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El Salamouni NS, Cater JH, Spenkelink LM, Yu H. Nanobody engineering: computational modelling and design for biomedical and therapeutic applications. FEBS Open Bio 2024. [PMID: 38898362 DOI: 10.1002/2211-5463.13850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/25/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
Nanobodies, the smallest functional antibody fragment derived from camelid heavy-chain-only antibodies, have emerged as powerful tools for diverse biomedical applications. In this comprehensive review, we discuss the structural characteristics, functional properties, and computational approaches driving the design and optimisation of synthetic nanobodies. We explore their unique antigen-binding domains, highlighting the critical role of complementarity-determining regions in target recognition and specificity. This review further underscores the advantages of nanobodies over conventional antibodies from a biosynthesis perspective, including their small size, stability, and solubility, which make them ideal candidates for economical antigen capture in diagnostics, therapeutics, and biosensing. We discuss the recent advancements in computational methods for nanobody modelling, epitope prediction, and affinity maturation, shedding light on their intricate antigen-binding mechanisms and conformational dynamics. Finally, we examine a direct example of how computational design strategies were implemented for improving a nanobody-based immunosensor, known as a Quenchbody. Through combining experimental findings and computational insights, this review elucidates the transformative impact of nanobodies in biotechnology and biomedical research, offering a roadmap for future advancements and applications in healthcare and diagnostics.
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Affiliation(s)
- Nehad S El Salamouni
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Australia
| | - Jordan H Cater
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Australia
| | - Haibo Yu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Australia
- ARC Centre of Excellence in Quantum Biotechnology, University of Wollongong, Australia
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2
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Deng Y, Liu J, Lu Y, Fan X, Yang Y, Xu Y, Qin X, Nian R, Liu W. Novel Polystyrene-Binding Nanobody for Enhancing Immunoassays: Insights into Affinity, Immobilization, and Application Potential. Anal Chem 2024; 96:1597-1605. [PMID: 38235613 DOI: 10.1021/acs.analchem.3c04375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Nanobodies, which represent the next generation of antibodies due to their unique properties, face a significant limitation in their poor physical adsorption on solid supports. In this study, we successfully discovered polystyrene binding nanobodies from a synthetic nanobody library. Notably, bivalent nanobody B2 exhibited high affinity for polystyrene (0.7 nM for ELISA saturation binding analysis and 15.6 nM for isothermal titration calorimetry), displaying a pH-dependent behavior. Remarkably, hydrophobic and electrostatic interactions contribute minimally to the binding process. Molecular modeling provided insights into the interaction between B2 and polystyrene, revealing that the Trp51 residue within the CDR2 loop formed an aromatic H-bond with polystyrene at a distance of 2.74 Å, thus explaining the observed reduction in B2 affinity caused by Trp51 mutations. To explore B2's potential in protein immobilization, we constructed a bispecific nanobody by fusing B2 to an anticarcinoembryonic antigen nanobody 11C12, which cannot be immobilized on polystyrene through passive adsorption. Remarkably, the fusion construct achieved effective immobilization on polystyrene within 5 min by passing the need for periplasmic protein purification despite its low expression level. Moreover, the fusion construct demonstrated excellent linearity in the chemiluminescent enzyme immunoassay. For the first time, this study reports a simplified and seamless platform for the oriented immobilization of nanobody. Importantly, the entire process eliminated the need for protein purification, enabling efficient and rapid immobilization of fusion proteins directly from crude cell extracts, even when the expression level was low. Our developed process dramatically reduced the processing time from 2.5 days to just 5 min.
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Affiliation(s)
- Yang Deng
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189, Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189, Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, No. 189, Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, No 19(A), Yuquan Road, Beijing 100049, China
| | - Jinyan Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189, Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189, Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, No. 189, Songling Road, Qingdao 266101, China
| | - Yaoping Lu
- WEGO Holding Co., Ltd., No. 18, Xingshan Road, Torch Hi-tech Science Park, Weihai 264210, China
| | - Xiying Fan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189, Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189, Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, No. 189, Songling Road, Qingdao 266101, China
| | - Yuansheng Yang
- Agency for Science, Technology and Research (A*STAR), Bioprocessing Technology Institute, 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore
| | - Yaozheng Xu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang 110004, China
- Liaoning Clinical Research Center for Laboratory Medicine, No. 36, Sanhao Street, Shenyang 110004, China
| | - Xiaosong Qin
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang 110004, China
- Liaoning Clinical Research Center for Laboratory Medicine, No. 36, Sanhao Street, Shenyang 110004, China
| | - Rui Nian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189, Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189, Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, No. 189, Songling Road, Qingdao 266101, China
| | - Wenshuai Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189, Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189, Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, No. 189, Songling Road, Qingdao 266101, China
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3
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Zhao TT, Hu HJ, Gao LX, Zhou YB, Zhu YL, Zhang C, Li J, Wang WL. Exploring the mechanism of the PTP1B inhibitors by molecular dynamics and experimental study. J Mol Graph Model 2023; 125:108585. [PMID: 37544021 DOI: 10.1016/j.jmgm.2023.108585] [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: 06/14/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) has proven to be an attractive target for the treatment of cancer, diabetes and other diseases. Although many PTP1B inhibitors with various scaffolds have been developed, there is still a lack of PTP1B inhibitor with high specificity and acceptable pharmacological properties. Therefore, it is urgent to develop more methods to explore complex action mode of PTP1B and ligands for designing ideal PTP1B modulators. In this work, we developed a potential molecular dynamics (MD) analytic mode to analyze the mechanism of active compounds 6a and 6e against PTP1B from different perspectives, including the stable ability, interactions and binding site of ligand and protein, the binding energy, relative movement between residues and changes in protein internal interactions. The simulated results demonstrated that compound 6a bound more stably to the active pocket of PTP1B than 6e due to its smaller molecular volume (326 Å3), matched electronegativity, and enhanced the positive correlation motion of residues, especially for WPD loop and P loop. Lastly, compound 6a as a competitive inhibitor for PTP1B was verified by enzyme kinetic assay. This work successfully studied the mechanism of compound 6a against PTP1B from various aspects, enriched the analysis of interaction mode between PTP1B and inhibitors. In summary, we hope that this work could provide more theoretical information for designing and developing more novel and ideal PTP1B inhibitors in the future.
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Affiliation(s)
- Tian-Tian Zhao
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China
| | - Hao-Jie Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China
| | - Li-Xin Gao
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yu-Bo Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yun-Long Zhu
- Wuxi Maternal and Child Health Hospital, Wuxi School of Medicine, Jiangnan University, Jiangsu, 214002, China.
| | - Chun Zhang
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China.
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Wen-Long Wang
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China.
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Kumar V, Dahiya S, Budania S, Gupta AK, Sangwan P, Lather A, Kumar P, Kakker NK, Singh A. Characterization of Foot-and-Mouth Disease Virus Serotype O-Specific Single Domain Antibody Expressed in the pET Expression System. Indian J Microbiol 2023; 63:337-343. [PMID: 37781019 PMCID: PMC10533770 DOI: 10.1007/s12088-023-01095-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/16/2023] [Indexed: 10/03/2023] Open
Abstract
Foot and mouth disease (FMD) is an extremely contagious disease of cloven-hoofed domesticated and wild animals, resulting in significant economic losses in many parts of the world. FMD virus (FMDV) serotype O is responsible for approximately 70% of global outbreaks. For detection of FMDV antigen or antibody, ELISAs are used worldwide and have several limitations, such as batch-to-batch variation in generating immunobiologicals, high production cost and ethical concerns over animal sacrifice. The use of single domain antibody (sdAb) or variable N-terminal domain of the heavy chain of heavy chain antibody (VHH) found naturally in camels has proven their effectiveness in diagnostics and therapeutics. In the present study, the anti-FMDV serotype O-specific VHH-C1 gene sequence (Accession no. KJ751546) was retrieved from the NCBI database. The gene was synthesized commercially in the pBluescript KS+ cloning vector and expressed in E. coli BL21 (DE3) cells using the pET303/CT-His expression system with a C-terminal 6X-His tag. The expressed sdAb, verified by SDS‒PAGE and western blotting, was purified by Ni-chelate chromatography and used as a coating antibody in double antibody sandwich (DAS) ELISA for FMDV detection and typing. The sdAb exhibited a high binding affinity for FMDV serotype O, without any cross-reactivity toward serotypes A and Asia-1. It exhibited better thermostability up to 85 °C than conventional rabbit polyclonal anti-FMDV sera. The potential of sdAbs thus produced without sacrificing lab animals could be explored for replacing polyclonal sera in DAS-ELISA as well as for developing biosensors or lateral flow devices for FMDV type O detection.
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Affiliation(s)
- Vijay Kumar
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Swati Dahiya
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Savita Budania
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Akhil Kumar Gupta
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Punesh Sangwan
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Anshul Lather
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Pawan Kumar
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Naresh Kumar Kakker
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Ajit Singh
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
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Jin BK, Odongo S, Radwanska M, Magez S. NANOBODIES®: A Review of Diagnostic and Therapeutic Applications. Int J Mol Sci 2023; 24:5994. [PMID: 36983063 PMCID: PMC10057852 DOI: 10.3390/ijms24065994] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
NANOBODY® (a registered trademark of Ablynx N.V) molecules (Nbs), also referred to as single domain-based VHHs, are antibody fragments derived from heavy-chain only IgG antibodies found in the Camelidae family. Due to their small size, simple structure, high antigen binding affinity, and remarkable stability in extreme conditions, nanobodies possess the potential to overcome several of the limitations of conventional monoclonal antibodies. For many years, nanobodies have been of great interest in a wide variety of research fields, particularly in the diagnosis and treatment of diseases. This culminated in the approval of the world's first nanobody based drug (Caplacizumab) in 2018 with others following soon thereafter. This review will provide an overview, with examples, of (i) the structure and advantages of nanobodies compared to conventional monoclonal antibodies, (ii) methods used to generate and produce antigen-specific nanobodies, (iii) applications for diagnostics, and (iv) ongoing clinical trials for nanobody therapeutics as well as promising candidates for clinical development.
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Affiliation(s)
- Bo-kyung Jin
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon 21985, Republic of Korea
| | - Steven Odongo
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon 21985, Republic of Korea
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala 7062, Uganda
- Center for Biosecurity and Global Health, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala 7062, Uganda
| | - Magdalena Radwanska
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon 21985, Republic of Korea
- Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Stefan Magez
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon 21985, Republic of Korea
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
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6
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General Trends of the Camelidae Antibody V HHs Domain Dynamics. Int J Mol Sci 2023; 24:ijms24054511. [PMID: 36901942 PMCID: PMC10003728 DOI: 10.3390/ijms24054511] [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: 02/09/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Conformational flexibility plays an essential role in antibodies' functional and structural stability. They facilitate and determine the strength of antigen-antibody interactions. Camelidae express an interesting subtype of single-chain antibody, named Heavy Chain only Antibody. They have only one N-terminal Variable domain (VHH) per chain, composed of Frameworks (FRs) and Complementarity Determining regions (CDRs) like their VH and VL counterparts in IgG. Even when expressed independently, VHH domains display excellent solubility and (thermo)stability, which helps them to retain their impressive interaction capabilities. Sequence and structural features of VHH domains contributing to these abilities have already been studied compared to classical antibodies. To have the broadest view and understand the changes in dynamics of these macromolecules, large-scale molecular dynamics simulations for a large number of non-redundant VHH structures have been performed for the first time. This analysis reveals the most prevalent movements in these domains. It reveals the four main classes of VHHs dynamics. Diverse local changes were observed in CDRs with various intensities. Similarly, different types of constraints were observed in CDRs, while FRs close to CDRs were sometimes primarily impacted. This study sheds light on the changes in flexibility in different regions of VHH that may impact their in silico design.
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7
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V HH Structural Modelling Approaches: A Critical Review. Int J Mol Sci 2022; 23:ijms23073721. [PMID: 35409081 PMCID: PMC8998791 DOI: 10.3390/ijms23073721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 12/20/2022] Open
Abstract
VHH, i.e., VH domains of camelid single-chain antibodies, are very promising therapeutic agents due to their significant physicochemical advantages compared to classical mammalian antibodies. The number of experimentally solved VHH structures has significantly improved recently, which is of great help, because it offers the ability to directly work on 3D structures to humanise or improve them. Unfortunately, most VHHs do not have 3D structures. Thus, it is essential to find alternative ways to get structural information. The methods of structure prediction from the primary amino acid sequence appear essential to bypass this limitation. This review presents the most extensive overview of structure prediction methods applied for the 3D modelling of a given VHH sequence (a total of 21). Besides the historical overview, it aims at showing how model software programs have been shaping the structural predictions of VHHs. A brief explanation of each methodology is supplied, and pertinent examples of their usage are provided. Finally, we present a structure prediction case study of a recently solved VHH structure. According to some recent studies and the present analysis, AlphaFold 2 and NanoNet appear to be the best tools to predict a structural model of VHH from its sequence.
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8
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Comparative studies on the interaction of ascorbic acid with gastric enzyme using multispectroscopic and docking methods. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131270] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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9
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Fernandes CFC, Pereira SS, Luiz MB, Silva NKRL, Silva MCS, Marinho ACM, Fonseca MHG, Furtado GP, Trevizani R, Nicolete R, Soares AM, Zuliani JP, Stabeli RG. Engineering of single-domain antibodies for next-generation snakebite antivenoms. Int J Biol Macromol 2021; 185:240-250. [PMID: 34118288 DOI: 10.1016/j.ijbiomac.2021.06.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 12/29/2022]
Abstract
Given the magnitude of the global snakebite crisis, strategies to ensure the quality of antivenom, as well as the availability and sustainability of its supply are under development by several research groups. Recombinant DNA technology has allowed the engineering of monoclonal antibodies and recombinant fragments as alternatives to conventional antivenoms. Besides having higher therapeutic efficacy, with broad neutralization capacity against local and systemic toxicity, novel antivenoms need to be safe and cost-effective. Due to the biological and physical chemical properties of camelid single-domain antibodies, with high volume of distribution to distal tissue, their modular format, and their versatility, their biotechnological application has grown considerably in recent decades. This article presents the most up-to-date developments concerning camelid single-domain-based antibodies against major toxins from snake venoms, the main venomous animals responsible for reported envenoming cases and related human deaths. A brief discussion on the composition, challenges, and perspectives of antivenoms is presented, as well as the road ahead for next-generation antivenoms based on single-domain antibodies.
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Affiliation(s)
| | - Soraya S Pereira
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil
| | - Marcos B Luiz
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil
| | - Nauanny K R L Silva
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil
| | - Marcela Cristina S Silva
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil
| | | | | | | | | | | | - Andreimar M Soares
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil
| | - Juliana P Zuliani
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil; Universidade Federal de Rondônia, UNIR, Porto Velho, Rondônia, Brazil
| | - Rodrigo G Stabeli
- Plataforma Bi-Institucional de Medicina Translacional (Fiocruz-USP), Ribeirão Preto, São Paulo, Brazil
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Du S, Lu XH, Li WY, Li LP, Ma YC, Zhou L, Wu JW, Ma Y, Wang RL. Exploring the dynamic mechanism of allosteric drug SHP099 inhibiting SHP2 E69K. Mol Divers 2021; 25:1873-1887. [PMID: 33392964 DOI: 10.1007/s11030-020-10179-y] [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: 10/01/2020] [Accepted: 12/17/2020] [Indexed: 10/22/2022]
Abstract
The E69K mutation is one of the most frequent protein tyrosine phosphatase-2 (SHP2) mutations in leukemia, and it can cause the increase in the protein activity. Recent studies have shown that the E69K mutation was fairly sensitive to the allosteric inhibitor of SHP2 (SHP099). However, the molecular mechanism of the allosteric drug SHP099 inhibiting SHP2E69K remains unclear. Thus, the molecular dynamic simulations and the post-dynamics analyses (RMSF, PCA, DCCM, RIN and the binding free energies) for SHP2WT, SHP2WT-SHP099, SHP2E69K and SHP2E69K-SHP099 were carried out, respectively. Owing to the strong binding affinity of SHP099 to residues Thr219 and Arg220, the flexibility of linker region (residues Val209-Arg231) was reduced. Moreover, the presence of SHP099 kept the autoinhibition state of the SHP2 protein through enhancing the interactions between the linker region and Q loop in PTP domain, such as Thr219/Val490, Thr219/Asn491, Arg220/Ile488 and Leu254/Asn491. In addition, it was found that the residues (Thr219, Arg220, Leu254 and Asn491) might be the key residues responsible for the conformational changes of protein. Overall, this study may provide an important basis for understanding how the SHP099 effectively inhibited the SHP2E69K activity at the molecular level.
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Affiliation(s)
- Shan Du
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Xin-Hua Lu
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, Key Laboratory for New Drug Screening Technology of Shijiazhuang City, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang, 050015, Hebei, China
| | - Wei-Ya Li
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Li-Peng Li
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Yang-Chun Ma
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Liang Zhou
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Jing-Wei Wu
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Ying Ma
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
| | - Run-Ling Wang
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
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11
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Cheng Z, Lan Y, Guo J, Ma D, Jiang S, Lai Q, Zhou Z, Peplowski L. Computational Design of Nitrile Hydratase from Pseudonocardia thermophila JCM3095 for Improved Thermostability. Molecules 2020; 25:molecules25204806. [PMID: 33086715 PMCID: PMC7587978 DOI: 10.3390/molecules25204806] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/08/2020] [Accepted: 10/16/2020] [Indexed: 11/16/2022] Open
Abstract
High thermostability and catalytic activity are key properties for nitrile hydratase (NHase, EC 4.2.1.84) as a well-industrialized catalyst. In this study, rational design was applied to tailor the thermostability of NHase from Pseudonocardia thermophila JCM3095 (PtNHase) by combining FireProt server prediction and molecular dynamics (MD) simulation. Site-directed mutagenesis of non-catalytic residues provided by the rational design was subsequentially performed. The positive multiple-point mutant, namely, M10 (αI5P/αT18Y/αQ31L/αD92H/βA20P/βP38L/βF118W/βS130Y/βC189N/βC218V), was obtained and further analyzed. The Melting temperature (Tm) of the M10 mutant showed an increase by 3.2 °C and a substantial increase in residual activity of the enzyme at elevated temperatures was also observed. Moreover, the M10 mutant also showed a 2.1-fold increase in catalytic activity compared with the wild-type PtNHase. Molecular docking and MD simulations demonstrated better substrate affinity and improved thermostability for the mutant.
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Affiliation(s)
- Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Yao Lan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Junling Guo
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Dong Ma
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Shijin Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Qianpeng Lai
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
- Jiangnan University (Rugao) Food Biotechnology Research Institute, Rugao 226500, China
- Correspondence: (Z.Z.); (L.P.)
| | - Lukasz Peplowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland
- Correspondence: (Z.Z.); (L.P.)
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Torshin IY, Namiot VA, Esipova NG, Tumanyan VG. Numeric analysis of reversibility of classic movement equations and constructive criteria of estimating quality of molecular dynamic simulations. J Biomol Struct Dyn 2020; 39:4066-4076. [DOI: 10.1080/07391102.2020.1773927] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ivan Yu. Torshin
- Dorodnicyn Computing Centre, Russian Academy of Sciences, FIC IU RAS, Moscow, Russian Federation
| | - Vladimir A. Namiot
- Institute of Nuclear Physics, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Natalia G. Esipova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir G. Tumanyan
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
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Du S, Yang B, Wang X, Li WY, Lu XH, Zheng ZH, Ma Y, Wang RL. Identification of potential leukocyte antigen-related protein (PTP-LAR) inhibitors through 3D QSAR pharmacophore-based virtual screening and molecular dynamics simulation. J Biomol Struct Dyn 2019; 38:4232-4245. [PMID: 31588870 DOI: 10.1080/07391102.2019.1676825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Owing to its negative regulatory role in insulin signaling, protein tyrosine phosphatase of leukocyte antigen-related protein (PTP-LAR) was widely thought as a potential drug target for diabetes. Now, it was urgent to search for potential LAR inhibitors targeting diabetes. Initially, the pharmacophore models of LAR inhibitors were established with the application of the HypoGen module. The cost analysis, test set validation, as well as Fischer's test was used to verify the efficiency of pharmacophore model. Then, the best pharmacophore model (Hypo-1-LAR) was applied for the virtual screening of the ZINC database. And 30 compounds met the Lipinski's rule of five. Among them, 10 compounds with better binding affinity than the known LAR inhibitor (BDBM50296375) were discovered by docking studies. Finally, molecular dynamics simulations and post-analysis experiments (RMSD, RMSF, PCA, DCCM and RIN) were conducted to explore the effect of ligands (ZINC97018474 and Compound 1) on LAR and preliminary understand why ZINC97018474 had better inhibitory activity than Compound 1 (BDBM50296375). Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shan Du
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Bing Yang
- Department of Cell Biology, School of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Xin Wang
- Tasly Pharmaceutical Group Co., Ltd, Tianjin, China
| | - Wei-Ya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xin-Hua Lu
- Key Laboratory for New Drug Screening Technology of Shijiazhuang City, New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang, Hebei, China
| | - Zhi-Hui Zheng
- Key Laboratory for New Drug Screening Technology of Shijiazhuang City, New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang, Hebei, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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