Evolving Experimental Techniques for Structure-Based Drug Design

Aplin, Cody P.; Milano, Shawn K.; Zielinski, Kara A.; Pollack, Lois; Cerione, Richard A.

doi:10.1021/acs.jpcb.2c04344

Cited by 18 publications

(8 citation statements)

References 97 publications

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“…Nonetheless, there is still an urgent requirement to develop new anti-infective drugs. Virtual high-throughput screening and structure-based rational drug design have been established as powerful tools [ 62 ]. In addition, alternative non-antibiotic approaches must be actively sought, such as identifying new targets in pathogenic microbial cells (quorum sensing, riboswitches, transcriptional regulators, etc.)…”

Section: Liposomes and Lipid Nanoparticles (Lnps)mentioning

confidence: 99%

Approved Nanomedicine against Diseases

Jia

Jiang

et al. 2023

Pharmaceutics

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Nanomedicine is a branch of medicine using nanotechnology to prevent and treat diseases. Nanotechnology represents one of the most effective approaches in elevating a drug‘s treatment efficacy and reducing toxicity by improving drug solubility, altering biodistribution, and controlling the release. The development of nanotechnology and materials has brought a profound revolution to medicine, significantly affecting the treatment of various major diseases such as cancer, injection, and cardiovascular diseases. Nanomedicine has experienced explosive growth in the past few years. Although the clinical transition of nanomedicine is not very satisfactory, traditional drugs still occupy a dominant position in formulation development, but increasingly active drugs have adopted nanoscale forms to limit side effects and improve efficacy. The review summarized the approved nanomedicine, its indications, and the properties of commonly used nanocarriers and nanotechnology.

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Section: Liposomes and Lipid Nanoparticles (Lnps)mentioning

confidence: 99%

Approved Nanomedicine against Diseases

Jia

Jiang

et al. 2023

Pharmaceutics

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“…To robustly characterize the conformational dynamics that TG2 undergoes, we used cryoelectron microscopy (cryo-EM) and small angle X-ray scattering (SAXS) to study the effects of guanine nucleotides and calcium on its structure (55)(56)(57). Cryo-EM has evolved to become an important method for experimental protein structure determination and enables high-resolution reconstruction without the need for a protein crystal.…”

Section: Introductionmentioning

confidence: 99%

Defining the conformational states that enable transglutaminase 2 to promote cancer cell survival versus cell death

Aplin,

Zielinski,

Pabit

et al. 2024

Preprint

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Transglutaminase 2 (TG2) is a GTP-binding/protein-crosslinking enzyme that has been investigated as a therapeutic target for Celiac disease, neurological disorders, and aggressive cancers. TG2 has been suggested to adopt two conformational states that regulate its functions: a GTP-bound, closed conformation, and a calcium-bound, crosslinking-active open conformation. TG2 mutants that constitutively adopt an open conformation are cytotoxic to cancer cells. Thus, small molecules that maintain the open conformation of TG2 could offer a new therapeutic strategy. Here, we investigate TG2, using static and time-resolved small-angle X-ray scattering (SAXS) and single-particle cryoelectron microscopy (cryo-EM), to determine the conformational states responsible for conferring its biological effects. We also describe a newly developed TG2 inhibitor, LM11, that potently kills glioblastoma cells and use SAXS to investigate how LM11 affects the conformational states of TG2. Using SAXS and cryo-EM, we show that guanine nucleotide-bound TG2 adopts a monomeric closed conformation while calcium-bound TG2 assumes an open conformational state that can form higher order oligomers. SAXS analysis also suggests how a TG2 mutant that constitutively adopts the open state binds nucleotides through an alternative mechanism to wildtype TG2. Furthermore, we use time-resolved SAXS to show that LM11 increases the ability of calcium to drive TG2 to an open conformation, which is not reversible by guanine nucleotides and is cytotoxic to cancer cells. Taken together, our findings demonstrate that the conformational dynamics of TG2 are more complex than previously suggested and highlight how conformational stabilization of TG2 by LM11 maintains TG2 in a cytotoxic conformational state.Significance StatementThe multi-functional protein transglutaminase 2 (TG2) undergoes large conformational changes in response to nucleotide and calcium binding, resulting in diverse cellular effects that can differentially promote either cancer cell survival or cell death. Previous biochemical and structural characterizations have revealed that TG2 primarily adopts two conformational states, a closed nucleotide-bound conformation, and an open calcium-bound conformation. In this study, we use advanced structural methods to describe the conformational changes associated with TG2 activation and inhibition and define the mechanism by which small molecule inhibitors maintain TG2 in a structural state that kill cancer cells.

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“…Accelerating the practical and frequent application of cryo-EM for SBDD requires a comprehensive review of technical improvements in this field and successful case studies using cryo-EM for drug development. Recently, several papers have reviewed cryo-EM-based drug development from various perspectives ( Subramaniam et al, 2016 ; Venien-Bryan et al, 2017 ; Garcia-Nafria and Tate, 2020 ; Van Drie and Tong, 2020 ; Wigge et al, 2020 ; de Oliveira et al, 2021 ; Lees et al, 2021 ; Aplin et al, 2022 ; Robertson et al, 2022a ; Zhu et al, 2023 ). One review introduced the potency of cryo-EM applicable to drug development using protein structures with inhibitors ( Subramaniam et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

Cryo-electron microscopy-based drug design

Cebi,

Lee,

Subramani

et al. 2024

Front. Mol. Biosci.

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Structure-based drug design (SBDD) has gained popularity owing to its ability to develop more potent drugs compared to conventional drug-discovery methods. The success of SBDD relies heavily on obtaining the three-dimensional structures of drug targets. X-ray crystallography is the primary method used for solving structures and aiding the SBDD workflow; however, it is not suitable for all targets. With the resolution revolution, enabling routine high-resolution reconstruction of structures, cryogenic electron microscopy (cryo-EM) has emerged as a promising alternative and has attracted increasing attention in SBDD. Cryo-EM offers various advantages over X-ray crystallography and can potentially replace X-ray crystallography in SBDD. To fully utilize cryo-EM in drug discovery, understanding the strengths and weaknesses of this technique and noting the key advancements in the field are crucial. This review provides an overview of the general workflow of cryo-EM in SBDD and highlights technical innovations that enable its application in drug design. Furthermore, the most recent achievements in the cryo-EM methodology for drug discovery are discussed, demonstrating the potential of this technique for advancing drug development. By understanding the capabilities and advancements of cryo-EM, researchers can leverage the benefits of designing more effective drugs. This review concludes with a discussion of the future perspectives of cryo-EM-based SBDD, emphasizing the role of this technique in driving innovations in drug discovery and development. The integration of cryo-EM into the drug design process holds great promise for accelerating the discovery of new and improved therapeutic agents to combat various diseases.

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Evolving Experimental Techniques for Structure-Based Drug Design

Cited by 18 publications

References 97 publications

Approved Nanomedicine against Diseases

Approved Nanomedicine against Diseases

Defining the conformational states that enable transglutaminase 2 to promote cancer cell survival versus cell death

Cryo-electron microscopy-based drug design

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