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Fu Y, Bedő J, Papenfuss AT, Rubin AF. Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants. Gigascience 2022; 12:giad073. [PMID: 37721410 PMCID: PMC10506130 DOI: 10.1093/gigascience/giad073] [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: 02/14/2023] [Revised: 07/02/2023] [Accepted: 08/23/2023] [Indexed: 09/19/2023] Open
Abstract
BACKGROUND Evaluating the impact of amino acid variants has been a critical challenge for studying protein function and interpreting genomic data. High-throughput experimental methods like deep mutational scanning (DMS) can measure the effect of large numbers of variants in a target protein, but because DMS studies have not been performed on all proteins, researchers also model DMS data computationally to estimate variant impacts by predictors. RESULTS In this study, we extended a linear regression-based predictor to explore whether incorporating data from alanine scanning (AS), a widely used low-throughput mutagenesis method, would improve prediction results. To evaluate our model, we collected 146 AS datasets, mapping to 54 DMS datasets across 22 distinct proteins. CONCLUSIONS We show that improved model performance depends on the compatibility of the DMS and AS assays, and the scale of improvement is closely related to the correlation between DMS and AS results.
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Affiliation(s)
- Yunfan Fu
- The Walter and Eliza Hall Institute of Medical Research, Bioinformatics Division, 1G Royal Pde, Parkville, Victoria 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, Victoria 3010, Australia
| | - Justin Bedő
- The Walter and Eliza Hall Institute of Medical Research, Bioinformatics Division, 1G Royal Pde, Parkville, Victoria 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, Victoria 3010, Australia
| | - Anthony T Papenfuss
- The Walter and Eliza Hall Institute of Medical Research, Bioinformatics Division, 1G Royal Pde, Parkville, Victoria 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, Victoria 3010, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Alan F Rubin
- The Walter and Eliza Hall Institute of Medical Research, Bioinformatics Division, 1G Royal Pde, Parkville, Victoria 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, Victoria 3010, Australia
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Singh P, Kumar V, Lee G, Jung TS, Ha MW, Hong JC, Lee KW. Pharmacophore-Oriented Identification of Potential Leads as CCR5 Inhibitors to Block HIV Cellular Entry. Int J Mol Sci 2022; 23:ijms232416122. [PMID: 36555761 PMCID: PMC9784205 DOI: 10.3390/ijms232416122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Cysteine-cysteine chemokine receptor 5 (CCR5) has been discovered as a co-receptor for cellular entry of human immunodeficiency virus (HIV). Moreover, the role of CCR5 in a variety of cancers and various inflammatory responses was also discovered. Despite the fact that several CCR5 antagonists have been investigated in clinical trials, only Maraviroc has been licensed for use in the treatment of HIV patients. This indicates that there is a need for novel CCR5 antagonists. Keeping this in mind, the present study was designed. The active CCR5 inhibitors with known IC50 value were selected from the literature and utilized to develop a ligand-based common feature pharmacophore model. The validated pharmacophore model was further used for virtual screening of drug-like databases obtained from the Asinex, Specs, InterBioScreen, and Eximed chemical libraries. Utilizing computational methods such as molecular docking studies, molecular dynamics simulations, and binding free energy calculation, the binding mechanism of selected inhibitors was established. The identified Hits not only showed better binding energy when compared to Maraviroc, but also formed stable interactions with the key residues and showed stable behavior throughout the 100 ns MD simulation. Our findings suggest that Hit1 and Hit2 may be potential candidates for CCR5 inhibition, and, therefore, can be considered for further CCR5 inhibition programs.
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Affiliation(s)
- Pooja Singh
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Vikas Kumar
- Department of Bio & Medical Big Data (BK), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Gihwan Lee
- Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Tae Sung Jung
- Laboratory of Aquatic Animal Diseases, Research Institute of Natural Science, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Min Woo Ha
- Jeju Research Institute of Pharmaceutical Sciences, College of Pharmacy, Jeju National University, Jeju 63243, Republic of Korea
| | - Jong Chan Hong
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
- Correspondence: (J.C.H.); (K.W.L.)
| | - Keun Woo Lee
- Department of Bio & Medical Big Data (BK), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
- Correspondence: (J.C.H.); (K.W.L.)
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Anitha AK, Narayanan P, Ajayakumar N, Sivakumar KC, Kumar KS. Novel small synthetic HIV-1 V3 crown variants: CCR5 targeting ligands. J Biochem 2022; 172:149-164. [PMID: 35708645 PMCID: PMC9445593 DOI: 10.1093/jb/mvac052] [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: 01/03/2022] [Accepted: 06/02/2022] [Indexed: 11/23/2022] Open
Abstract
The CC chemokine receptor 5 (CCR5) antagonism represents a promising pharmacological strategy for therapeutic intervention as it plays a significant role in reducing the severity and progression of a wide range of pathological conditions. Here we designed and generated peptide ligands targeting the chemokine receptor, CCR5, that were derived from the critical interaction sites of the V3 crown domain of envelope protein glycoprotein gp120 (TRKSIHIGPGRAFYTTGEI) of HIV-1 using computational biology approach and the peptide sequence corresponding to this region was taken as the template peptide, designated as TMP-1. The peptide variants were synthesized by employing Fmoc chemistry using polymer support and were labelled with rhodamine B to study their interaction with the CCR5 receptor expressed on various cells. TMP-1 and TMP-2 were selected as the high-affinity ligands from in vitro receptor-binding assays. Specific receptor-binding experiments in activated peripheral blood mononuclear cells and HOS.CCR5 cells indicated that TMP-1 and TMP-2 had significant CCR5 specificity. Further, the functional analysis of TMP peptides using chemotactic migration assay showed that both peptides did not mediate the migration of responsive cells. Thus, template
TMP-1 and TMP-2 represent promising CCR5 targeting peptide candidates.
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Affiliation(s)
- Anju Krishnan Anitha
- Chemical Biology Laboratory, Pathogen biology research program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.,University of Kerala, Thiruvananthapuram, Kerala, 695014, India
| | - Pratibha Narayanan
- Chemical Biology Laboratory, Pathogen biology research program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.,University of Kerala, Thiruvananthapuram, Kerala, 695014, India
| | - Neethu Ajayakumar
- Chemical Biology Laboratory, Pathogen biology research program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.,University of Kerala, Thiruvananthapuram, Kerala, 695014, India
| | - Krishnankutty Chandrika Sivakumar
- Chemical Biology Laboratory, Pathogen biology research program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Kesavakurup Santhosh Kumar
- Chemical Biology Laboratory, Pathogen biology research program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
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Venuti A, Pastori C, Lopalco L. The Role of Natural Antibodies to CC Chemokine Receptor 5 in HIV Infection. Front Immunol 2017; 8:1358. [PMID: 29163468 PMCID: PMC5670346 DOI: 10.3389/fimmu.2017.01358] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/03/2017] [Indexed: 12/22/2022] Open
Abstract
The CC chemokine receptor 5 (CCR5) is responsible for immune and inflammatory responses by mediation of chemotactic activity in leukocytes, although it is expressed on different cell types. It has been shown to act as co-receptor for the human and simian immunodeficiency viruses (HIV-1, HIV-2, and SIV). Natural reactive antibodies (Abs) recognizing first loop (ECL1) of CCR5 have been detected in several pools of immunoglobulins from healthy donors and from several cohorts of either HIV-exposed but uninfected subjects (ESN) or HIV-infected individuals who control disease progression (LTNP) as well. The reason of development of anti-CCR5 Abs in the absence of autoimmune disease is still unknown; however, the presence of these Abs specific for CCR5 or for other immune receptors and mediators probably is related to homeostasis maintenance. The majority of anti-CCR5 Abs is directed to HIV binding site (N-terminus and ECL2) of the receptor. Conversely, it is well known that ECL1 of CCR5 does not bind HIV; thus, the anti-CCR5 Abs directed to ECL1 elicit a long-lasting internalization of CCR5 but not interfere with HIV binding directly; these Abs block HIV infection in either epithelial cells or CD4+ T lymphocytes and the mechanism differs from those ones described for all other CCR5-specific ligands. The Ab-mediated CCR5 internalization allows the formation of a stable signalosome by interaction of CCR5, β-arrestin2 and ERK1 proteins. The signalosome degradation and the subsequent de novo proteins synthesis determine the CCR5 reappearance on the cell membrane with a very long-lasting kinetics (8 days). The use of monoclonal Abs to CCR5 with particular characteristics and mode of action may represent a novel mode to fight viral infection in either vaccinal or therapeutic strategies.
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Affiliation(s)
- Assunta Venuti
- Division of Immunology, Transplantation and Infectious Diseases, DIBIT - San Raffaele Scientific Institute, Milan, Italy
| | - Claudia Pastori
- Division of Immunology, Transplantation and Infectious Diseases, DIBIT - San Raffaele Scientific Institute, Milan, Italy
| | - Lucia Lopalco
- Division of Immunology, Transplantation and Infectious Diseases, DIBIT - San Raffaele Scientific Institute, Milan, Italy
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