Perahia D, Scott LPB. Relation between flexibility and positively selected HIV-1 protease mutants against inhibitors. Proteins 2012; 80:2680-91. [DOI: 10.1002/prot.24151] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 05/31/2012] [Accepted: 07/11/2012] [Indexed: 11/09/2022]
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47
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Zhu Q, Shibata T, Kabashima T, Kai M. Inhibition of HIV-1 protease expression in T cells owing to DNA aptamer-mediated specific delivery of siRNA. Eur J Med Chem 2012; 56:396-9. [PMID: 22907035 DOI: 10.1016/j.ejmech.2012.07.045] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 06/28/2012] [Accepted: 07/25/2012] [Indexed: 10/28/2022]
Abstract
Targeted delivery is a promising way to improve the safety and efficiency of siRNA delivery. We show that a DNA aptamer could be used to deliver siRNA into CD4(+) T cells specifically. The DNA aptamer was obtained from the conversion of a reported RNA aptamer that binds to CD4 protein on the surface of T cells. It was covalently conjugated to the sense strand of the siRNA targeting HIV-1 protease (HIV-PR). The resulting DNA aptamer-siRNA chimera could specifically enter into CD4(+) T cells and efficiently knock down the expression of exogenous HIV-PR gene. This study provides the first evidence that the DNA aptamer with intrinsic stability has a greater potential to be used for siRNA delivery.
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Affiliation(s)
- Qinchang Zhu
- Faculty of Pharmaceutical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-Machi, Nagasaki 852-8521, Japan
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48
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Gadakh SK, Santhosh Reddy R, Sudalai A. Enantioselective synthesis of HIV protease inhibitor amprenavir via Co-catalyzed HKR of 2-(1-azido-2-phenylethyl)oxirane. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.tetasy.2012.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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49
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Venkatakrishnan B, Palii ML, Agbandje-McKenna M, McKenna R. Mining the protein data bank to differentiate error from structural variation in clustered static structures: an examination of HIV protease. Viruses 2012; 4:348-62. [PMID: 22590675 PMCID: PMC3347031 DOI: 10.3390/v4030348] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 02/29/2012] [Accepted: 03/01/2012] [Indexed: 11/22/2022] Open
Abstract
The Protein Data Bank (PDB) contains over 71,000 structures. Extensively studied proteins have hundreds of submissions available, including mutations, different complexes, and space groups, allowing for application of data-mining algorithms to analyze an array of static structures and gain insight about a protein’s structural variation and possibly its dynamics. This investigation is a case study of HIV protease (PR) using in-house algorithms for data mining and structure superposition through generalized formulæ that account for multiple conformations and fractional occupancies. Temperature factors (B-factors) are compared with spatial displacement from the mean structure over the entire study set and separately over bound and ligand-free structures, to assess the significance of structural deviation in a statistical context. Space group differences are also examined.
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50
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Tanimoto S, Sakai S, Kudo E, Okada S, Matsumura S, Takahashi D, Toshima K. Target-Selective Photodegradation of HIV-1 Protease and Inhibition of HIV-1 Replication in Living Cells by Designed Fullerene-Sugar Hybrids. Chem Asian J 2012; 7:911-4. [DOI: 10.1002/asia.201101043] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Indexed: 11/06/2022]
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