List of Publications

Research Articles

2025

1. Islam, S. M.; Stennette, J.; Hasan, M. M.; Shah, K. Computational Study of Pathogenic Variants in Phenylalanine-4-Hydroxylase (PAH): Insights into Structure, Dynamics, and BH4 Binding. ACS Omega 2025. https://doi.org/10.1021/acsomega.5c01993.

2. Akbari, B.; Hasan, M. M.; Islam, S. M. Advances in Targeted Therapy for Triple-Negative Breast Cancer: A Review of Key Antigens and Recent Advances. Journal of Drug Targeting 2025. https://doi.org/10.1080/1061186X.2025.2520306. 

3. Hasan, M. M.; Tarkhaneh, O.; Bungay, S. D.; Poirier, R. A.; Islam, S. M. Predicting HOMO–LUMO Gaps Using Hartree–Fock Calculated Data and Machine Learning Models. J Chem Inf Model 2025, 65 (18), 9497–9515. https://doi.org/10.1021/ACS.JCIM.5C01412.

2024 

1. Islam, S. M.; Hasan, Md. M.; Alam, J.; Dey, A.; Molineaux, D. In Silico Screening, Molecular Dynamics Simulation and Binding Free Energy Identify Single-Point Mutations That Destabilize P53 and Reduce Binding to DNA. Proteins: Structure, Function, and Bioinformatics 2024. https://doi.org/10.1002/PROT.26747. 

2. Hwang, W.; Austin, S. L.; Blondel, A.; Boittier, E. D.; Boresch, S.; Buck, M.; Buckner, J.; Caflisch, A.; Chang, H.-T.; Cheng, X.; Choi, Y. K.; Chu, J.-W.; Crowley, M. F.; Cui, Q.; Damjanovic, A.; Deng, Y.; Devereux, M.; Ding, X.; Feig, M. F.; Gao, J.; Glowacki, D. R.; Gonzales, J. E. I. I.; Hamaneh, M. B.; Harder, E. D.; Hayes, R. L.; Huang, J.; Huang, Y.; Hudson, P. S.; Im, W.; Islam, S. M.; Jiang, W.; Jones, M. R.; Käser, S.; Kearns, F. L.; Kern, N. R.; Klauda, J. B.; Lazaridis, T.; Lee, J.; Lemkul, J. A.; Liu, X.; Luo, Y.; MacKerell, A. D. Jr.; Major, D. T.; Meuwly, M.; Nam, K.; Nilsson, L.; Ovchinnikov, V.; Paci, E.; Park, S.; Pastor, R. W.; Pittman, A. R.; Post, C. B.; Prasad, S.; Pu, J.; Qi, Y.; Rathinavelan, T.; Roe, D. R.; Roux, B.; Rowley, C. N.; Shen, J.; Simmonett, A. C.; Sodt, A. J.; Töpfer, K.; Upadhyay, M.; van der Vaart, A.; Vazquez-Salazar, L. I.; Venable, R. M.; Warrensford, L. C.; Woodcock, H. L.; Wu, Y.; Brooks, C. L. I. I. I.; Brooks, B. R.; Karplus, M. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. J Phys Chem B 2024. https://doi.org/10.1021/acs.jpcb.4c04100.

3. Holmes, J.; Islam, S. M.; Milligan, K. A. Exploring Cannabinoids as Potential Inhibitors of SARS-CoV-2 Papain-like Protease: Insights from Computational Analysis and Molecular Dynamics Simulations. Viruses 2024, Vol. 16, Page 878 2024, 16 (6), 878. https://doi.org/10.3390/V16060878. 

4. Lopez, U. M.; Hasan, M. M.; Havranek, B.; Islam, S. M. SARS-CoV-2 Resistance to Small Molecule Inhibitors. Curr Clin Microbiol Rep 2024, 1–13. https://doi.org/10.1007/S40588-024-00229-6. 

2023

5. Abousamra, W. H.; Thomas, D.; Yang, D.; Islam, S. M.; Winstead, C.; Kim, Y. G. Synthesis and Characterization of the Donor-Acceptor Conjugated Polymer PBDB-T Implementing Group IV Element Germanium. Polymers 2023, Vol. 15, Page 2429 2023, 15 (11), 2429. https://doi.org/10.3390/POLYM15112429.

6. Uddin, K. M.; Islam, M. S.; Islam, S. M.; Poirier, R. A. New Insight into the Substituent Effects on the Hydrolytic Deamination of Saturated and Unsaturated Cytosine. Int J Quantum Chem 2023, 123 (2), e27014. https://doi.org/10.1002/QUA.27014.

7. Morgan, J.; Yun, Y. J.; Jamhawi, A. M.; Islam, S. M.; Ayitou, A. J. L. Photophysical Insights of Halogenated Dipyrrolonaphthyridine-Diones as Potential Photodynamic Therapy Agents†. Photochem Photobiol 2023, 99 (2), 761–768. https://doi.org/10.1111/PHP.13757.

8. Havranek, B.; Lindsey, G. W.; Higuchi, Y.; Itoh, Y.; Suzuki, T.; Okamoto, T.; Hoshino, A.; Procko, E.; Islam, S. M. A Computationally Designed ACE2 Decoy Has Broad Efficacy against SARS-CoV-2 Omicron Variants and Related Viruses in Vitro and in Vivo. Communications Biology 2023 6:1 2023, 6 (1), 1–16. https://doi.org/10.1038/s42003-023-04860-9.

9. Havranek, B.; Demissie, R.; Lee, H.; Lan, S.; Zhang, H.; Sarafianos, S.; Ayitou, A. J. L.; Islam, S. M. Discovery of Nirmatrelvir Resistance Mutations in SARS-CoV-2 3CLpro: A Computational-Experimental Approach. J Chem Inf Model 2023, 63 (22), 7180–7188. https://doi.org/10.1021/ACS.JCIM.3C01269.

2021

10. Havranek, B.; Islam, S. M. An in Silico Approach for Identification of Novel Inhibitors as Potential Therapeutics Targeting COVID-19 Main Protease. Journal of Biomolecular Structure and Dynamics 2021, 39 (12), 4304–4315. https://doi.org/10.1080/07391102.2020.1776158.

11. Havranek, B.; Islam, S. M. Prediction and Evaluation of Deleterious and Disease Causing Non-Synonymous SNPs (NsSNPs) in Human NF2 Gene Responsible for Neurofibromatosis Type 2 (NF2). Journal of Biomolecular Structure and Dynamics 2021, 39 (18), 7044–7055. https://doi.org/10.1080/07391102.2020.1805018.

12. Chowdhury, F. I.; Islam, J.; Arof, A. K.; Khandaker, M. U.; Zabed, H. M.; Khalil, I.; Rahman, M. R.; Islam, S. M.; Karim, M. R.; Uddin, J. Electrocatalytic and Structural Properties and Computational Calculation of PAN-EC-PC-TPAI-I 2 Gel Polymer Electrolytes for Dye Sensitized Solar Cell Application. RSC Advances 2021, 11 (37), 22937–22950. https://doi.org/10.1039/D1RA01983J.

13. Al-Busaidi, I. J.; Haque, A.; Al-Balushi, R. A.; Rather, J. A.; Munam, A.; Ilmi, R.; Raithby, P. R.; Zhang, Y.; Fu, Y.; Xie, Z.; Chen, S.; Islam, S. M.; Wong, W. Y.; Skelton, J. M.; Khan, M. S. Synthesis, Characterization, and Optoelectronic Properties of Phenothiazine-Based Organic Co-Poly-Ynes. New Journal of Chemistry 2021, 45 (33), 15082–15095. https://doi.org/10.1039/D1NJ00925G.

14. Almanasra, A.; Havranek, B.; Islam, S. M. In-Silico Screening and Microsecond Molecular Dynamics Simulations to Identify Single Point Mutations That Destabilize β-Hexosaminidase A Causing Tay-Sachs Disease. Proteins: Structure, Function and Bioinformatics 2021, 89 (11), 1587–1601. https://doi.org/10.1002/PROT.26180.

15. Havranek, B.; Chan, K. K.; Wu, A.; Procko, E.; Islam, S. M. Computationally Designed ACE2 Decoy Receptor Binds SARS-CoV-2 Spike (S) Protein with Tight Nanomolar Affinity. Journal of Chemical Information and Modeling 2021, 61 (9), 4656–4669. https://doi.org/10.1021/ACS.JCIM.1C00783.

16. Lopez, A.; Havranek, B.; Papadantonakis, G. A.; Islam, S. M. In Silico Screening and Molecular Dynamics Simulation of Deleterious PAH Mutations Responsible for Phenylketonuria Genetic Disorder. Proteins: Structure, Function and Bioinformatics 2021, 89 (6), 683–696. https://doi.org/10.1002/PROT.26051.

17. Zhang, G.; Alshreimi, A. S.; Alonso, L.; Antar, A.; Yu, H. C.; Islam, S. M.; Anderson, L. L. Nitrone and Alkyne Cascade Reactions for Regio- and Diastereoselective 1-Pyrroline Synthesis. Angewandte Chemie - International Edition 2021, 60 (23), 13089–13097. https://doi.org/10.1002/ANIE.202101511.

2020

18. Rathnayaka, S. C.; Islam, S. M.; DiMucci, I. M.; MacMillan, S. N.; Lancaster, K. M.; Mankad, N. P. Probing the Electronic and Mechanistic Roles of the Μ4-Sulfur Atom in a Synthetic CuZ Model System. Chemical Science 2020, 11 (13), 3441–3447. https://doi.org/10.1039/C9SC06251C.

19. Islam, S. M.; Ibnat, Z. New Insights into the Structure and Reactivity of Uracil Derivatives in Different Solvents-a Computational Study. ACS Omega 2020, 5 (35), 22449–22458. https://doi.org/10.1021/ACSOMEGA.0C02943.

20. Almatarneh, M. H.; Omeir, R. A.; AL Demour, S.; Elayan, I. A.; Islam, S.; Poirier, R. A. Hydrolytic Deamination Mechanisms of Guanosine Monophosphate: A Computational Study. Computational and Theoretical Chemistry 2020, 1175, 112732. https://doi.org/10.1016/J.COMPTC.2020.112732.

21. Qi, Y.; Lee, J.; Cheng, X.; Shen, R.; Islam, S. M.; Roux, B.; Im, W. CHARMM-GUI DEER Facilitator for Spin-Pair Distance Distribution Calculations and Preparation of Restrained-Ensemble Molecular Dynamics Simulations. Journal of Computational Chemistry 2020, 41 (5), 415–420. https://doi.org/10.1002/JCC.26032.

22. Yu, H. C.; Islam, S. M.; Mankad, N. P. Cooperative Heterobimetallic Substrate Activation Enhances Catalytic Activity and Amplifies Regioselectivity in 1,4-Hydroboration of Pyridines. ACS Catalysis 2020, 10 (6), 3670–3675. https://doi.org/10.1021/ACSCATAL.0C00515.

23. Islam, S. M.; Havranek, B.; Ibnat, Z.; Roy, P. N. New Insights into the Role of Hydrogen Bonding in Furanoside Binding to Protein. Journal of Physical Chemistry B 2020, 124 (10), 1919–1927. https://doi.org/10.1021/ACS.JPCB.9B11924.

24. Hsu, C.-W.; Rathnayaka, S. C.; Islam, S. M.; MacMillan, S. N.; Mankad, N. P. N2O Reductase Activity of a [Cu4S] Cluster in the 4CuI Redox State Modulated by Hydrogen Bond Donors and Proton Relays in the Secondary Coordination Sphere. Angewandte Chemie 2020, 132 (2), 637–641. https://doi.org/10.1002/ANGE.201906327.

25. Alshreimi, A. S.; Zhang, G.; Reidl, T. W.; Peña, R. L.; Koto, N. G.; Islam, S. M.; Wink, D. J.; Anderson, L. L. Synthesis of Spirocyclic 1-Pyrrolines from Nitrones and Arynes through a Dearomative [3,3′]-Sigmatropic Rearrangement. Angewandte Chemie - International Edition 2020, 59 (35), 15244–15248. https://doi.org/10.1002/ANIE.202004652.

2018

26. Cheng, L. J.; Islam, S. M.; Mankad, N. P. Synthesis of Allylic Alcohols via Cu-Catalyzed Hydrocarbonylative Coupling of Alkynes with Alkyl Halides. Journal of the American Chemical Society 2018, 140 (3), 1159–1164. https://doi.org/10.1021/JACS.7B12582.

27. Jayapal, M.; Haque, A.; Al-Busaidi, I. J.; Al-Rasbi, N.; Al-Suti, M. K.; Khan, M. S.; Al-Balushi, R.; Islam, S. M.; Xin, C.; Wu, W.; Wong, W. Y.; Marken, F.; Raithby, P. R. Dicopper(I) Complexes Incorporating Acetylide-Functionalized Pyridinyl-Based Ligands: Synthesis, Structural, and Photovoltaic Studies. Inorganic Chemistry 2018, 57 (19), 12113–12124. https://doi.org/10.1021/ACS.INORGCHEM.8B01684.

2017

28. Jayapal, M.; Haque, A.; Al-Busaidi, I. J.; Al-Balushi, R.; Al-Suti, M. K.; Islam, S. M.; Khan, M. S.; Dittmer, J. J. Synthesis and Characterization of a Thienopyrazine-Based Low Band-Gap Poly(Arylene Ethynylene) and Photocell Studies of the Poly-Yne/Perylene Dye Blend with Broad Photocurrent Spectrum. Current Organic Chemistry 2017, 21 (19), 2017–2027. https://doi.org/10.2174/1385272821666170420152645.

29. Jayapal, M.; Haque, A.; Al-Busaidi, I. J.; Al-Balushi, R.; Al-Suti, M. K.; Islam, S. M.; Khan, M. S. Synthesis, Characterization and Photocell Studies of a Pt(II) Poly-Yne Covalently Attached to a Fullerene. Journal of Organometallic Chemistry 2017, 842, 32–38. https://doi.org/10.1016/J.JORGANCHEM.2017.05.012.

30. Deng, Y.; Kauser, N. I.; Islam, S. M.; Mohr, J. T. AgII-Mediated Synthesis of β-Fluoroketones by Oxidative Cyclopropanol Opening. European Journal of Organic Chemistry 2017, 2017 (39), 5872–5879. https://doi.org/10.1002/EJOC.201700899.

2016

31. Matthies, D.; Dalmas, O.; Borgnia, M. J.; Dominik, P. K.; Merk, A.; Rao, P.; Reddy, B. G.; Islam, S. M.; Bartesaghi, A.; Perozo, E.; Subramaniam, S. Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating. Cell 2016, 164 (4), 747–756. https://doi.org/10.1016/J.CELL.2015.12.055.

32. Khan, M. F.; Rashid, R. Bin; Islam, S. M.; Rashid, M. A. Computational Study of Geometry, Solvation Free Energy, Dipole Moment, Polarizability, Hyperpolarizability and Molecular Properties of 2-Methylimidazole. Sultan Qaboos University Journal for Science [SQUJS] 2016, 21 (2), 89–101. https://doi.org/10.24200/SQUJS.VOL21ISS2PP89-101.

33. Abraham, S. J.; Chavan, T.; Cheng, R. C.; Fenollar-Ferrer, C.; Han, W.; Islam, S. M.; Jiang, T.; Khantwal, C. M.; Mathews, I. I.; Stein, R. A.; Roux, B.; Forrest, L. R.; Mchaourab, H. S.; Tajkhorshid, E.; Maduke, M. An Outward-Facing Open Conformational State in a CLC Transporter. Biophysical Journal 2016, 110 (3), 178a. https://doi.org/10.1016/j.bpj.2015.11.994.

2015

34. Islam, S. M.; Roux, B. Simulating the Distance Distribution between Spin-Labels Attached to Proteins. Journal of Physical Chemistry B 2015, 119 (10), 3901–3911. https://doi.org/10.1021/JP510745D.

35. Shen, R.; Han, W.; Fiorin, G.; Islam, S. M.; Schulten, K.; Roux, B. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-Interacting Molecular Fragments. PLOS Computational Biology 2015, 11 (10), e1004368. https://doi.org/10.1371/JOURNAL.PCBI.1004368.

2014

36. Raghuraman, H.; Islam, S. M.; Mukherjee, S.; Roux, B.; Perozo, E. Dynamics Transitions at the Outer Vestibule of the KcsA Potassium Channel during Gating. Proceedings of the National Academy of Sciences of the United States of America 2014, 111 (5), 1831–1836. https://doi.org/10.1073/PNAS.1314875111.

37. Kazmier, K.; Sharma, S.; Quick, M.; Islam, S. M.; Roux, B.; Weinstein, H.; Javitch, J. A.; McHaourab, H. S. Conformational Dynamics of Ligand-Dependent Alternating Access in LeuT. Nature Structural & Molecular Biology 2014 21:5 2014, 21 (5), 472–479. https://doi.org/10.1038/nsmb.2816.

38. Kazmier, K.; Sharma, S.; Islam, S. M.; Roux, B.; Mchaourab, H. S.; Wright, E. M. Conformational Cycle and Ion-Coupling Mechanism of the Na+/Hydantoin Transporter Mhp1. Proceedings of the National Academy of Sciences of the United States of America 2014, 111 (41), 14752–14757. https://doi.org/10.1073/PNAS.1410431111.

2013

39. Roux, B.; Islam, S. M. Restrained-Ensemble Molecular Dynamics Simulations Based on Distance Histograms from Double Electron-Electron Resonance Spectroscopy. Journal of Physical Chemistry B 2013, 117 (17), 4733–4739. https://doi.org/10.1021/JP3110369.

40. Islam, S. M.; Stein, R. A.; McHaourab, H. S.; Roux, B. Structural Refinement from Restrained-Ensemble Simulations Based on EPR/DEER Data: Application to T4 Lysozyme. Journal of Physical Chemistry B 2013, 117 (17), 4740–4754. https://doi.org/10.1021/JP311723A.

2012

41. Islam, S. M.; Roy, P. N. Performance of the SCC-DFTB Model for Description of Five-Membered Ring Carbohydrate Conformations: Comparison to Force Fields, High-Level Electronic Structure Methods, and Experiment. Journal of Chemical Theory and Computation 2012, 8 (7), 2412–2423. https://doi.org/10.1021/CT200789W. 

2011

42. Islam, S. M.; Richards, M. R.; Taha, H. A.; Byrns, S. C.; Lowary, T. L.; Roy, P. N. Conformational Analysis of Oligoarabinofuranosides: Overcoming Torsional Barriers with Umbrella Sampling. Journal of Chemical Theory and Computation 2011, 7 (9), 2989–3000. https://doi.org/10.1021/CT200333P. 

2010

43. Islam, S. M.; Saleh, M. A. Thermodynamic Activation Parameters for Viscous Flow of Dilute Aqueous Solutions of Ethylenediamine, Trimethylenediamine and N,N-Dimethyltrimethylenediamine. Physics and Chemistry of Liquids 2010, 48 (2), 156–170. https://doi.org/10.1080/00319100802654347. 

2008

44. Islam, S. M.; Huelin, S. D.; Dawe, M.; Poirier, R. A. Comparison of the Standard 6-31G and Binning-Curtiss Basis Sets for Third Row Elements. Journal of Chemical Theory and Computation 2008, 4 (1), 86–100. https://doi.org/10.1021/CT700224J.

45. Westaway, K. C.; Fang, Y. R.; MacMillar, S.; Matsson, O.; Poirier, R. A.; Islam, S. M. Determining the Transition-State Structure for Different SN2 Reactions Using Experimental Nucleophile Carbon and Secondary α-Deuterium Kinetic Isotope Effects and Theory. Journal of Physical Chemistry A 2008, 112 (41), 10264–10273. https://doi.org/10.1021/JP804237G.

46. Islam, S. M.; Poirier, R. A. Addition Reaction of Adamantylideneadamantane with Br2 and 2Br2: A Computational Study. Journal of Physical Chemistry A 2008, 112 (1), 152–159. https://doi.org/10.1021/JP077306D.

2007

47. Islam, S. M.; Hollett, J. W.; Poirier, R. A. Computational Study of the Reactions of SiH3X (X = H, Cl, Br, I) with HCN. Journal of Physical Chemistry A 2007, 111 (3), 526–540. https://doi.org/10.1021/JP066524O.

48. Westaway, K. C.; Fang, Y. R.; MacMillar, S.; Matsson, O.; Poirier, R. A.; Islam, S. M. A New Insight into Using Chlorine Leaving Group and Nucleophile Carbon Kinetic Isotope Effects To Determine Substituent Effects on the Structure of SN2 Transition States. Journal of Physical Chemistry A 2007, 111 (33), 8110–8120. https://doi.org/10.1021/JP0729765.

49. Islam, S. M.; Poirier, R. A. New Insights into the Bromination Reaction for a Series of Alkenes a Computational Study. Journal of Physical Chemistry A 2007, 111 (50), 13218–13232. https://doi.org/10.1021/JP075674B.

2002

50. Saleh, M. A.; Ahmed, M. S.; Islam, S. M. Viscosity and Excess Viscosity of Dilute Aqueous Solutions of Ethylenediamine, Trimethylenediamine and N , N -Dimethyltrimethylenediamine. Physics and Chemistry of Liquids 2002, 40 (4), 477–490. https://doi.org/10.1080/00319100290010392. 

Book Chapter and Publication on Website

1. Jo, S.; Cheng, X.; Islam, S. M.; Huang, L.; Rui, H.; Zhu, A.; Lee, H. S.; Qi, Y.; Han, W.; Vanommeslaeghe, K.; MacKerell, A. D.; Roux, B.; Im, W. CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues; Academic Press, 2014; Vol. 96. https://doi.org/10.1016/BS.APCSB.2014.06.002.

2. Overview: Structural Refinement Based on EPR Data from Restrained-Ensemble Simulation | Membrane Protein Structural Dynamics Gateway. http://memprotein.org/structural-refinement-based-on-epr-data-from-restrained-ensemble-simulation  (accessed 2024-09-04).