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Rizarullah, Aditama R, Giri-Rachman EA, Hertadi R. Designing a Novel Multiepitope Vaccine from the Human Papilloma Virus E1 and E2 Proteins for Indonesia with Immunoinformatics and Molecular Dynamics Approaches. ACS OMEGA 2024; 9:16547-16562. [PMID: 38617694 PMCID: PMC11007845 DOI: 10.1021/acsomega.4c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 04/16/2024]
Abstract
One of the deadliest malignant cancer in women globally is cervical cancer. Specifically, cervical cancer is the second most common type of cancer in Indonesia. The main infectious agent of cervical cancer is the human papilloma virus (HPV). Although licensed prophylactic vaccines are available, cervical cancer cases are on the rise. Therapy using multiepitope-based vaccines is a very promising therapy for cervical cancer. This study aimed to develop a multiepitope vaccine based on the E1 and E2 proteins of HPV 16, 18, 45, and 52 using in silico. In this study, we develop a novel multiepitope vaccine candidate using an immunoinformatic approach. We predicted the epitopes of the cytotoxic T lymphocyte (CTL) and helper T lymphocyte (HTL) and evaluated their immunogenic properties. Population coverage analysis of qualified epitopes was conducted to determine the successful use of the vaccine worldwide. The epitopes were constructed into a multiepitope vaccine by using AAY linkers between the CTL epitopes and GPGPG linkers between the HTL epitopes. The tertiary structure of the multiepitope vaccine was modeled with AlphaFold and was evaluated by Prosa-web. The results of vaccine construction were analyzed for B-cell epitope prediction, molecular docking with Toll like receptor-4 (TLR4), and molecular dynamics simulation. The results of epitope prediction obtained 4 CTL epitopes and 7 HTL epitopes that are eligible for construction of multiepitope vaccines. Prediction of the physicochemical properties of multiepitope vaccines obtained good results for recombinant protein production. The interaction showed that the interaction of the multiepitope vaccine-TLR4 complex is stable based on the binding free energy value -106.5 kcal/mol. The results of the immune response simulation show that multiepitope vaccine candidates could activate the adaptive and humoral immune systems and generate long-term B-cell memory. According to these results, the development of a multiepitope vaccine with a reverse vaccinology approach is a breakthrough to develop potential cervical cancer therapeutic vaccines.
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Affiliation(s)
- Rizarullah
- Biochemistry
and Biomolecular Engineering Research Division, Faculty of Mathematics
and Natural Sciences, Bandung Institute
of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
- Department
of Biochemistry, Faculty of Medicine, Abulyatama
University, Jl. Blangbintang Lama, Aceh Besar 23372, Indonesia
| | - Reza Aditama
- Biochemistry
and Biomolecular Engineering Research Division, Faculty of Mathematics
and Natural Sciences, Bandung Institute
of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
| | - Ernawati Arifin Giri-Rachman
- Genetics
and Molecular Biotechnology Research Division, School of Life Sciences
and Technology, Bandung Institute of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
| | - Rukman Hertadi
- Biochemistry
and Biomolecular Engineering Research Division, Faculty of Mathematics
and Natural Sciences, Bandung Institute
of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
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Peluso P, Chankvetadze B. Recent developments in molecular modeling tools and applications related to pharmaceutical and biomedical research. J Pharm Biomed Anal 2024; 238:115836. [PMID: 37939549 DOI: 10.1016/j.jpba.2023.115836] [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: 08/05/2023] [Revised: 09/21/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023]
Abstract
In modern pharmaceutical and biomedical research, molecular modeling represents a useful tool to explore processes and their mechanistic bases at the molecular level. Integrating experimental and virtual analysis is a fruitful approach to study ligand-receptor interaction in chemical, biochemical and biological environments. In these fields, molecular docking and molecular dynamics are considered privileged techniques for modeling (bio)macromolecules and related complexes. This review aims to present the current landscape of molecular modeling in pharmaceutical and biomedical research by examining selected representative applications published in the last years and highlighting current topics and trends of this field. Thus, a systematic compilation of all published literature has not been attempted herein. After a brief overview of the main theoretical and computational tools used to investigate mechanisms at molecular level, recent applications of molecular modeling in drug discovery, ligand binding and for studying protein conformation and function will be discussed. Furthermore, specific sections will be devoted to the application of molecular modeling for unravelling enantioselective mechanisms underlying the enantioseparation of chiral compounds of pharmaceutical and biomedical interest as well as for studying new forms of noncovalent interactivity identified in biochemical and biological environments. The general aim of this review is to provide the reader with a modern overview of the topic, highlighting advancements and outlooks as well as drawbacks and pitfalls still affecting the applicability of theoretical and computational methods in the field of pharmaceutical and biomedical research.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB-CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy.
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Ave 3, 0179 Tbilisi, Georgia
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Rabdano SO, Ruzanova EA, Pletyukhina IV, Saveliev NS, Kryshen KL, Katelnikova AE, Beltyukov PP, Fakhretdinova LN, Safi AS, Rudakov GO, Arakelov SA, Andreev IV, Kofiadi IA, Khaitov MR, Valenta R, Kryuchko DS, Berzin IA, Belozerova NS, Evtushenko AE, Truhin VP, Skvortsova VI. Immunogenicity and In Vivo Protective Effects of Recombinant Nucleocapsid-Based SARS-CoV-2 Vaccine Convacell ®. Vaccines (Basel) 2023; 11:vaccines11040874. [PMID: 37112786 PMCID: PMC10141225 DOI: 10.3390/vaccines11040874] [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: 04/02/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The vast majority of SARS-CoV-2 vaccines which are licensed or under development focus on the spike (S) protein and its receptor binding domain (RBD). However, the S protein shows considerable sequence variations among variants of concern. The aim of this study was to develop and characterize a SARS-CoV-2 vaccine targeting the highly conserved nucleocapsid (N) protein. Recombinant N protein was expressed in Escherichia coli, purified to homogeneity by chromatography and characterized by SDS-PAGE, immunoblotting, mass spectrometry, dynamic light scattering and differential scanning calorimetry. The vaccine, formulated as a squalane-based emulsion, was used to immunize Balb/c mice and NOD SCID gamma (NSG) mice engrafted with human PBMCs, rabbits and marmoset monkeys. Safety and immunogenicity of the vaccine was assessed via ELISA, cytokine titer assays and CFSE dilution assays. The protective effect of the vaccine was studied in SARS-CoV-2-infected Syrian hamsters. Immunization induced sustainable N-specific IgG responses and an N-specific mixed Th1/Th2 cytokine response. In marmoset monkeys, an N-specific CD4+/CD8+ T cell response was observed. Vaccinated Syrian hamsters showed reduced lung histopathology, lower virus proliferation, lower lung weight relative to the body, and faster body weight recovery. Convacell® thus is shown to be effective and may augment the existing armamentarium of vaccines against COVID-19.
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Affiliation(s)
- Sevastyan O Rabdano
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia
| | - Ellina A Ruzanova
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia
| | - Iuliia V Pletyukhina
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia
| | - Nikita S Saveliev
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia
| | | | | | - Petr P Beltyukov
- Scientific Research Institute of Hygiene, Occupational Pathology and Human Ecology of the Federal Medical-Biological Agency of Russia (SRIHOPHE), Kuzmolovsky 188663, Russia
| | - Liliya N Fakhretdinova
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia
| | - Ariana S Safi
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia
| | - German O Rudakov
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia
| | - Sergei A Arakelov
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia
| | - Igor V Andreev
- National Research Center Institute of Immunology (NRCII), Federal Medical-Biological Agency of Russia, Moscow 115522, Russia
| | - Ilya A Kofiadi
- National Research Center Institute of Immunology (NRCII), Federal Medical-Biological Agency of Russia, Moscow 115522, Russia
- Department of Immunology, N.I. Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, Moscow 117997, Russia
| | - Musa R Khaitov
- National Research Center Institute of Immunology (NRCII), Federal Medical-Biological Agency of Russia, Moscow 115522, Russia
- Department of Immunology, N.I. Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, Moscow 117997, Russia
| | - Rudolf Valenta
- National Research Center Institute of Immunology (NRCII), Federal Medical-Biological Agency of Russia, Moscow 115522, Russia
- Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria
- Laboratory of Immunopathology, Department of Clinical Immunology and Allergology, I.M. Sechenov First Moscow State Medical University, Moscow 119435, Russia
- Karl Landsteiner University of Health Sciences, 3500 Krems, Austria
| | - Daria S Kryuchko
- Federal Medical-Biological Agency of Russia, Moscow 125310, Russia
| | - Igor A Berzin
- Federal Medical-Biological Agency of Russia, Moscow 125310, Russia
| | - Natalia S Belozerova
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia
| | - Anatoly E Evtushenko
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia
| | - Viktor P Truhin
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia
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Salod Z, Mahomed O. Mapping Potential Vaccine Candidates Predicted by VaxiJen for Different Viral Pathogens between 2017-2021-A Scoping Review. Vaccines (Basel) 2022; 10:1785. [PMID: 36366294 PMCID: PMC9695814 DOI: 10.3390/vaccines10111785] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 09/29/2023] Open
Abstract
Reverse vaccinology (RV) is a promising alternative to traditional vaccinology. RV focuses on in silico methods to identify antigens or potential vaccine candidates (PVCs) from a pathogen's proteome. Researchers use VaxiJen, the most well-known RV tool, to predict PVCs for various pathogens. The purpose of this scoping review is to provide an overview of PVCs predicted by VaxiJen for different viruses between 2017 and 2021 using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic Reviews extension for Scoping Reviews (PRISMA-ScR) guidelines. We used the term 'vaxijen' to search PubMed, Scopus, Web of Science, EBSCOhost, and ProQuest One Academic. The protocol was registered at the Open Science Framework (OSF). We identified articles on this topic, charted them, and discussed the key findings. The database searches yielded 1033 articles, of which 275 were eligible. Most studies focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), published between 2020 and 2021. Only a few articles (8/275; 2.9%) conducted experimental validations to confirm the predictions as vaccine candidates, with 2.2% (6/275) articles mentioning recombinant protein expression. Researchers commonly targeted parts of the SARS-CoV-2 spike (S) protein, with the frequently predicted epitopes as PVCs being major histocompatibility complex (MHC) class I T cell epitopes WTAGAAAYY, RQIAPGQTG, IAIVMVTIM, and B cell epitope IAPGQTGKIADY, among others. The findings of this review are promising for the development of novel vaccines. We recommend that vaccinologists use these findings as a guide to performing experimental validation for various viruses, with SARS-CoV-2 as a priority, because better vaccines are needed, especially to stay ahead of the emergence of new variants. If successful, these vaccines could provide broader protection than traditional vaccines.
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Affiliation(s)
- Zakia Salod
- Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban 4051, South Africa
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Kumar S, Dutta D, Ravichandiran V, Sukla S. Monoclonal antibodies: a remedial approach to prevent SARS-CoV-2 infection. 3 Biotech 2022; 12:227. [PMID: 35982759 PMCID: PMC9383686 DOI: 10.1007/s13205-022-03281-5] [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: 01/09/2022] [Accepted: 07/26/2022] [Indexed: 11/07/2022] Open
Abstract
SARS-CoV-2, the newly emerged virus of the Coronaviridae family is causing havoc worldwide. The novel coronavirus 2019 was first reported in Wuhan, China marked as the third highly infectious pathogenic virus of the twenty-first century. The typical manifestations of COVID-19 include cough, sore throat, fever, fatigue, loss of sense of taste and difficulties in breathing. Large numbers of SARS-CoV-2 infected patients have mild to moderate symptoms, however severe and life-threatening cases occur in about 5-10% of infections with an approximately 2% mortality rate. For the treatment of SARS-CoV-2, the use of neutralizing monoclonal antibodies (mAbs) could be one approach. The receptor binding domain (RBD) and N-terminal domain (NTD) situated on the peak of the spike protein (S-Protein) of SARS-CoV-2 are immunogenic in nature, therefore, can be targeted by neutralizing monoclonal antibodies. Several bioinformatics approaches highlight the identification of novel SARS-CoV-2 epitopes which can be targeted for the development of COVID-19 therapeutics. Here we present a summary of neutralizing mAbs isolated from COVID-19 infected patients which are anticipated to be a better therapeutic alternative against SARS-CoV-2. However, provided the vast escalation of the disease worldwide affecting people from all strata, affording expensive mAb therapy will not be feasible. Hence other strategies are also being employed to find suitable vaccine candidates and antivirals against SARS-CoV-2 that can be made easily available to the population.
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Affiliation(s)
- Sonu Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
| | - Debrupa Dutta
- Department of Pharmacology and Toxicology, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
| | - Velayutham Ravichandiran
- Department of Natural Products, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
| | - Soumi Sukla
- Department of Pharmacology and Toxicology, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
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6
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Zelenova M, Ivanova A, Semyonov S, Gankin Y. Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Comput Biol Med 2021; 139:104981. [PMID: 34735950 PMCID: PMC8547852 DOI: 10.1016/j.compbiomed.2021.104981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/17/2021] [Accepted: 10/22/2021] [Indexed: 01/06/2023]
Abstract
BACKGROUND The SARS-CoV-2 virus caused a worldwide pandemic - although none of its predecessors from the coronavirus family ever achieved such a scale. The key to understanding the global success of SARS-CoV-2 is hidden in its genome. MATERIALS AND METHODS We retrieved data for 329,942 SARS-CoV-2 records uploaded to the GISAID database from the beginning of the pandemic until the January 8, 2021. A Python variant detection script was developed to process the data using pairwise2 from the BioPython library. Sequence alignments were performed for every gene separately (except ORF1ab, which was not studied). Genomes less than 26,000 nucleotides long were excluded from the research. Clustering was performed using HDBScan. RESULTS Here, we addressed the genetic variability of SARS-CoV-2 using 329,942 samples. The analysis yielded 155 SNPs and deletions in more than 0.3% of the sequences. Clustering results suggested that a proportion of people (2.46%) was infected with a distinct subtype of the B.1.1.7 variant, which contained four to six additional mutations (G28881A, G28882A, G28883С, A23403G, A28095T, G25437T). Two clusters were formed by mutations in the samples uploaded predominantly by Denmark and Australia (1.48% and 2.51%, respectively). A correlation coefficient matrix detected 160 pairs of mutations (correlation coefficient greater than 0.7). We also addressed the completeness of the GISAID database, patient gender, and age. Finally, we found ORF6 and E to be the most conserved genes (96.15% and 94.66% of the sequences totally match the reference, respectively). Our results indicate multiple areas for further research in both SARS-CoV-2 studies and health science.
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Affiliation(s)
- Maria Zelenova
- Quantori, 625 Massachusetts Ave, Cambridge, MA, 02139, USA; Mental Health Research Center, Kashirskoe Shosse 34, 115522, Moscow, Russia.
| | - Anna Ivanova
- Quantori, 625 Massachusetts Ave, Cambridge, MA, 02139, USA.
| | | | - Yuriy Gankin
- Quantori, 625 Massachusetts Ave, Cambridge, MA, 02139, USA.
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Mazumder S, Rastogi R, Undale A, Arora K, Arora NM, Pratim B, Kumar D, Joseph A, Mali B, Arya VB, Kalyanaraman S, Mukherjee A, Gupta A, Potdar S, Roy SS, Parashar D, Paliwal J, Singh SK, Naqvi A, Srivastava A, Singh MK, Kumar D, Bansal S, Rautray S, Saini M, Jain K, Gupta R, Kundu PK. PRAK-03202: A triple antigen virus-like particle vaccine candidate against SARS CoV-2. Heliyon 2021; 7:e08124. [PMID: 34632131 PMCID: PMC8487870 DOI: 10.1016/j.heliyon.2021.e08124] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/17/2021] [Accepted: 09/30/2021] [Indexed: 11/22/2022] Open
Abstract
The rapid development of safe and effective vaccines against severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) is a necessary response to coronavirus outbreak. Here, we developed PRAK-03202, the world's first triple antigen virus-like particle vaccine candidate, by cloning and transforming SARS-CoV-2 gene segments into a highly characterized S. cerevisiae-based D-Crypt™ platform, which induced SARS CoV-2 specific neutralizing antibodies in BALB/c mice. Immunization using three different doses of PRAK-03202 induced an antigen-specific (spike, envelope, and membrane proteins) humoral response and neutralizing potential. Peripheral blood mononuclear cells from convalescent patients showed lymphocyte proliferation and elevated interferon levels suggestive of epitope conservation and induction of T helper 1-biased cellular immune response when exposed to PRAK-03202. These data support further clinical development and testing of PRAK-03202 for use in humans.
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Affiliation(s)
| | | | | | | | | | - Biswa Pratim
- Premas Biotech Private Limited, Manesar, Gurugram, India
| | - Dilip Kumar
- Premas Biotech Private Limited, Manesar, Gurugram, India
| | - Abyson Joseph
- Premas Biotech Private Limited, Manesar, Gurugram, India
| | - Bhupesh Mali
- Premas Biotech Private Limited, Manesar, Gurugram, India
| | | | | | | | - Aditi Gupta
- Premas Biotech Private Limited, Manesar, Gurugram, India
| | - Swaroop Potdar
- Premas Biotech Private Limited, Manesar, Gurugram, India
| | | | | | - Jeny Paliwal
- Premas Biotech Private Limited, Manesar, Gurugram, India
| | | | - Aelia Naqvi
- Premas Biotech Private Limited, Manesar, Gurugram, India
| | | | | | - Devanand Kumar
- Premas Biotech Private Limited, Manesar, Gurugram, India
| | - Sarthi Bansal
- Premas Biotech Private Limited, Manesar, Gurugram, India
| | | | - Manish Saini
- Premas Biotech Private Limited, Manesar, Gurugram, India
| | - Kshipra Jain
- Premas Biotech Private Limited, Manesar, Gurugram, India
| | - Reeshu Gupta
- Premas Biotech Private Limited, Manesar, Gurugram, India
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