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Hu Z, Martí J. Isomer-sourced structure iteration methods for in silico development of inhibitors: Inducing GTP-bound NRAS-Q61 oncogenic mutations to an "off-like" state. Comput Struct Biotechnol J 2024; 23:2418-2428. [PMID: 38882681 PMCID: PMC11176632 DOI: 10.1016/j.csbj.2024.05.038] [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: 03/25/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The NRAS-mutant subset of melanoma represent some of the most aggressive and deadliest types associated with poor overall survival. Unfortunately, for more than 40 years, no therapeutic agent directly targeting NRAS mutations has been clinically approved. In this work, based on microsecond scale molecular dynamics simulations, the effect of Q61 mutations on NRAS conformational characteristics is revealed at the atomic level. The GTP-bound NRAS-Q61R and Q61K mutations show a specific targetable pocket between Switch-II and α-helix 3 whereas the NRAS-Q61L non-polar mutation category shows a different targetable pocket. Moreover, a new isomer-sourced structure iteration method has been developed for the in silico design of potential inhibitor prototypes for oncogenes. We show the possibility of a designed prototype HM-387 to target activated NRAS-Q61R and that it can gradually induce the transition from the activated NRAS-Q61R to an "off-like" state.
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Affiliation(s)
- Zheyao Hu
- Department of Physics, Polytechnic University of Catalonia-Barcelona Tech, B4-B5 Northern Campus UPC, Barcelona, 08034, Catalonia, Spain
| | - Jordi Martí
- Department of Physics, Polytechnic University of Catalonia-Barcelona Tech, B4-B5 Northern Campus UPC, Barcelona, 08034, Catalonia, Spain
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Arora N, Mu H, Liang H, Zhao W, Zhou Y. RAS G-domains allosterically contribute to the recognition of lipid headgroups and acyl chains. J Cell Biol 2024; 223:e202307121. [PMID: 38334958 PMCID: PMC10857904 DOI: 10.1083/jcb.202307121] [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: 08/17/2023] [Revised: 12/15/2023] [Accepted: 01/29/2024] [Indexed: 02/10/2024] Open
Abstract
Mutant RAS are major contributors to cancer and signal primarily from nanoclusters on the plasma membrane (PM). Their C-terminal membrane anchors are main features of membrane association. However, the same RAS isoform bound to different guanine nucleotides spatially segregate. Different RAS nanoclusters all enrich a phospholipid, phosphatidylserine (PS). These findings suggest more complex membrane interactions. Our electron microscopy-spatial analysis shows that wild-types, G12V mutants, and membrane anchors of isoforms HRAS, KRAS4A, and KRAS4B prefer distinct PS species. Mechanistically, reorientation of KRAS4B G-domain exposes distinct residues, such as Arg 135 in orientation state 1 (OS1) and Arg 73/Arg 102 in OS2, to the PM and differentially facilitates the recognition of PS acyl chains. Allele-specific oncogenic mutations of KRAS4B also shift G-domain reorientation equilibrium. Indeed, KRAS4BG12V, KRAS4BG12D, KRAS4BG12C, KRAS4BG13D, and KRAS4BQ61H associate with PM lipids with headgroup and acyl chain specificities. Distribution of these KRAS4B oncogenic mutants favors different nanoscale membrane topography. Thus, RAS G-domains allosterically facilitate membrane lateral distribution.
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Affiliation(s)
- Neha Arora
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Huanwen Mu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Hong Liang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Wenting Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore, Singapore
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
- Program of Molecular and Translational Biology, Graduate School of Biological Sciences, M.D. Anderson Cancer Center and University of Texas Health Science Center, Houston, TX, USA
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Mosa FES, AlRawashdeh S, El-Kadi AOS, Barakat K. Investigating the Aryl Hydrocarbon Receptor Agonist/Antagonist Conformational Switch Using Well-Tempered Metadynamics Simulations. J Chem Inf Model 2024; 64:2021-2034. [PMID: 38457778 DOI: 10.1021/acs.jcim.4c00169] [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: 03/10/2024]
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that mediates biological signals to control various complicated cellular functions. It plays a crucial role in environmental sensing and xenobiotic metabolism. Dysregulation of AhR is associated with health concerns, including cancer and immune system disorders. Upon binding to AhR ligands, AhR, along with heat shock protein 90 and other partner proteins undergoes a transformation in the nucleus, heterodimerizes with the aryl hydrocarbon receptor nuclear translocator (ARNT), and mediates numerous biological functions by inducing the transcription of various AhR-responsive genes. In this manuscript, the 3-dimensional structure of the entire human AhR is obtained using an artificial intelligence tool, and molecular dynamics (MD) simulations are performed to study different structural conformations. These conformations provide insights into the protein's function and movement in response to ligand binding. Understanding the dynamic behavior of AhR will contribute to the development of targeted therapies for associated health conditions. Therefore, we employ well-tempered metadynamics (WTE-metaD) simulations to explore the conformational landscape of AhR and obtain a better understanding of its functional behavior. Our computational results are in excellent agreement with previous experimental findings, revealing the closed and open states of helix α1 in the basic helix-loop-helix (bHLH domain) in the cytoplasm at the atomic level. We also predict the inactive form of AhR and identify Arginine 42 as a key residue that regulates switching between closed and open conformations in existing AhR modulators.
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Affiliation(s)
- Farag E S Mosa
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Sara AlRawashdeh
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Ayman O S El-Kadi
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada
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Lu H, Hu Z, Faraudo J, Martí J. In silico design of a lipid-like compound targeting KRAS4B-G12D through non-covalent bonds. NANOSCALE 2023; 15:19359-19368. [PMID: 38014474 DOI: 10.1039/d3nr04513g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
One of the most common drivers in human cancer is the peripheral membrane protein KRAS4B, able to promote oncogenic signalling. To signal, oncogenic KRAS4B not only requires a sufficient nucleotide exchange, but also needs to recruit effectors by exposing its effector-binding sites while anchoring to the phospholipid bilayer where KRAS4B-mediated signalling events occur. The enzyme phosphodiesterase-δ plays an important role in sequestering KRAS4B from the cytoplasm and targeting it to cellular membranes of different cell species. In this work, we present an in silico design of a lipid-like compound that has the remarkable feature of being able to target both an oncogenic KRAS4B-G12D mutant and the phosphodiesterase-δ enzyme. This double action is accomplished by adding a lipid tail (analogous to the farnesyl group of the KRAS4B protein) to an previously known active compound (2H-1,2,4-benzothiadiazine, 3,4-dihydro-,1,1-dioxide). The proposed lipid-like molecule was found to lock KRAS4B-G12D in its GDP-bound state by adjusting the effector-binding domain to be blocked by the interface of the lipid bilayer. Meanwhile, it can tune GTP-bound KRAS4B-G12D to shift from the active orientation state to the inactive state. The proposed compound is also observed to stably accommodate itself in the prenyl-binding pocket of phosphodiesterase-δ, which impairs KRAS4B enrichment at the lipid bilayer, potentially reducing the proliferation of KRAS4B inside the cytoplasm and its anchoring at the bilayer. In conclusion, we report a potential inhibitor of KRAS4B-G12D with a lipid tail attached to a specific warhead, a compound which has not yet been considered for drugs targeting RAS mutants. Our work provides new ways to target KRAS4B-G12D and can also foster drug discovery efforts for the targeting of oncogenes of the RAS family and beyond.
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Affiliation(s)
- Huixia Lu
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, Bellaterra, Barcelona E-08193, Spain.
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B5-209 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain.
| | - Zheyao Hu
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B5-209 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain.
| | - Jordi Faraudo
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, Bellaterra, Barcelona E-08193, Spain.
| | - Jordi Martí
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B5-209 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain.
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Feng S, Park S, Choi YK, Im W. CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications. J Chem Theory Comput 2023; 19:2161-2185. [PMID: 37014931 PMCID: PMC10174225 DOI: 10.1021/acs.jctc.2c01246] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drug-binding and dynamics, protein-lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.
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Affiliation(s)
- Shasha Feng
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Soohyung Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Yeol Kyo Choi
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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Discovering and Targeting Dynamic Drugging Pockets of Oncogenic Proteins: The Role of Magnesium in Conformational Changes of the G12D Mutated Kirsten Rat Sarcoma-Guanosine Diphosphate Complex. Int J Mol Sci 2022; 23:ijms232213865. [PMID: 36430338 PMCID: PMC9692486 DOI: 10.3390/ijms232213865] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022] Open
Abstract
KRAS-G12D mutations are the one of most frequent oncogenic drivers in human cancers. Unfortunately, no therapeutic agent directly targeting KRAS-G12D has been clinically approved yet, with such mutated species remaining undrugged. Notably, cofactor Mg2+ is closely related to the function of small GTPases, but no investigation has been conducted yet on Mg2+ when associated with KRAS. Herein, through microsecond scale molecular dynamics simulations, we found that Mg2+ plays a crucial role in the conformational changes of the KRAS-GDP complex. We located two brand new druggable dynamic pockets exclusive to KRAS-G12D. Using the structural characteristics of these two dynamic pockets, we designed in silico the inhibitor DBD15-21-22, which can specifically and tightly target the KRAS-G12D-GDP-Mg2+ ternary complex. Overall, we provide two brand new druggable pockets located on KRAS-G12D and suitable strategies for its inhibition.
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