Halogen substitution strengthens Z944 binding to the human Cav3.1 calcium channel pore domain: Insights from molecular dynamics simulations

Theodore Feisal Khoushab; Panisak Boonamnaj; Pisit Lerttanakij; Ras Pandey; Pornthep Sompornpisut; Theodore Feisal Khoushab; Panisak Boonamnaj; Pisit Lerttanakij; Ras Pandey; Pornthep Sompornpisut

doi:10.3934/biophy.2026020

AIMS Biophysics

2026, Volume 13, Issue 3: 368-395. doi: 10.3934/biophy.2026020

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Research article

Halogen substitution strengthens Z944 binding to the human Cav3.1 calcium channel pore domain: Insights from molecular dynamics simulations

1.
Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
2.
Program in Bioinformatics and Computational Biology, College of Interdisciplinary and Integrative Studies, Chulalongkorn University, Bangkok 10330, Thailand
3.
School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States

Received: 10 August 2026 Revised: 12 September 2026 Accepted: 23 September 2026 Published: 28 September 2026

Voltage-gated T-type calcium channels (Cav3.1) are important therapeutic targets for neurological and cardiovascular disorders; the selective blocker Z944 is among the most potent inhibitors currently available. However, the molecular basis underlying the contribution of its halogen substituents to ligand recognition remains poorly understood. In this study, all-atom molecular dynamics simulations totaling 4.8 µs were performed to investigate the binding dynamics of the human Cav3.1 pore domain in the apo state and in complex with Z944 or a dehalogenated analogue lacking the chlorine and fluorine substituents (mZ944). Ligand binding preserved the overall pore architecture while locally stabilizing the blocker-binding cavity without inducing large-scale conformational changes. Relative MM/GBSA binding-energy calculations showed more favorable calculated binding energetics for Z944 than for mZ944, primarily because of greater dispersion interactions, with domain II residues, particularly Phe956, Asn952, Leu920, and Thr921, forming the dominant energetic contributions. Dynamic interaction analyses further revealed that Z944 maintains a broader protein–ligand interaction network, whereas mZ944 displayed greater positional and conformational variability within the binding cavity. Because mZ944 was initialized from the experimentally determined Z944 pose, its persistence within the same binding cavity over the simulated timescale does not exclude alternative binding modes. Moreover, because chlorine and fluorine were removed simultaneously, the observed differences reflect their combined removal rather than their individual contributions. Analysis of ligand conformational dynamics showed that the halogenated ligand occupies a more restricted conformational ensemble, favoring well-defined torsional states compatible with stable binding. Overall, these findings indicate that the presence of the chlorine and fluorine substituents is associated with more favorable calculated binding energetics, more favorable dispersion interactions, differences in direct and water-mediated interaction patterns, and reduced ligand conformational heterogeneity. This work provides atomistic insight into the molecular mechanism of Z944 recognition and establishes structural principles that may guide the rational design of next-generation Cav3.1 inhibitors.
- T-type calcium channel,
- Cav3.1,
- Z944,
- channel blocker,
- molecular dynamics
Citation: Theodore Feisal Khoushab, Panisak Boonamnaj, Pisit Lerttanakij, Ras Pandey, Pornthep Sompornpisut. Halogen substitution strengthens Z944 binding to the human Cav3.1 calcium channel pore domain: Insights from molecular dynamics simulations[J]. AIMS Biophysics, 2026, 13(3): 368-395. doi: 10.3934/biophy.2026020

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Abstract

Voltage-gated T-type calcium channels (Cav3.1) are important therapeutic targets for neurological and cardiovascular disorders; the selective blocker Z944 is among the most potent inhibitors currently available. However, the molecular basis underlying the contribution of its halogen substituents to ligand recognition remains poorly understood. In this study, all-atom molecular dynamics simulations totaling 4.8 µs were performed to investigate the binding dynamics of the human Cav3.1 pore domain in the apo state and in complex with Z944 or a dehalogenated analogue lacking the chlorine and fluorine substituents (mZ944). Ligand binding preserved the overall pore architecture while locally stabilizing the blocker-binding cavity without inducing large-scale conformational changes. Relative MM/GBSA binding-energy calculations showed more favorable calculated binding energetics for Z944 than for mZ944, primarily because of greater dispersion interactions, with domain II residues, particularly Phe956, Asn952, Leu920, and Thr921, forming the dominant energetic contributions. Dynamic interaction analyses further revealed that Z944 maintains a broader protein–ligand interaction network, whereas mZ944 displayed greater positional and conformational variability within the binding cavity. Because mZ944 was initialized from the experimentally determined Z944 pose, its persistence within the same binding cavity over the simulated timescale does not exclude alternative binding modes. Moreover, because chlorine and fluorine were removed simultaneously, the observed differences reflect their combined removal rather than their individual contributions. Analysis of ligand conformational dynamics showed that the halogenated ligand occupies a more restricted conformational ensemble, favoring well-defined torsional states compatible with stable binding. Overall, these findings indicate that the presence of the chlorine and fluorine substituents is associated with more favorable calculated binding energetics, more favorable dispersion interactions, differences in direct and water-mediated interaction patterns, and reduced ligand conformational heterogeneity. This work provides atomistic insight into the molecular mechanism of Z944 recognition and establishes structural principles that may guide the rational design of next-generation Cav3.1 inhibitors.

Acknowledgments

This research is supported by the Thailand Science Research and Innovation Fund Chulalongkorn University (HEA_FF_69_244_2300_055).

Conflict of interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Author contributions

T.F.K. performed the molecular dynamics simulations, conducted the computational analyses, and interpreted the data. P.L. and P.B. contributed to data analysis. T.F.K., P.B. and P.S. conceived the study, wrote the manuscript, and prepared all figures. R.B.P. provided critical discussions and intellectual input. All authors reviewed and approved the final manuscript.

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