1
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Lu H, Zhu Z, Fields L, Zhang H, Li L. Mass Spectrometry Structural Proteomics Enabled by Limited Proteolysis and Cross-Linking. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39300771 DOI: 10.1002/mas.21908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 08/31/2024] [Accepted: 09/02/2024] [Indexed: 09/22/2024]
Abstract
The exploration of protein structure and function stands at the forefront of life science and represents an ever-expanding focus in the development of proteomics. As mass spectrometry (MS) offers readout of protein conformational changes at both the protein and peptide levels, MS-based structural proteomics is making significant strides in the realms of structural and molecular biology, complementing traditional structural biology techniques. This review focuses on two powerful MS-based techniques for peptide-level readout, namely limited proteolysis-mass spectrometry (LiP-MS) and cross-linking mass spectrometry (XL-MS). First, we discuss the principles, features, and different workflows of these two methods. Subsequently, we delve into the bioinformatics strategies and software tools used for interpreting data associated with these protein conformation readouts and how the data can be integrated with other computational tools. Furthermore, we provide a comprehensive summary of the noteworthy applications of LiP-MS and XL-MS in diverse areas including neurodegenerative diseases, interactome studies, membrane proteins, and artificial intelligence-based structural analysis. Finally, we discuss the factors that modulate protein conformational changes. We also highlight the remaining challenges in understanding the intricacies of protein conformational changes by LiP-MS and XL-MS technologies.
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Affiliation(s)
- Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Zexin Zhu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
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2
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Matsuzaka Y, Yashiro R. Therapeutic Application and Structural Features of Adeno-Associated Virus Vector. Curr Issues Mol Biol 2024; 46:8464-8498. [PMID: 39194716 DOI: 10.3390/cimb46080499] [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: 06/10/2024] [Revised: 07/02/2024] [Accepted: 07/12/2024] [Indexed: 08/29/2024] Open
Abstract
Adeno-associated virus (AAV) is characterized by non-pathogenicity, long-term infection, and broad tropism and is actively developed as a vector virus for gene therapy products. AAV is classified into more than 100 serotypes based on differences in the amino acid sequence of the capsid protein. Endocytosis involves the uptake of viral particles by AAV and accessory receptors during AAV infection. After entry into the cell, they are transported to the nucleus through the nuclear pore complex. AAVs mainly use proteoglycans as receptors to enter cells, but the types of sugar chains in proteoglycans that have binding ability are different. Therefore, it is necessary to properly evaluate the primary structure of receptor proteins, such as amino acid sequences and post-translational modifications, including glycosylation, and the higher-order structure of proteins, such as the folding of the entire capsid structure and the three-dimensional (3D) structure of functional domains, to ensure the efficacy and safety of biopharmaceuticals. To further enhance safety, it is necessary to further improve the efficiency of gene transfer into target cells, reduce the amount of vector administered, and prevent infection of non-target cells.
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Affiliation(s)
- Yasunari Matsuzaka
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
- Administrative Section of Radiation Protection, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira 187-8551, Japan
| | - Ryu Yashiro
- Administrative Section of Radiation Protection, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira 187-8551, Japan
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
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3
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Venanzi NE, Basciu A, Vargiu AV, Kiparissides A, Dalby PA, Dikicioglu D. Machine Learning Integrating Protein Structure, Sequence, and Dynamics to Predict the Enzyme Activity of Bovine Enterokinase Variants. J Chem Inf Model 2024; 64:2681-2694. [PMID: 38386417 PMCID: PMC11005043 DOI: 10.1021/acs.jcim.3c00999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
Despite recent advances in computational protein science, the dynamic behavior of proteins, which directly governs their biological activity, cannot be gleaned from sequence information alone. To overcome this challenge, we propose a framework that integrates the peptide sequence, protein structure, and protein dynamics descriptors into machine learning algorithms to enhance their predictive capabilities and achieve improved prediction of the protein variant function. The resulting machine learning pipeline integrates traditional sequence and structure information with molecular dynamics simulation data to predict the effects of multiple point mutations on the fold improvement of the activity of bovine enterokinase variants. This study highlights how the combination of structural and dynamic data can provide predictive insights into protein functionality and address protein engineering challenges in industrial contexts.
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Affiliation(s)
| | - Andrea Basciu
- Department
of Physics, University of Cagliari, Cittadella
Universitaria, I-09042 Monserrato, Cagliari, Italy
| | - Attilio Vittorio Vargiu
- Department
of Physics, University of Cagliari, Cittadella
Universitaria, I-09042 Monserrato, Cagliari, Italy
| | - Alexandros Kiparissides
- Department
of Biochemical Engineering, University College
London, Gower Street, WC1E 6BT London, U.K.
- Department
of Chemical Engineering, Aristotle University
of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Paul A. Dalby
- Department
of Biochemical Engineering, University College
London, Gower Street, WC1E 6BT London, U.K.
| | - Duygu Dikicioglu
- Department
of Biochemical Engineering, University College
London, Gower Street, WC1E 6BT London, U.K.
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4
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Pillai AS, Hochberg GK, Thornton JW. Simple mechanisms for the evolution of protein complexity. Protein Sci 2022; 31:e4449. [PMID: 36107026 PMCID: PMC9601886 DOI: 10.1002/pro.4449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/01/2022] [Accepted: 09/10/2022] [Indexed: 01/26/2023]
Abstract
Proteins are tiny models of biological complexity: specific interactions among their many amino acids cause proteins to fold into elaborate structures, assemble with other proteins into higher-order complexes, and change their functions and structures upon binding other molecules. These complex features are classically thought to evolve via long and gradual trajectories driven by persistent natural selection. But a growing body of evidence from biochemistry, protein engineering, and molecular evolution shows that naturally occurring proteins often exist at or near the genetic edge of multimerization, allostery, and even new folds, so just one or a few mutations can trigger acquisition of these properties. These sudden transitions can occur because many of the physical properties that underlie these features are present in simpler proteins as fortuitous by-products of their architecture. Moreover, complex features of proteins can be encoded by huge arrays of sequences, so they are accessible from many different starting points via many possible paths. Because the bridges to these features are both short and numerous, random chance can join selection as a key factor in explaining the evolution of molecular complexity.
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Affiliation(s)
- Arvind S. Pillai
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
- Institute for Protein DesignUniversity of WashingtonSeattleWAUSA
| | - Georg K.A. Hochberg
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Department of Chemistry, Center for Synthetic MicrobiologyPhilipps University MarburgMarburgGermany
| | - Joseph W. Thornton
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
- Departments of Human Genetics and Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
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5
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Zhang R, Han Y, Xie W, Liu F, Chen S. Advances in Protein-Based Nanocarriers of Bioactive Compounds: From Microscopic Molecular Principles to Macroscopical Structural and Functional Attributes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6354-6367. [PMID: 35603429 DOI: 10.1021/acs.jafc.2c01936] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Many proteins can be used to fabricate nanocarriers for encapsulation, protection, and controlled release of nutraceuticals. This review examined the protein-based nanocarriers from microscopic molecular characteristics to the macroscopical structural and functional attributes. Structural, physical, and chemical properties of protein-based nanocarriers were introduced in detail. The spatial size, shape, water dispersibility, colloidal stability, etc. of protein-based nanocarriers were largely determined by the molecular physicochemical principles of protein. Different preparative techniques, including antisolvent precipitation, pH-driven, electrospray, and gelation methods, among others, can be used to fabricate different protein-based nanocarriers. Various modifications based on physical, chemical, and enzymatic approaches can be used to improve the functional performance of these nanocarriers. Protein is a natural resource with a wide range of sources, including plant, animal, and microbial, which are usually used to fabricate the nanocarriers. Protein-based nanocarriers have many advantages in aid of the application of bioactive ingredients to the medical, food, and cosmetic industries.
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Affiliation(s)
- Ruyi Zhang
- School of Public Health, Wuhan University, 115 Donghu Road, Wuchang District, Wuhan, Hubei 430071, People's Republic of China
| | - Yahong Han
- Key Laboratory of Aquaculture Facilities Engineering, Ministry of Agriculture and Rural Affairs, College of Engineering, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Weijie Xie
- Shanghai Mental Health Centre, School of Medicine, Shanghai Jiao Tong University, Shanghai 200011, People's Republic of China
| | - Fuguo Liu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Shuai Chen
- School of Public Health, Wuhan University, 115 Donghu Road, Wuchang District, Wuhan, Hubei 430071, People's Republic of China
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6
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Djokovic N, Ruzic D, Rahnasto-Rilla M, Srdic-Rajic T, Lahtela-Kakkonen M, Nikolic K. Expanding the Accessible Chemical Space of SIRT2 Inhibitors through Exploration of Binding Pocket Dynamics. J Chem Inf Model 2022; 62:2571-2585. [PMID: 35467856 DOI: 10.1021/acs.jcim.2c00241] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Considerations of binding pocket dynamics are one of the crucial aspects of the rational design of binders. Identification of alternative conformational states or cryptic subpockets could lead to the discovery of completely novel groups of the ligands. However, experimental characterization of pocket dynamics, besides being expensive, may not be able to elucidate all of the conformational states relevant for drug discovery projects. In this study, we propose the protocol for computational simulations of sirtuin 2 (SIRT2) binding pocket dynamics and its integration into the structure-based virtual screening (SBVS) pipeline. Initially, unbiased molecular dynamics simulations of SIRT2:inhibitor complexes were performed using optimized force field parameters of SIRT2 inhibitors. Time-lagged independent component analysis (tICA) was used to design pocket-related collective variables (CVs) for enhanced sampling of SIRT2 pocket dynamics. Metadynamics simulations in the tICA eigenvector space revealed alternative conformational states of the SIRT2 binding pocket and the existence of a cryptic subpocket. Newly identified SIRT2 conformational states outperformed experimentally resolved states in retrospective SBVS validation. After performing prospective SBVS, compounds from the under-represented portions of the SIRT2 inhibitor chemical space were selected for in vitro evaluation. Two compounds, NDJ18 and NDJ85, were identified as potent and selective SIRT2 inhibitors, which validated the in silico protocol and opened up the possibility for generalization and broadening of its application. The anticancer effects of the most potent compound NDJ18 were examined on the triple-negative breast cancer cell line. Results indicated that NDJ18 represents a promising structure suitable for further evaluation.
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Affiliation(s)
- Nemanja Djokovic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Minna Rahnasto-Rilla
- School of Pharmacy, University of Eastern Finland, P.O. Box 1627, 70210 Kuopio, Finland
| | - Tatjana Srdic-Rajic
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | | | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
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7
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Chalopin Y, Sparfel J. Energy Bilocalization Effect and the Emergence of Molecular Functions in Proteins. Front Mol Biosci 2022; 8:736376. [PMID: 35004841 PMCID: PMC8733615 DOI: 10.3389/fmolb.2021.736376] [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: 07/05/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
Proteins are among the most complex molecular structures, which have evolved to develop broad functions, such as energy conversion and transport, information storage and processing, communication, and regulation of chemical reactions. However, the mechanisms by which these dynamical entities coordinate themselves to perform biological tasks remain hotly debated. Here, a physical theory is presented to explain how functional dynamical behavior possibly emerge in complex/macro molecules, thanks to the effect that we term bilocalization of thermal vibrations. More specifically, our approach allows us to understand how structural irregularities lead to a partitioning of the energy of the vibrations into two distinct sets of molecular domains, corresponding to slow and fast motions. This shape-encoded spectral allocation, associated to the genetic sequence, provides a close access to a wide reservoir of dynamical patterns, and eventually allows the emergence of biological functions by natural selection. To illustrate our approach, the SPIKE protein structure of SARS-COV2 is considered.
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Affiliation(s)
- Yann Chalopin
- Laboratoire EM2C-CNRS and CentraleSupélec, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Julien Sparfel
- Laboratoire EM2C-CNRS and CentraleSupélec, University of Paris-Saclay, Gif-sur-Yvette, France
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8
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Damry AM, Jackson CJ. The evolution and engineering of enzyme activity through tuning conformational landscapes. Protein Eng Des Sel 2021; 34:6254467. [PMID: 33903911 DOI: 10.1093/protein/gzab009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 11/12/2022] Open
Abstract
Proteins are dynamic molecules whose structures consist of an ensemble of conformational states. Dynamics contribute to protein function and a link to protein evolution has begun to emerge. This increased appreciation for the evolutionary impact of conformational sampling has grown from our developing structural biology capabilities and the exploration of directed evolution approaches, which have allowed evolutionary trajectories to be mapped. Recent studies have provided empirical examples of how proteins can evolve via conformational landscape alterations. Moreover, minor conformational substates have been shown to be involved in the emergence of new enzyme functions as they can become enriched through evolution. The role of remote mutations in stabilizing new active site geometries has also granted insight into the molecular basis underpinning poorly understood epistatic effects that guide protein evolution. Finally, we discuss how the growth of our understanding of remote mutations is beginning to refine our approach to engineering enzymes.
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Affiliation(s)
- Adam M Damry
- Research School of Chemistry, The Australian National University, Canberra, 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, The Australian National University, Canberra, 2601, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, 2601, ACT, Australia.,Australian Research Council Centre of Excellence in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, 2601, ACT, Australia
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9
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Adolf-Bryfogle J, Teets FD, Bahl CD. Toward complete rational control over protein structure and function through computational design. Curr Opin Struct Biol 2020; 66:170-177. [PMID: 33276237 DOI: 10.1016/j.sbi.2020.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/08/2020] [Accepted: 10/19/2020] [Indexed: 11/28/2022]
Abstract
The grand challenge of protein design is a general method for producing a polypeptide with arbitrary functionality, conformation, and biochemical properties. To that end, a wide variety of methods have been developed for the improvement of native proteins, the design of ideal proteins de novo, and the redesign of suboptimal proteins with better-performing substructures. These methods employ informatic comparisons of function-structure-sequence relationships as well as knowledge-based evaluation of protein properties to narrow the immense protein sequence search space down to an enumerable and often manually evaluable set of structures that meet specified criteria. While arbitrary manipulation of protein-protein interfaces and molecular catalysis remains an unsolved problem, and no protein shape or behavior manipulation algorithm is universally applicable, the promising results thus far are a strong indicator that a general approach to the arbitrary manipulation of polypeptides is within reach.
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Affiliation(s)
- Jared Adolf-Bryfogle
- Institute for Protein Innovation, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Frank D Teets
- Institute for Protein Innovation, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Christopher D Bahl
- Institute for Protein Innovation, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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10
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Alaofi AL. Exploring structural dynamics of the MERS-CoV receptor DPP4 and mutant DPP4 receptors. J Biomol Struct Dyn 2020; 40:752-763. [PMID: 32909925 DOI: 10.1080/07391102.2020.1818626] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mouse DPP4 (mDPP4) receptor is not a functional receptor for MERS-CoV while human DPP4 (hDPP4) is, despite the high similarities between hDPP4 and mDPP4 receptors. The variability of DPP4 receptors against MERS-CoV is not fully investigated, especially conformational and structural differences. Therefore, investigating the conformational differences of the DPP4 receptors can aid in developing new small animal models for MERS-CoV vaccines and antiviral agents evaluation. Here we used MD simulations and docking techniques to investigate these structural differences in DPP4 receptors. The results showed chimeric mouse mDPP4 (cmDPP4) has a similar compact conformation as wild-type hDPP4 based on the structural analysis. Interestingly, a single Thr288Ala mutation induced a relaxed conformation in chimeric 2 hDPP4 (c2hDPP4) and chimeric 2 mDPP4 (c2mDPP4); in addition to its significant effect on the DPP4 flexibility. The Thr288 residue is known for its critical function in MERS-CoV RBD interaction. Moreover, MERS-CoV RBD adopts a "standing" conformation when docked to hDPP4 and cmDPP4 in blade IV and V regions. In conclusion, the results could explain the functionality differences between mouse and human DPP4 receptors against MERS-CoV. However, further structural studies are needed to evaluate how DPP4 conformations affects MERS-CoV RBD binding and affinity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ahmed L Alaofi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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