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Priyadarsinee L, Jamir E, Nagamani S, Mahanta HJ, Kumar N, John L, Sarma H, Kumar A, Gaur AS, Sahoo R, Vaikundamani S, Murugan NA, Priyakumar UD, Raghava GPS, Bharatam PV, Parthasarathi R, Subramanian V, Sastry GM, Sastry GN. Molecular Property Diagnostic Suite for COVID-19 (MPDS COVID-19): an open-source disease-specific drug discovery portal. GIGABYTE 2024; 2024:gigabyte114. [PMID: 38525218 PMCID: PMC10958779 DOI: 10.46471/gigabyte.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/11/2024] [Indexed: 03/26/2024] Open
Abstract
Molecular Property Diagnostic Suite (MPDS) was conceived and developed as an open-source disease-specific web portal based on Galaxy. MPDSCOVID-19 was developed for COVID-19 as a one-stop solution for drug discovery research. Galaxy platforms enable the creation of customized workflows connecting various modules in the web server. The architecture of MPDSCOVID-19 effectively employs Galaxy v22.04 features, which are ported on CentOS 7.8 and Python 3.7. MPDSCOVID-19 provides significant updates and the addition of several new tools updated after six years. Tools developed by our group in Perl/Python and open-source tools are collated and integrated into MPDSCOVID-19 using XML scripts. Our MPDS suite aims to facilitate transparent and open innovation. This approach significantly helps bring inclusiveness in the community while promoting free access and participation in software development. Availability & Implementation The MPDSCOVID-19 portal can be accessed at https://mpds.neist.res.in:8085/.
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Affiliation(s)
- Lipsa Priyadarsinee
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Esther Jamir
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - Selvaraman Nagamani
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Hridoy Jyoti Mahanta
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Nandan Kumar
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - Lijo John
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - Himakshi Sarma
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - Asheesh Kumar
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - Anamika Singh Gaur
- CSIR-Indian Institute of Toxicology Research, Lucknow, 226001, Uttar Pradesh, India
| | - Rosaleen Sahoo
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - S. Vaikundamani
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - N. Arul Murugan
- Indraprastha Institute of Information Technology, Delhi, 110020, India
| | - U. Deva Priyakumar
- International Institute of Information Technology, Gachibowli, Hyderabad, 500032, India
| | - G. P. S. Raghava
- Indraprastha Institute of Information Technology, Delhi, 110020, India
| | - Prasad V. Bharatam
- National Institute of Pharmaceutical Education and Research, S.A.S. Nagar (Mohali), 160062, India
| | - Ramakrishnan Parthasarathi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- CSIR-Indian Institute of Toxicology Research, Lucknow, 226001, Uttar Pradesh, India
| | - V. Subramanian
- Department of Chemistry, Indian Institute of Technology, Chennai, 600036, India
| | - G. Madhavi Sastry
- Schrödinger Inc., Octave, Salarpuria Sattva Knowledge City, 1st Floor, Unit 3A, Hyderabad, 500081, India
| | - G. Narahari Sastry
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Indian Institute of Technology (IIT) Hyderabad, Kandi, Sangareddy, Telangana, 502284, India
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Yousefbeigi S, Marsusi F. Structural insights into ACE2 interactions and immune activation of SARS-CoV-2 and its variants: an in-silico study. J Biomol Struct Dyn 2023:1-14. [PMID: 37982275 DOI: 10.1080/07391102.2023.2283158] [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: 10/15/2022] [Accepted: 11/08/2023] [Indexed: 11/21/2023]
Abstract
The initial interaction between COVID-19 and the human body involves the receptor-binding domain (RBD) of the viral spike protein with the angiotensin-converting enzyme 2 (ACE2) receptor. Likewise, the spike protein can engage with immune-related proteins, such as toll-like receptors (TLRs) and pulmonary surfactant proteins A (SP-A) and D (SP-D), thereby triggering immune responses. In this study, we utilize computational methods to investigate the interactions between the spike protein and TLRs (specifically TLR2 and TLR4), as well as (SP-A) and (SP-D). The study is conducted on four variants of concern (VOC) to differentiate and identify common virus behaviours. An assessment of the structural stability of various variants indicates slight changes attributed to mutations, yet overall structural integrity remains preserved. Our findings reveal the spike protein's ability to bind with TLR4 and TLR2, prompting immune activation. In addition, our in-silico results reveal almost similar docking scores and therefore affinity for both ACE2-spike and TLR4-spike complexes. We demonstrate that even minor changes due to mutations in all variants, surfactant A and D proteins can function as inhibitors against the spike in all variants, hindering the ACE2-RBD interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sarina Yousefbeigi
- Department of Physics and Energy Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Farah Marsusi
- Department of Physics and Energy Engineering, Amirkabir University of Technology, Tehran, Iran
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Sarma H, Kiewhuo K, Jamir E, Sastry GN. In silico investigation on the mutational analysis of BRCA1-BARD1 RING domains and its effect on nucleosome recognition and ubiquitination. Biophys Chem 2023; 300:107070. [PMID: 37339533 DOI: 10.1016/j.bpc.2023.107070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/24/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023]
Abstract
The BRCA1-BARD1 complex is a crucial tumor suppressor E3 ubiquitin ligase involved in DNA double-stranded break repair. The BRCA1-BARD1 RING domains interact with UBE2D3 through the BRCA1 interface and this complex flexibly tether to the nucleosome core particle (NCP), where BRCA1 and BARD1 interacts with histone H2A and H2B of NCP. Mutations in the BRCA1-BARD1 RING domains have been linked to familial breast and ovarian cancer. Seven mutations were analyzed to understand their effect on the binding interface of protein partners and changes in conformational dynamics. Molecular dynamics simulations revealed that mutant complexes were less conformationally flexible than the wildtype complex. Protein-protein interaction profiling showed the importance of specific molecular interactions, hotspot and hub residues, and some of these were lost in the mutant complexes. Two mutations (BRCA1L51W-K65R and BARD1C53W) hindered significant interaction between protein partners and may prevent signaling for ubiquitination of histones in NCP and other cellular targets. The structural compactness and reduced significant interaction in mutant complexes may be the possible reason of preventing ubiquitination and hinder DNA repair, resulting cancer.
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Affiliation(s)
- Himakshi Sarma
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, India.
| | - Kikrusenuo Kiewhuo
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Esther Jamir
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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Kiewhuo K, Priyadarsinee L, Sarma H, Sastry GN. Molecular dynamics simulations reveal the effect of mutations in the RING domains of BRCA1-BARD1 complex and its relevance to the prognosis of breast cancer. J Biomol Struct Dyn 2023; 41:12734-12752. [PMID: 36775657 DOI: 10.1080/07391102.2023.2175383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/05/2023] [Indexed: 02/14/2023]
Abstract
The N-terminal RING-RING domain of BRCA1-BARD1 is an E3 ubiquitin ligase complex that plays a critical role in tumor suppression through DNA double stranded repair mechanism. Mutations in the BRCA1-BARD1 heterodimer RING domains were found to have an association with breast and ovarian cancer by a way of hampering the E3 ubiquitin ligase activity. Herein, the molecular mechanism of interaction, conformational change due to the specific mutations on the BRCA1-BARD1 complex at atomic level has been examined by employing molecular modeling techniques. Sixteen mutations have been selected for the study. Molecular dynamics simulation results reveal that the mutant complexes have more local perturbation with a high residual fluctuation in the zinc binding sites and central helix. A few of the BRCA1 (V11A, I21V, I42V, R71G, I31M and L51W) mutants have been experimentally identified that do not impair E3 ligase activity, display an enhanced number of H-bonds and non-bonded contacts at the interacting interface as revealed by MD simulation. The mutation of BRCA1 (C61G, C64Y, C39Y and C24R) and BARD1 (C53W, C71Y and C83R) zinc binding residues displayed a smaller number of significant H-bonds, other interactions and also loss of some of the hotspot residues. Additionally, most of the mutant complexes display relatively lower electrostatic energy, H-bonding and total stabilizing energy as compared to wild-type. The current study attempts to unravel the role of BRCA1-BARD1 mutations and delineates the structural and conformational dynamics in the progression of breast cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kikrusenuo Kiewhuo
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Lipsa Priyadarsinee
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Himakshi Sarma
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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