Publications

Peer-reviewed research spanning computational chemistry, medicinal chemistry, antibiotic resistance, and machine learning.

2026

The CDIN1-Codanin-1 Complex, Defective in Congenital Dyserythropoietic Anaemia Type I, is an RNA Nuclease

Sanja Brolih, Hafiz Saqib Ali, Caroline Scott, Aude-Anais Olijnik, Hazel Aitkenhead, Gemma Moir-Meyer, Angeline E. Gavard, Yuliana Yosaatmadja, Douglas R. Higgs, Veronica Buckle, Noemi Roy, Opher Gileadi, Joseph A. Newman, Fernanda Duarte, Christian Babbs, Peter J. McHugh

Nature Communications, 2026 (Accepted/in-press)

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Novel Indole-based Sulfonate and Sulfamate Derivatives as Potent and Selective Urease Inhibitors Targeting Helicobacter Pylori: A Promising Therapeutic Strategy

Ghalia Khoder, Esra M. Mustafa, Sumera Zaib, Anil Ravi, Afnan I. Shahin, Seyed-Omar Zaraei, Nehal Rana, Hanan S. Anbar, Hafiz Saqib Ali, Shamsul Qumar, Merylin Sebastian, Ragheb Alsheikh Zein, Mohammed I. El-Gamal

Gut Pathogens, 2026, 18, 27

2025

Binding Assays Enable Discovery of Tet(X) Inhibitors that Combat Tetracycline Destructase Resistance

Matthew J. Beech, Edmond C. Toma, Helen G. Smith, Maria M. Trush, Jit H.J. Ang, Mei Y. Wong, Chung H.J. Wong, Hafiz Saqib Ali, Zakia Butt, Viha Goel, Fernanda Duarte, Alistair J.M. Farley, Timothy R. Walsh, Christopher J. Schofield

Chemical Science, 2025, 16, 9691–9704

Synthesis, In-vitro and In-vivo Evaluation, and Computational Modeling Analysis of Thioxothiazolidine Derivatives as Highly Potent and Selective α-amylase Inhibitors

Anil Ravi, Sumera Zaib, Shabab Zahra, Imtiaz Khan, Hafiz Saqib Ali, Mohammed Ibrahim El-Gamal, Hanan Sayed Anbar

European Journal of Medicinal Chemistry, 2025, 291, 117584

Synergistic Effect of Hydrogen Bonding and C–H…π Interactions to Modulate the Supramolecular Assemblies of Isobenzofuranones: X-ray Crystallography, DFT Analysis and Antihyperglycemic Potential

Sumera Zaib, Imtiaz Khan, Aliya Ibrar, Hafiz Saqib Ali, Nehal Rana, Rubina Munir, Shabab Zahra, Abdel-Basit Al-Odayni, John Mcadam, Tuncer Hökelek, Antonio Frontera

Journal of Molecular Structure, 2025, 1321, 140263

2024

QM/MM Study Into the Mechanism of Oxidative C=C Double Bond Cleavage by Lignostilbene-alpha,beta-Dioxygenase

Hafiz Saqib Ali, Sam P. de Visser

Chemistry: A European Journal, 2024, e202304172

Catalytic Divergencies in the Mechanism of L-Arginine Hydroxylating Nonheme Iron Enzymes

Hafiz Saqib Ali, Sam P. de Visser

Frontiers in Chemistry, 2024, 12, 1–14

Probing Ferryl Reactivity in a Nonheme Iron Oxygenase Using an Expanded Genetic Code

Florence J. Hardy, Matthew G. Quesne, Emilie F. Gérard, Jingming Zhao, Mary Ortmayer, Christopher J. Taylor, Hafiz Saqib Ali, Jeffrey W. Slater, Colin W. Levy, Derren J. Heyes, J. Martin Bollinger, Jr., Sam P. de Visser, Anthony P. Green

ACS Catalysis, 2024, 14, 11584–11590

Using BpyAla to Generate Copper Artificial Metalloenzymes: A Catalytic and Structural Study

Eva Klemencic, Richard Brewster, Hafiz Saqib Ali, Julia Richardson, Amanda Jarvis

Catalysis Science & Technology, 2024, 14, 1622-1632

Emerging Perception of Activity Cliffs: A Brief Review

Hafiz Saqib Ali

UCP Journal of Science & Technology, 2024, 1, 15-29

Design and Discovery of Anthranilamide Derivatives as a Potential Treatment for Neurodegenerative Disorders via Targeting Cholinesterases and Monoamine Oxidases

Sumera Zaib, Imtiaz Khan, Hafiz Saqib Ali, Muhammad Tayyab Younas, Aliya Ibrar, Abdel-Basit Al-Odayni, Abdullah A. Al-Kahtani

International Journal of Biological Macromolecules, 2024, 272, 132784.

Mitochondrial Oxidative Phosphorylation (mtOXPHOS) Serves as a Sentinel to Gauge Fluctuations Under Heat Stress in Arabidopsis Thaliana Elucidated by Comparative Transcriptomics

Muhammad Riaz, Erum Yasmeen, Moyang Liu, Hafiz Saqib Ali, Mengli Lv, Hu Shi, Chuanhui Du, Tiantian Dong, Zhenxin Liu, Qingwei Song, QiJun Ma, Kaijing Zuo

Plant Stress, 2024, 14, 100613

Hydrogen Bonding, Halogen Bonding and C–H…π Interactions Governing the Supramolecular Architecture of 1-(4-(4-bromophenyl)piperazin-1-yl)-2-chloroethan-1-one: Insights from X-ray Crystallography, DFT Calculations and Urease Inhibitory Assessment

Sumera Zaib, Imtiaz Khan, Aliya Ibrar, Nehal Rana, Hafiz Saqib Ali, Christopher J. McAdam, Rosa M. Gomila, Islam H. El Azab, M.H.H. Mahmoud, Zeinhom M. El-Bahy, Antonio Frontera

Journal of Molecular Structure, 2024, 1317, 139065

Regioselective Metal-free Synthesis of Sulfostyril-Quinoline Hybrid Framework: Experimental and Computational Mechanistic Insights

Rubina Munir, Imtiaz Khan, Leena Siddiqui, Noman Javid, Muhammad Zia-ur-Rehman, Hafiz Saqib Ali, Memoona Saeed, Sumera Zaib, Nasser S. Awwad, Hala A. Ibrahium, Colleen Hui Shiuan Yeow, Jonathan M. White, Ayed A. Dera

Journal of Molecular Structure, 2024, 1315, 138894

Computational Exploration of Nonlinear Optical Properties in Supramolecular Naphthalene Diimides and Nucleotide Complexes

Wajid Hussain, Muhammad Sulaman, Yahya Sandali, Chuanbo Li, Muhammad Shahid Iqbal, Muhammad Rashid Bashir, Maroof Ahmad Khan, Hafiz Saqib Ali, Ahmad Irfan, Hui Li

Materials Science and Engineering: B, 2024, 305, 117429

Exploring Nonlinear Optical Properties of Perylene Diimide and Biomolecules Complexes: A Computational Supramolecular Study

Wajid Hussain, Hafiz Saqib Ali, Muhammad Shahid Iqbal, Muhammad Rashid Bashir, Maroof Ahmad Khan, Muhammad Hanif, Yahya Sandali, Ahmad Irfan, Hui Li

Theoretical Chemistry Accounts, 2024, 143, 1-23

2023

How Does the Nonheme Iron Enzyme NapI React through L-Arginine Desaturation Rather Than Hydroxylation? A QM/MM Study

Hafiz Saqib Ali, Jim Warwicker, Sam P. de Visser

ACS Catalysis, 2023, 13, 10705–10721

Energy-Entropy Multiscale Cell Correlation Method to Predict Toluene-Water LogP in the SAMPL9 Challenge

Hafiz Saqib Ali, Richard Henchman

Physical Chemistry Chemical Physics, 2023, 25, 27524–27531

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Impact of Counteranions on N-heterocyclic Carbene Gold(I)-Catalyzed Cyclization of Propargylic Amide

Hafiz Saqib Ali, Aqeel A. Hussein, Mohammed Obies

RSC Advances, 2023, 13, 2896–2902

Identification of Potential Inhibitors Targeting Yellow Fever Virus Helicase Through Ligand and Structure-based Computational Studies

Sumera Zaib, Nehal Rana, Hafiz Saqib Ali, Mujeeb ur Rehman, Nasser S. Awwad, Hala A. Ibrahium, Imtiaz Khan

Journal of Biomolecular Structure and Dynamics, 2023, 253, 127379

Discovery of Druggable Potent Inhibitors of Serine Proteases and Farnesoid X-Receptor by Ligand-based Virtual Screening to Obstruct SARS-CoV-2

Sumera Zaib, Nehal Rana, Hafiz Saqib Ali, Nadia Hussain, Areeba, Hanan A. Ogaly, Fatimah A.M. Al-Zahrani, Imtiaz Khan

International Journal of Biological Macromolecules, 2023, 253, 127379

Pyrimidine-Morpholine Hybrids as Potent Druggable Therapeutics for Alzheimer’s Disease: Synthesis, Biochemical and In-Silico Analyses

Sumera Zaib, Muhammad T. Younas, Imtiaz Khan, Hafiz Saqib Ali, Christopher J. McAdam, Jonathan M. White, Fadi Jaber, Nasser S. Awwad, Hala A. Ibrahium

Bioorganic Chemistry, 2023, 141, 106868

Dehydrogenative α-Oxygenation of Cyclic Ethers by a High-Valent Manganese(IV)-Oxo Species

M. Qadri E. Mubarak, Hafiz Saqib Ali, Jimei Zhou, Chaoqun Li, Jianliang Xiao, Sam P. de Visser

European Journal of Inorganic Chemistry, 2023, 26, e202200621

Spectroscopic and Conductometric Investigation of Mixed Micellar-Assisted Solubilization of Nile Blue Sulfate

Mudussar Ali, Muhammad Usman, Afzal Shah, Abdul Rehman, Hafiz Saqib Ali

Journal of Molecular Liquids, 2023, 386, 122507

A Comprehensive Analysis of Electronic Transitions in Naphthalene and Perylene Diimide Derivatives Through Computational Methods

Wajid Hussain, Muhammad S. Iqbal, Hui Li, Muhammad Sulaman, Honglian Guo, Chuanbo Li, Yahya Sandali, Ahmad Irfan, Hafiz Saqib Ali

International Journal of Quantum Chemistry, 2023, 124, e27223

Computational and Theoretical Chemistry of Newly Synthesized and Characterized 2,2’-(5,5’-(1,4-Phenylene)bis(1H-Tetrazole-5,1-diyl))bis-N-Acetamides

Syeda A. Ejaz, Aftab Farid, Seema Zargar, Pervaiz A. Channar, Mubashir Aziz, Tanveer A. Wani, Hafiz M. Attaullah, Rabail Ujhan, Arfa Tehzeeb, Aamer Saeed, Hafiz Saqib Ali, Mauricio F. Erben

BMC Chemistry, 2023, 17, 97

2022

Electrostatic Perturbations in the Substrate-Binding Pocket of Taurine/α-Ketoglutarate Dioxygenase Determine its Selectivity

Hafiz Saqib Ali, Sam P. de Visser

Chemistry: A European Journal, 2022, 16, e202104167

Density Functional Theory Study into the Reaction Mechanism of Isonitrile Biosynthesis by the Nonheme Iron Enzyme ScoE

Hafiz Saqib Ali, Sidra Ghafoor, Sam P. de Visser

Topics in Catalysis, 2022, 65, 528–543

Density Functional Theory Study into the Reaction Mechanism of Isonitrile Biosynthesis by the Nonheme Iron Enzyme ScoE

Yen-Ting Lin, Hafiz Saqib Ali, Sam P. de Visser

Chemistry: A European Journal, 2022, 28, e202103982

A Mechanistic Study on the Gold(I)-Catalyzed Cyclization of Propargylic Amide: Revealing the Impact of Expanded-ring N-Heterocyclic Carbenes

Yumiao Ma, Hafiz Saqib Ali, Aqeel A. Hussein

Catalysis Science & Technology, 2022, 12, 674-685

A Combined Experimental and Theoretical Study of Alkyl 2-(3-benzoyl-4‑hydroxy-1,1-dioxido-2H-benzo[e][1,2]thiazin-2-yl)Acetates: Synthesis, X-ray Crystallography and DFT

Sana Aslam, Hafiz Saqib Ali, Matloob Ahmad, Asim Mansha, Narmeen Ali, Sana Khan, Syed Ali Raza Naqvi, Zunera Khalid, Sadia Asim, Masood Parvez, Muhammad Khalid

Catalysis Science & Technology, 2022, 1258, 132671

2021

Energy–Entropy Method Using Multiscale Cell Correlation to Calculate Binding Free Energies in the SAMPL8 Host–Guest Challenge

Hafiz Saqib Ali, Arghya Chakravorty, Jas Kalayan, Samuel P. de Visser, Richard H. Henchman

Journal of Computer-Aided Molecular Design, 2021, 35, 911-921

How Do Electrostatic Perturbations of the Protein Affect the Bifurcation Pathways of Substrate Hydroxylation versus Desaturation in the Nonheme Iron-Dependent Viomycin Biosynthesis Enzyme?

Hafiz Saqib Ali, Richard Henchman, Jim Warwicker, and Sam P. de Visser

The Journal of Physical Chemistry A, 2021, 125, 1720-1737

What Determines the Selectivity of Arginine Dihydroxylation by the Nonheme Iron Enzyme OrfP?

Hafiz Saqib Ali, Richard Henchman, Sam P. de Visser

Chemistry: A European Journal, 2021, 27, 1795-1809

Mechanism of Oxidative Ring-Closure as Part of the Hygromycin Biosynthesis Step by a Nonheme Iron Dioxygenase

Hafiz Saqib Ali, Richard Henchman, Sam P. de Visser

ChemCatChem, 2021, 13, 3054-3066

Local Charge Distributions, Electric Dipole Moments, and Local Electric Fields Influence Reactivity Patterns and Guide Regioselectivities in α-Ketoglutarate-Dependent Non-heme Iron Dioxygenases

Sam P. de Visser, Gourab Mukherjee, Hafiz Saqib Ali, Chivukula V. Sastri

Accounts of Chemical Research, 2021, 55, 65-74

Negative Catalysis / Non-Bell-Evans-Polanyi Reactivity by Metalloenzymes: Examples from Mononuclear Heme and Non-Heme Iron Oxygenases

Sam P. de Visser, Yen-Ting Lin, Hafiz Saqib Ali, Umesh Kumar Bagha, Gourab Mukherjee, Chivukula V. Sastri

Coordination Chemistry Reviews, 2021, 439, 213914

Electrostatic Perturbations from the Protein Affect C−H Bond Strengths of the Substrate and Enable Negative Catalysis in the TmpA Biosynthesis Enzyme

Yen-Ting Lin, Hafiz Saqib Ali, Sam P. de Visser

Chemistry: A European Journal, 2021, 27, 8851-8864

Glutarate Hydroxylation by the Carbon Starvation-Induced Protein D: A Computational Study into the Stereo- and Regioselectivities of the Reaction

Sungho Bosco Han, Hafiz Saqib Ali, Sam P. de Visser

Inorganic Chemistry, 2021, 60, 4800–4815

Rhodanine-3-Acetamide Derivatives as Aldose and Aldehyde Reductase Inhibitors to Treat Diabetic Complications: Synthesis, Biological Evaluation, Molecular Docking and Simulation Studies

Mohsinul Mulk Bacha, Humaira Nadeem, Sumera Zaib, Sadia Sarwar, Aqeel Imran, Shafiq Ur Rahman, Hafiz Saqib Ali, Muazzam Arif, Jamshed Iqbal

BMC Chemistry, 2021, 1258, 132671

Theoretical and Computational Insight into the Supramolecular Assemblies of Schiff Bases Involving Hydrogen Bonding and C-H…π Interactions: Synthesis, X-ray Characterization, Hirshfeld Surface Analysis, Anticancer Activity and Molecular Docking Analysis

Hina Andleeb, Lubna Danish, Shiza Munawar, Muhammad N. Ahmed, Imtiaz Khan, Hafiz Saqib Ali, Muhammad N. Tahir, Jim Simpson, Shahid Hameed

Journal of Molecular Structure, 2021, 1235, 130223

Structure-Based Virtual Screening of Dipeptidyl Peptidase-4 Inhibitors and Their In-vitro Analysis

Shafiq Ur Rahman, Hafiz Saqib Ali, Behzad Jafari, Sumera Zaib, Abdul Hameed, Yasser M.S.A Al-Kahraman, Peter Langer, Jamshed Iqbal

ournal of Molecular Structure, 2021, 91, 107326

2020

Lignin Biodegradation by a Cytochrome P450 Enzyme: A Computational Study into Syringol Activation by GcoA

Hafiz Saqib Ali, Richard H. Henchman, Samuel P. de Visser

Chemistry: A European Journal, 2020 26, 13093-13102

Cross-linking of Aromatic Phenolate Groups by Cytochrome P450 Enzymes: A Model for the Biosynthesis of Vancomycin by OxyB

Hafiz Saqib Ali, Richard H. Henchman, Samuel P. de Visser

Organic & Biomolecular Chemistry, 2020, 18, 4610-4618

Comparison of Free-Energy Methods to Calculate the Barriers for the Nucleophilic Substitution of Alkyl Halides by Hydroxide

Hafiz Saqib Ali, Jonathan Higham, Sam P. de Visser, Richard H. Henchman

The Journal of Physical Chemistry B, 2020, 124, 6835–6842

Catalytic Mechanism of Aromatic Nitration by Cytochrome P450 TxtE: Involvement of a Ferric-Peroxynitrite Intermediate

Savvas Louka, Sarah M. Barry, Derren J. Heyes, M. Qadri E. Mubarak, Hafiz Saqib Ali, Lona M. Alkhalaf, Andrew W. Munro, Nigel S. Scrutton, Gregory L. Challis, Sam P. de Visser

Journal of the American Chemical Society, 2020, 142, 15764–15779

How External Perturbations Affect the Chemoselectivity of Substrate Activation by Cytochrome P450 OleTJE

Ahmed Shahria Chowdhury, Hafiz Saqib Ali, Abayomi S. Faponle, Samuel P. de Visser

Physical Chemistry Chemical Physics, 2020, 22, 27178-27190

Revealing the Mechanism and Origin of Reactivity of Au(I)-Catalyzed Functionalized Indenone Formation of Cyclic and Acyclic Acetals of Alkynylaldehydes

Aqeel A. Hussein, Hafiz Saqib Ali

The Journal of Organic Chemistry, 2020, 85, 12682–12691

Insight into the Molecular Characterization and Spectral Properties of 2-Methoxy-1,4-Naphthoquinone: A Computational Approach

Narmeen Ali, Asim Mansha, Sadia Asim, Hafiz Saqib Ali, Muhammad Usman

Journal of Structural Chemistry, 2020, 61, 182–196

The Structural, Spectral, Frontier Molecular Orbital and Thermodynamic Analysis of 2-Hydroxy 2-Methyl Propiophenone by MP2 and B3LYP Methods

Sidra Ghafoor, Asim Mansha, Sadia Asim, Muhammad Usman, Ameer Fawad Zahoor, Hafiz Saqib Ali

Journal of Theoretical and Computational Chemistry, 2020, 19, 2050020

Spectroscopic, Quantum Chemical and Molecular Docking Studies on 2,4-dimethoxy-1,3,5-triazine: A Potent Inhibitor of Protein Kinase CK2 for the Development of Breast Cancer Drug

Noreen Akram, Asim Mansha, R. Premkumar, A. Milton Franklin Benial, Sadia Asim, Shahzad Zafar Iqbal, Hafiz Saqib Ali

Molecular Simulation, 2020, 46, 1340-1353

2019

Entropy of Simulated Liquids Using Multiscale Cell Correlation

Hafiz Saqib Ali, Jonathan Higham, Richard H. Henchman

Entropy, 2019 21, 750

A Combined Experimental and Theoretical Analysis of the Solid-state Supramolecular Self-assembly of N-(2,4-Dichlorophenyl)-1-Naphthamide: Synthesis, Anticholinesterase Potential and Molecular Docking Analysis

Madiha Kazmi, Aliya Ibrar, Hafiz Saqib Ali, Mehreen Ghufran, Abdul Wadood, Ulrich Flörke, Jim Simpson, Aamer Saeed, Antonio Frontera, Imtiaz Khan

Journal of Molecular Structure, 2019, 1197, 458-470

4-(4-Bromophenyl)Thiazol-2-Amine: Crystal Structure Determination, DFT Calculations, Visualizing Intermolecular Interactions Using Hirshfeld Surface Analysis, and DNA Binding Studies

Pervaiz A. Channar, Nasima Arshad, Fayaz A. Larik, Shahid I. Farooqi, Aamer Saeed, Tuncer Hökelek, Bakhtawar Batool, Rabail Ujan, Hafiz Saqib Ali, Ulrich Flörke

Journal of Physical Organic Chemistry, 2019, 32, e3968