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Parise A, Cresca S, Magistrato A. Molecular dynamics simulations for the structure-based drug design: targeting small-GTPases proteins. Expert Opin Drug Discov 2024:1-21. [PMID: 39105536 DOI: 10.1080/17460441.2024.2387856] [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: 04/18/2024] [Accepted: 07/30/2024] [Indexed: 08/07/2024]
Abstract
INTRODUCTION Molecular Dynamics (MD) simulations can support mechanism-based drug design. Indeed, MD simulations by capturing biomolecule motions at finite temperatures can reveal hidden binding sites, accurately predict drug-binding poses, and estimate the thermodynamics and kinetics, crucial information for drug discovery campaigns. Small-Guanosine Triphosphate Phosphohydrolases (GTPases) regulate a cascade of signaling events, that affect most cellular processes. Their deregulation is linked to several diseases, making them appealing drug targets. The broad roles of small-GTPases in cellular processes and the recent approval of a covalent KRas inhibitor as an anticancer agent renewed the interest in targeting small-GTPase with small molecules. AREA COVERED This review emphasizes the role of MD simulations in elucidating small-GTPase mechanisms, assessing the impact of cancer-related variants, and discovering novel inhibitors. EXPERT OPINION The application of MD simulations to small-GTPases exemplifies the role of MD simulations in the structure-based drug design process for challenging biomolecular targets. Furthermore, AI and machine learning-enhanced MD simulations, coupled with the upcoming power of quantum computing, are promising instruments to target elusive small-GTPases mutations and splice variants. This powerful synergy will aid in developing innovative therapeutic strategies associated to small-GTPases deregulation, which could potentially be used for personalized therapies and in a tissue-agnostic manner to treat tumors with mutations in small-GTPases.
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Affiliation(s)
- Angela Parise
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
| | - Sofia Cresca
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
| | - Alessandra Magistrato
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
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Rinaldi S, Moroni E, Rozza R, Magistrato A. Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation. J Chem Theory Comput 2024; 20:993-1018. [PMID: 38287883 DOI: 10.1021/acs.jctc.3c01239] [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: 01/31/2024]
Abstract
Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute 98-99% of the human genome. Non-coding RNAs encompass diverse functional classes, including microRNAs, small interfering RNAs, PIWI-interacting RNAs, small nuclear RNAs, small nucleolar RNAs, and long non-coding RNAs. With critical involvement in gene expression and regulation across various biological and physiopathological contexts, such as neuronal disorders, immune responses, cardiovascular diseases, and cancer, non-coding RNAs are emerging as disease biomarkers and therapeutic targets. In this review, after providing an overview of non-coding RNAs' role in cell homeostasis, we illustrate the potential and the challenges of state-of-the-art computational methods exploited to study non-coding RNAs biogenesis, function, and modulation. This can be done by directly targeting them with small molecules or by altering their expression by targeting the cellular engines underlying their biosynthesis. Drawing from applications, also taken from our work, we showcase the significance and role of computer simulations in uncovering fundamental facets of ncRNA mechanisms and modulation. This information may set the basis to advance gene modulation tools and therapeutic strategies to address unmet medical needs.
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Affiliation(s)
- Silvia Rinaldi
- National Research Council of Italy (CNR) - Institute of Chemistry of OrganoMetallic Compounds (ICCOM), c/o Area di Ricerca CNR di Firenze Via Madonna del Piano 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Elisabetta Moroni
- National Research Council of Italy (CNR) - Institute of Chemical Sciences and Technologies (SCITEC), via Mario Bianco 9, 20131 Milano, Italy
| | - Riccardo Rozza
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
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Rozza R, Janoš P, Magistrato A. Assessing the Binding Mode of a Splicing Modulator Stimulating Pre-mRNA Binding to the Plastic U2AF2 Splicing Factor. J Chem Inf Model 2023; 63:7508-7517. [PMID: 37967032 DOI: 10.1021/acs.jcim.3c01204] [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: 11/17/2023]
Abstract
RNA recognition motifs (RRMs) play a pivotal role in RNA metabolism and the regulation of gene expression. Owing to their plasticity and fuzziness, targeting RRM/RNA interfaces with small molecules is a daunting challenge for drug discovery campaigns. The U2AF2 splicing factor, which recognizes the polypyrimidine (polyPy) sequence of premature messenger (pre-m)RNA, exhibits a dynamic architecture consisting of two RRMs joined by a disordered linker. An inhibitor, NSC-194308, was shown to enhance the binding of pre-mRNA to U2AF2, selectively triggering cell death in leukemia cell lines containing spliceosome mutations. The NSC-194308 binding mode remains elusive; yet, unraveling its knowledge may offer intriguing insights for effectively targeting U2AF2 and other flexible protein/protein/RNA interfaces with small molecules. To infer plausible NSC-194308 binding poses to U2AF2, here, we applied and benchmarked the performance of static and dynamic docking approaches, elucidating the molecular basis of the NSC-194308-induced pre-mRNA stabilization on U2AF2. We demonstrate that introducing dynamic effects is mandatory to assess the binding mode of the inhibitors when they target plastic and modular architectures, such as those formed by interacting RRMs. The latter are widespread across RNA binding proteins; therefore, this mechanism may be broadly applicable to discover new therapeutics aimed at selectively modulating the RNA function by targeting protein/protein/RNA interfaces.
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Affiliation(s)
- Riccardo Rozza
- National Research Council of Italy (CNR)-Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| | - Pavel Janoš
- National Research Council of Italy (CNR)-Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR)-Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
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Singh Y, Hocky GM, Nolen BJ. Molecular dynamics simulations support a multistep pathway for activation of branched actin filament nucleation by Arp2/3 complex. J Biol Chem 2023; 299:105169. [PMID: 37595874 PMCID: PMC10514467 DOI: 10.1016/j.jbc.2023.105169] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/10/2023] [Accepted: 08/12/2023] [Indexed: 08/20/2023] Open
Abstract
Actin-related protein 2/3 complex (Arp2/3 complex) catalyzes the nucleation of branched actin filaments that push against membranes in processes like cellular motility and endocytosis. During activation by WASP proteins, the complex must bind WASP and engage the side of a pre-existing (mother) filament before a branched filament is nucleated. Recent high-resolution structures of activated Arp2/3 complex revealed two major sets of activating conformational changes. How these activating conformational changes are triggered by interactions of Arp2/3 complex with actin filaments and WASP remains unclear. Here we use a recent high-resolution structure of Arp2/3 complex at a branch junction to design all-atom molecular dynamics simulations that elucidate the pathway between the active and inactive states. We ran a total of ∼4.6 microseconds of both unbiased and steered all-atom molecular dynamics simulations starting from three different binding states, including Arp2/3 complex within a branch junction, bound only to a mother filament, and alone in solution. These simulations indicate that the contacts with the mother filament are mostly insensitive to the massive rigid body motion that moves Arp2 and Arp3 into a short pitch helical (filament-like) arrangement, suggesting actin filaments alone do not stimulate the short pitch conformational change. In contrast, contacts with the mother filament stabilize subunit flattening in Arp3, an intrasubunit change that converts Arp3 from a conformation that mimics an actin monomer to one that mimics a filamentous actin subunit. Our results support a multistep activation pathway that has important implications for understanding how WASP-mediated activation allows Arp2/3 complex to assemble force-producing actin networks.
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Affiliation(s)
| | - Glen M Hocky
- Department of Chemistry, New York University; Simons Center for Computational Physical Chemistry, New York University.
| | - Brad J Nolen
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon.
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Zhang S, Vavylonis D. Steps of actin filament branch formation by Arp2/3 complex investigated with coarse-grained molecular dynamics. Front Cell Dev Biol 2023; 11:1071977. [PMID: 36733458 PMCID: PMC9887124 DOI: 10.3389/fcell.2023.1071977] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
The nucleation of actin filament branches by the Arp2/3 complex involves activation through nucleation promotion factors (NPFs), recruitment of actin monomers, and binding of the complex to the side of actin filaments. Because of the large system size and processes that involve flexible regions and diffuse components, simulations of branch formation using all-atom molecular dynamics are challenging. We applied a coarse-grained model that retains amino-acid level information and allows molecular dynamics simulations in implicit solvent, with globular domains represented as rigid bodies and flexible regions allowed to fluctuate. We used recent electron microscopy structures of the inactive Arp2/3 complex bound to NPF domains and to mother actin filament for the activated Arp2/3 complex. We studied interactions of Arp2/3 complex with the activating VCA domain of the NPF Wiskott-Aldrich syndrome protein, actin monomers, and actin filament. We found stable configurations with one or two actin monomers bound along the branch filament direction and with CA domain of VCA associated to the strong and weak binding sites of the Arp2/3 complex, supporting prior structural studies and validating our approach. We reproduced delivery of actin monomers and CA to the Arp2/3 complex under different conditions, providing insight into mechanisms proposed in previous studies. Simulations of active Arp2/3 complex bound to a mother actin filament indicate the contribution of each subunit to the binding. Addition of the C-terminal tail of Arp2/3 complex subunit ArpC2, which is missing in the cryo-EM structure, increased binding affinity, indicating a possible stabilizing role of this tail.
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Affiliation(s)
- Shuting Zhang
- Department of Physics, Lehigh University, Bethlehem, PA, United States
| | - Dimitrios Vavylonis
- Department of Physics, Lehigh University, Bethlehem, PA, United States,Center for Computational Biology, Flatiron Institute, New York, NY, United States,*Correspondence: Dimitrios Vavylonis ,
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Rozza R, Saltalamacchia A, Orrico C, Janoš P, Magistrato A. All-Atom Simulations Elucidate the Impact of U2AF2 Cancer-Associated Mutations on Pre-mRNA Recognition. J Chem Inf Model 2022; 62:6691-6703. [PMID: 36040856 DOI: 10.1021/acs.jcim.2c00511] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The U2AF2 splicing factor, made of two tandem RNA recognition motifs (RRMs) joined by a flexible linker, selects the intronic polypyrimidine sequence of premature mRNA, thus ensuring splicing fidelity. Increasing evidence links mutations of key splicing factors, including U2AF2, to a variety of cancers. Nevertheless, the impact of U2AF2 cancer-associated mutations on polypyrimidine recognition remains unclear. Here, we combined extensive (18 μs-long) all-atom molecular dynamics simulations and dynamical network theory analysis (NWA) of U2AF2, in its wild-type form and in the presence of the six most frequent cancer-associated mutations, bound to a poly-U strand. Our results reveal that the selected mutations affect the pre-mRNA binding at two hot spot regions, irrespectively of where these mutants are placed on the distinct U2AF2 domains. Complementarily, NWA traced the existence of cross-communication pathways, connecting each mutation site to these recognition hot spots, whose strength is altered by the mutations. Our outcomes suggest the existence of a structural/dynamical interplay of the two U2AF2's RRMs underlying the recognition of the polypyrimidine tract and reveal that the cancer-associated mutations affect the polypyrimidine selection by altering the RRMs' cooperativity. This mechanism may be shared by other RNA binding proteins hallmarked, like U2AF2, by multidomain architecture and high plasticity.
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Affiliation(s)
- Riccardo Rozza
- National Research Council of Italy (CNR)-IOM c/o International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| | - Andrea Saltalamacchia
- International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| | - Clarissa Orrico
- International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| | - Pavel Janoš
- National Research Council of Italy (CNR)-IOM c/o International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR)-IOM c/o International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
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Castelli M, Serapian SA, Marchetti F, Triveri A, Pirota V, Torielli L, Collina S, Doria F, Freccero M, Colombo G. New perspectives in cancer drug development: computational advances with an eye to design. RSC Med Chem 2021; 12:1491-1502. [PMID: 34671733 PMCID: PMC8459323 DOI: 10.1039/d1md00192b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
Computational chemistry has come of age in drug discovery. Indeed, most pharmaceutical development programs rely on computer-based data and results at some point. Herein, we discuss recent applications of advanced simulation techniques to difficult challenges in drug discovery. These entail the characterization of allosteric mechanisms and the identification of allosteric sites or cryptic pockets determined by protein motions, which are not immediately evident in the experimental structure of the target; the study of ligand binding mechanisms and their kinetic profiles; and the evaluation of drug-target affinities. We analyze different approaches to tackle challenging and emerging biological targets. Finally, we discuss the possible perspectives of future application of computation in drug discovery.
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Affiliation(s)
- Matteo Castelli
- Department of Chemistry, University of Pavia via Taramelli 12 27100 Pavia Italy
| | - Stefano A Serapian
- Department of Chemistry, University of Pavia via Taramelli 12 27100 Pavia Italy
| | - Filippo Marchetti
- Department of Chemistry, University of Pavia via Taramelli 12 27100 Pavia Italy
| | - Alice Triveri
- Department of Chemistry, University of Pavia via Taramelli 12 27100 Pavia Italy
| | - Valentina Pirota
- Department of Chemistry, University of Pavia via Taramelli 12 27100 Pavia Italy
| | - Luca Torielli
- Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section, University of Pavia via Taramelli 12 27100 Pavia Italy
| | - Simona Collina
- Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section, University of Pavia via Taramelli 12 27100 Pavia Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia via Taramelli 12 27100 Pavia Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia via Taramelli 12 27100 Pavia Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia via Taramelli 12 27100 Pavia Italy
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Spinello A, Saltalamacchia A, Borišek J, Magistrato A. Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. J Phys Chem Lett 2021; 12:5987-5993. [PMID: 34161095 PMCID: PMC8247780 DOI: 10.1021/acs.jpclett.1c01415] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 06/21/2021] [Indexed: 05/23/2023]
Abstract
The rapid and relentless emergence of novel highly transmissible SARS-CoV-2 variants, possibly decreasing vaccine efficacy, currently represents a formidable medical and societal challenge. These variants frequently hold mutations on the Spike protein's receptor-binding domain (RBD), which, binding to the angiotensin-converting enzyme 2 (ACE2) receptor, mediates viral entry into host cells. Here, all-atom molecular dynamics simulations and dynamical network theory of the wild-type and mutant RBD/ACE2 adducts disclose that while the N501Y mutation (UK variant) enhances the Spike's binding affinity toward ACE2, the concomitant N501Y, E484K, and K417N mutations (South African variant) aptly adapt to increase SARS-CoV-2 propagation via a two-pronged strategy: (i) effectively grasping ACE2 through an allosteric signaling between pivotal RBD structural elements and (ii) impairing the binding of antibodies elicited by infected or vaccinated patients. This information unlocks the molecular terms and evolutionary strategies underlying the increased virulence of emerging SARS-CoV-2 variants, setting the basis for developing the next-generation anti-COVID-19 therapeutics.
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Affiliation(s)
| | - Andrea Saltalamacchia
- International
School for Advanced Studies SISSA, via Bonomea 265, 34136 Trieste, Italy
| | - Jure Borišek
- National
Institute of Chemistry, Hajdrihova ulica 19, 1000 Ljubljana, Slovenia
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