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Sonawani A, Kharche S, Dasgupta D, Sengupta D. Insights into the dynamic interactions at chemokine-receptor interfaces and mechanistic models of chemokine binding. J Struct Biol 2022; 214:107877. [PMID: 35750237 DOI: 10.1016/j.jsb.2022.107877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/20/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022]
Abstract
Chemokine receptors are the central signaling hubs of several processes such as cell migration, chemotaxis and cell positioning. In this graphical review, we provide an overview of the structural and mechanistic principles governing chemokine recognition that are currently emerging. Structural models of chemokine-receptor co-complexes with endogenous chemokines, viral chemokines and therapeutics have been resolved that highlight multiple interaction sites, termed as CRS1, CRS1.5 etc. The first site of interaction has been shown to be the N-terminal domain of the receptors (CRS1 site). A large structural flexibility of the N-terminal domain has been reported that was supported by both experimental and simulation studies. Upon chemokine binding, the N-terminal domain appears to show constricted dynamics and opens up to interact with the chemokine via a large interface. The subsequent sites such as CRS1.5 and CRS2 sites have been structurally well resolved although differences arise such as the localization of the N-terminus of the ligand to a major or minor pocket of the orthosteric binding site. Several computational studies have highlighted the dynamic protein-protein interface at the CRS1 site that seemingly appears to resolve the differences in NMR and mutagenesis studies. Interestingly, the differential dynamics at the CRS1 site suggests a mixed model of binding with complex signatures of both conformational selection and induced fit models. Integrative experimental and computational approaches could help unravel the structural basis of promiscuity and specificity in chemokine-receptor binding and open up new avenues of therapeutic design.
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Affiliation(s)
- Archana Sonawani
- School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to be University, CBD Belapur, Navi Mumbai 400614, India
| | - Shalmali Kharche
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| | - Debjani Dasgupta
- School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to be University, CBD Belapur, Navi Mumbai 400614, India
| | - Durba Sengupta
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India.
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Sutar J, Padwal V, Sonawani A, Nagar V, Patil P, Kulkarni B, Hingankar N, Deshpande S, Idicula-Thomas S, Jagtap D, Bhattacharya J, Bandivdekar A, Patel V. Effect of diversity in gp41 membrane proximal external region of primary HIV-1 Indian subtype C sequences on interaction with broadly neutralizing antibodies 4E10 and 10E8. Virus Res 2019; 273:197763. [PMID: 31553924 DOI: 10.1016/j.virusres.2019.197763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 10/25/2022]
Abstract
Human Immunodeficiency Virus-1 Clade C (HIV-1C) dominates the AIDS epidemic in India, afflicting 2.1 million individuals within the country and more than 15 million people worldwide. Membrane proximal external region (MPER) is an attractive target for broadly neutralizing antibody (bNAb) based therapies. However, information on MPER sequence diversity from India is meagre due to limited sampling of primary viral sequences. In the present study, we examined the variation in MPER of HIV-1C from 24 individuals in Mumbai, India by high throughput sequencing of uncultured viral sequences. Deep sequencing of MPER (662-683; HXB2 envelope amino acid numbering) allowed quantification of intra-individual variation up to 65% at positions 662, 665, 668, 674 and 677 within this region. These variable positions included contact sites targeted by bNAbs 2F5, Z13e1, 4E10 as well as 10E8. Both major and minor epitope variants i.e. 'haplotypes' were generated for each sample dataset. A total of 23, 34 and 25 unique epitope haplotypes could be identified for bNAbs 2F5, Z13e1 and 4E10/10E8 respectively. Further analysis of 4E10 and 10E8 epitopes from our dataset and meta-analysis of previously reported HIV-1 sequences from India revealed 26 epitopes (7 India-specific), heretofore untested for neutralization sensitivity. Peptide-Ab docking predicted 13 of these to be non-binding to 10E8. ELISA, Surface Plasmon Resonance and peptide inhibition of HIV-1 neutralization assays were then performed which validated predicted weak/non-binding interactions for peptides corresponding to six of these epitopes. These results highlight the under-representation of 10E8 non-binding HIV-1C MPER sequences from India. Our study thus underscores the need for increased surveillance of primary circulating envelope sequences for development of efficacious bNAb-based interventions in India.
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Affiliation(s)
- Jyoti Sutar
- Department of Biochemistry, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India
| | - Varsha Padwal
- Department of Biochemistry, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India
| | - Archana Sonawani
- ICMR Biomedical Informatics Centre, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India
| | - Vidya Nagar
- Department of Medicine, Grant Government Medical College, Byculla, Mumbai, India
| | - Priya Patil
- Department of Medicine, Grant Government Medical College, Byculla, Mumbai, India
| | - Bhalachandra Kulkarni
- Department of Structural Biology, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India
| | - Nitin Hingankar
- HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Suprit Deshpande
- HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Susan Idicula-Thomas
- ICMR Biomedical Informatics Centre, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India
| | - Dhanashree Jagtap
- Department of Structural Biology, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India
| | - Jayanta Bhattacharya
- HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Atmaram Bandivdekar
- Department of Biochemistry, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India.
| | - Vainav Patel
- Department of Biochemistry, National Institute for Research in Reproductive Health (ICMR-NIRRH), Parel, Mumbai, India.
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Niazi S, Purohit M, Sonawani A, Niazi JH. Revealing the molecular interactions of aptamers that specifically bind to the extracellular domain of HER2 cancer biomarker protein: An in silico assessment. J Mol Graph Model 2018; 83:112-121. [DOI: 10.1016/j.jmgm.2018.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/03/2018] [Accepted: 06/04/2018] [Indexed: 12/16/2022]
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Dodagatta-Marri E, Mitchell DA, Pandit H, Sonawani A, Murugaiah V, Idicula-Thomas S, Nal B, Al-Mozaini MM, Kaur A, Madan T, Kishore U. Protein-Protein Interaction between Surfactant Protein D and DC-SIGN via C-Type Lectin Domain Can Suppress HIV-1 Transfer. Front Immunol 2017; 8:834. [PMID: 28824609 PMCID: PMC5534670 DOI: 10.3389/fimmu.2017.00834] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 07/03/2017] [Indexed: 01/01/2023] Open
Abstract
Surfactant protein D (SP-D) is a soluble C-type lectin, belonging to the collectin (collagen-containing calcium-dependent lectin) family, which acts as an innate immune pattern recognition molecule in the lungs at other mucosal surfaces. Immune regulation and surfactant homeostasis are salient functions of SP-D. SP-D can bind to a range of viral, bacterial, and fungal pathogens and trigger clearance mechanisms. SP-D binds to gp120, the envelope protein expressed on HIV-1, through its C-type lectin or carbohydrate recognition domain. This is of importance since SP-D is secreted by human mucosal epithelial cells and is present in the female reproductive tract, including vagina. Another C-type lectin, dendritic cell (DC)-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN), present on the surface of the DCs, also binds to HIV-1 gp120 and facilitates viral transfer to the lymphoid tissues. DCs are also present at the site of HIV-1 entry, embedded in vaginal or rectal mucosa. In the present study, we report a direct protein-protein interaction between recombinant forms of SP-D (rfhSP-D) and DC-SIGN via their C-type lectin domains. Both SP-D and DC-SIGN competed for binding to immobilized HIV-1 gp120. Pre-incubation of human embryonic kidney cells expressing surface DC-SIGN with rfhSP-D significantly inhibited the HIV-1 transfer to activated peripheral blood mononuclear cells. In silico analysis revealed that SP-D and gp120 may occupy same sites on DC-SIGN, which may explain the reduced transfer of HIV-1. In summary, we demonstrate, for the first time, that DC-SIGN is a novel binding partner of SP-D, and this interaction can modulate HIV-1 capture and transfer to CD4+ T cells. In addition, the present study also reveals a novel and distinct mechanism of host defense by SP-D against HIV-1.
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Affiliation(s)
- Eswari Dodagatta-Marri
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Daniel A Mitchell
- Clinical Sciences Research Laboratories, Warwick Medical School, University Hospital Coventry and Warwickshire Campus, Coventry, United Kingdom
| | - Hrishikesh Pandit
- Department of Innate Immunity, National Institute for Research in Reproductive Health, Indian Council of Medical Research, Mumbai, India
| | - Archana Sonawani
- Department of Innate Immunity, National Institute for Research in Reproductive Health, Indian Council of Medical Research, Mumbai, India
| | - Valarmathy Murugaiah
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Susan Idicula-Thomas
- Department of Innate Immunity, National Institute for Research in Reproductive Health, Indian Council of Medical Research, Mumbai, India
| | - Béatrice Nal
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom.,Institute of Environment, Health and Societies, Brunel University London, Uxbridge, United Kingdom
| | - Maha M Al-Mozaini
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Anuvinder Kaur
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Taruna Madan
- Department of Innate Immunity, National Institute for Research in Reproductive Health, Indian Council of Medical Research, Mumbai, India
| | - Uday Kishore
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
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Suryawanshi R, Jadhav S, Makwana N, Desai D, Chaturbhuj D, Sonawani A, Idicula-Thomas S, Murugesan V, Katti SB, Tripathy S, Paranjape R, Kulkarni S. Evaluation of 4-thiazolidinone derivatives as potential reverse transcriptase inhibitors against HIV-1 drug resistant strains. Bioorg Chem 2017; 71:211-218. [PMID: 28236450 DOI: 10.1016/j.bioorg.2017.02.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/10/2017] [Accepted: 02/13/2017] [Indexed: 02/03/2023]
Abstract
Rapid emergence of drug resistance is crucial in management of HIV infection limiting implementation of efficacious drugs in the ART regimen. Designing new molecules against HIV drug resistant strains is utmost essential. Based on the anti-HIV-1 activity, we selected four 4-thiazolidinone derivatives (S009-1908, S009-1909, S009-1911, S009-1912) and studied their interaction with reverse transcriptase (RT) from a panel of 10 clinical isolates (8 nevirapine resistant and two susceptible) using in silico methods, and inhibition pattern using in vitro cell based assays. On the basis of binding affinity observed in in silico analysis, 2-(2-chloro-6-nitrophenyl)-3-(4, 6-dimethylpyridin-2-yl) thiazolidin-4-one (S009-1912) was identified as the lead molecule followed by S009-1908, S009-1909 and S009-1911. The in vitro activity against the same panel was assessed using TZM-bl assay (IC50: 0.4-11.44µg/ml, TI: 4-126) and subsequently in PBMC assay against a nevirapine resistant clinical isolate (IC50: 0.8-6.65µg/ml, TI: 8.31-11.43) and standard strain from NIH ARRRP (IC50: 0.95-3.6µg/ml, TI: 9-26). The study shows analogue with pyrimidin-2-yl amino substitution at N-3 position of thiazolidin-4-one ring (S009-1908, S009-1909, S009-1911) exhibited enhanced activity as compared to pyridin-2-yl substituted derivatives (S009-1912), suggesting the use 4-thiazolidinones for developing potent inhibitors against HIV-1 drug resistant strains.
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Affiliation(s)
| | | | | | - Dipen Desai
- National AIDS Research Institute, Pune, India
| | | | - Archana Sonawani
- National Institute for Research in Reproductive Health, Mumbai, India
| | | | - Vanangamudi Murugesan
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute (CDRI), Jankipuram Extension, Sector-10, Lucknow 226031, Uttar Pradesh, India
| | - Seturam B Katti
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute (CDRI), Jankipuram Extension, Sector-10, Lucknow 226031, Uttar Pradesh, India
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Pandit H, Gopal S, Sonawani A, Yadav AK, Qaseem AS, Warke H, Patil A, Gajbhiye R, Kulkarni V, Al-Mozaini MA, Idicula-Thomas S, Kishore U, Madan T. Surfactant protein D inhibits HIV-1 infection of target cells via interference with gp120-CD4 interaction and modulates pro-inflammatory cytokine production. PLoS One 2014; 9:e102395. [PMID: 25036364 PMCID: PMC4103819 DOI: 10.1371/journal.pone.0102395] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 06/17/2014] [Indexed: 01/12/2023] Open
Abstract
Surfactant Protein SP-D, a member of the collectin family, is a pattern recognition protein, secreted by mucosal epithelial cells and has an important role in innate immunity against various pathogens. In this study, we confirm that native human SP-D and a recombinant fragment of human SP-D (rhSP-D) bind to gp120 of HIV-1 and significantly inhibit viral replication in vitro in a calcium and dose-dependent manner. We show, for the first time, that SP-D and rhSP-D act as potent inhibitors of HIV-1 entry in to target cells and block the interaction between CD4 and gp120 in a dose-dependent manner. The rhSP-D-mediated inhibition of viral replication was examined using three clinical isolates of HIV-1 and three target cells: Jurkat T cells, U937 monocytic cells and PBMCs. HIV-1 induced cytokine storm in the three target cells was significantly suppressed by rhSP-D. Phosphorylation of key kinases p38, Erk1/2 and AKT, which contribute to HIV-1 induced immune activation, was significantly reduced in vitro in the presence of rhSP-D. Notably, anti-HIV-1 activity of rhSP-D was retained in the presence of biological fluids such as cervico-vaginal lavage and seminal plasma. Our study illustrates the multi-faceted role of human SP-D against HIV-1 and potential of rhSP-D for immunotherapy to inhibit viral entry and immune activation in acute HIV infection.
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Affiliation(s)
- Hrishikesh Pandit
- Department of Innate Immunity, National Institute for Research in Reproductive Health (ICMR), Mumbai, Maharashtra, India
| | - Sandhya Gopal
- Department of Innate Immunity, National Institute for Research in Reproductive Health (ICMR), Mumbai, Maharashtra, India
| | - Archana Sonawani
- Biomedical Informatics Centre, National Institute for Research in Reproductive Health (ICMR), Mumbai, Maharashtra, India
| | - Ajit Kumar Yadav
- Department of Innate Immunity, National Institute for Research in Reproductive Health (ICMR), Mumbai, Maharashtra, India
| | - Asif S. Qaseem
- Centre for Infection, Immunity and Disease Mechanisms, Brunel University, London, United Kingdom
| | - Himangi Warke
- Department of Obstetrics and Gynecology, Seth G S Medical College and K E M Hospital, Mumbai, Maharashtra, India
| | - Anushree Patil
- Department of Clinical Research, National Institute for Research in Reproductive Health (ICMR), Mumbai, Maharashtra, India
| | - Rahul Gajbhiye
- Department of Clinical Research, National Institute for Research in Reproductive Health (ICMR), Mumbai, Maharashtra, India
| | - Vijay Kulkarni
- Department of Clinical Research, National Institute for Research in Reproductive Health (ICMR), Mumbai, Maharashtra, India
| | - Maha Ahmed Al-Mozaini
- Immunocompromised Host Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Susan Idicula-Thomas
- Biomedical Informatics Centre, National Institute for Research in Reproductive Health (ICMR), Mumbai, Maharashtra, India
| | - Uday Kishore
- Centre for Infection, Immunity and Disease Mechanisms, Brunel University, London, United Kingdom
| | - Taruna Madan
- Department of Innate Immunity, National Institute for Research in Reproductive Health (ICMR), Mumbai, Maharashtra, India
- * E-mail:
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Sonawani A, Niazi S, Idicula-Thomas S. In silico study on binding specificity of gonadotropins and their receptors: design of a novel and selective peptidomimetic for human follicle stimulating hormone receptor. PLoS One 2013; 8:e64475. [PMID: 23700481 PMCID: PMC3659097 DOI: 10.1371/journal.pone.0064475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 04/15/2013] [Indexed: 01/13/2023] Open
Abstract
Gonadotropins bind to specific receptors in spite of sharing a high level of sequence and structural similarity. This specific binding is crucial for maintaining the reproductive health of an organism. In this study, residues that dictate the receptor binding specificity of the gonadotropins (FSH and LH) have been identified using combination of in silico methods. Docking studies (ZDOCK), based on the systematic replacement of these residues, confirmed its importance in receptor binding. An interesting observation is that the relative positioning of the residues conferring binding specificity varied for the gonadotropin-receptor complexes. This spatial difference of the key residues could be exploited for design of specific modulators. Based on the identified residues, we have rationally designed a peptidomimetic (FSHP) that displays good binding affinity and specificity for hFSHR. FSHP was developed by screening 3.9 million compounds using pharmacophore-shape similarity followed by fragment-based approach. It was observed that FSHP and hFSHâ can share the same receptor binding site thereby mimicking the native hFSHR-FSH interactions. FSHP also displayed higher binding affinity to hFSHR as compared to two reported hFSHR antagonists. MD simulation studies on hFSHR-FSHP complex revealed that FSHP is conformationally rigid and the intermolecular interactions are maintained during the course of simulation.
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Affiliation(s)
- Archana Sonawani
- Biomedical Informatics Center of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai, India
| | - Sarfaraj Niazi
- Biomedical Informatics Center of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai, India
| | - Susan Idicula-Thomas
- Biomedical Informatics Center of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai, India
- * E-mail:
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Vaidya S, Sonawani A, Idicula-Thomas S, Vundinti BR, Ghosh K. Imatinib resistance due to a novel tri-nucleotide insertion in the SH2/C lobe interface of BCR/ABL kinase domain between position K357 and N358. Leuk Res 2012; 36:e110-2. [PMID: 22387050 DOI: 10.1016/j.leukres.2012.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 01/27/2012] [Accepted: 02/07/2012] [Indexed: 11/19/2022]
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Gajbhiye R, Sonawani A, Khan S, Suryawanshi A, Kadam S, Warty N, Raut V, Khole V. Identification and validation of novel serum markers for early diagnosis of endometriosis. Hum Reprod 2011; 27:408-17. [DOI: 10.1093/humrep/der410] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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