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List of Publications per Year

S Ahmad, MU Mirza, JF Trant. Dock-able linear and homodetic di, tri, tetra, and pentapeptide library from canonical amino acids: SARS-CoV-2 Mpro as a case studyJournal of Pharmaceutical Analysis 13 (5), 523-534

Andrew S P Sharp, Tim Kinnaird, Nick Curzen, Ruba Ayyub, Jorge Emilio Alfonso, Mamas A Mamas, Henri Vanden Bavière, Cost-effectiveness of intravascular ultrasound-guided percutaneous intervention in patients with acute coronary syndromes: a UK perspective, European Heart Journal - Quality of Care and Clinical Outcomes, 2023;, qcad073,

Saira Naseem, Samra Khan, Safdar Hussain, Muhammad Usman Mirza, Muhammad Ashraf, Zahid Shafiq & John F. Trant (2023) Synthesis, biological evaluation, and molecular docking study of xanthene-linked thiosemicarbazones as cholinesterase inhibitors, Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2023.2274981

Pasha U, Hanif K, Nisar H, Abid R, Mirza MU, Wajid B, Sadaf S. A novel missense compound heterozygous variant in TLR1 gene is associated with susceptibility to rheumatoid arthritis - structural perspective and functional annotations. Clin Rheumatol. 2023 Nov;42(11):3097-3111. doi: 10.1007/s10067-023-06702-9. Epub 2023 Jul 21. PMID: 37479888.

Ahmad S, Sajjad M, Altayb HN, Sarim Imam S, Alshehri S, Ghoneim MM, Shahid S, Usman Mirza M, Shahid Nadeem M, Kazmi I, Waheed Akhtar M. Engineering processive cellulase of Clostridium thermocellum to divulge the role of the carbohydrate-binding module. Biotechnol Appl Biochem. 2023 Feb;70(1):290-305. doi: 10.1002/bab.2352. Epub 2022 May 25. PMID: 35483889.

Abdul Majeed, Muhammad Tahir ul Qamar, Arooma Maryam, Muhammad Usman Mirza, Laila Alhussain, Seham Obaid Al Otaibi, Ahmad Almatroudi, Khaled S. Allemailem, Faris Alrumaihi, Abdulaziz A. Aloliqi & Faez Falah Alshehri (2023) Structural insights into the mechanism of resistance to bicalutamide by the clinical mutations in androgen receptor in chemo-treatment resistant prostate cancer, Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2023.2208203

Muhammad N, Hussain SI, Rehman ZU, Khan SA, Jan S, Khan N, Muzammal M, Abbasi SW, Kakar N, Rehman ZU, Khan MA, Mirza MU, Muhammad N, Khan S, Wasif N. Autosomal recessive variants c.953A>C and c.97-1G>C in NSUN2 causing intellectual disability: a molecular dynamics simulation study of loss-of-function mechanisms. Front Neurol. 2023 May 25;14:1168307. doi: 10.3389/fneur.2023.1168307. PMID: 37305761; PMCID: PMC10249782. 

Sadia Saeed, Lijiao Ning, Alaa Badreddine, Muhammad Usman Mirza, Mathilde Boissel, Roohia Khanam, Jaida Manzoor, Qasim M. Janjua, Waqas I. Khan, Bénédicte Toussaint, Emmanuel Vaillant, Souhila Amanzougarene, Mehdi Derhourhi, John F. Trant, Anna-Maria Siegert, Brian Y.H. Lam, Giles S.H. Yeo, Layachi Chabraoui, Asmae Touzani, Abhishek Kulkarni, I. Sadaf Farooqi, Amélie Bonnefond, Muhammad Arslan, Philippe Froguel; Biallelic Mutations in P4HTM Cause Syndromic Obesity. Diabetes 1 September 2023; 72 (9): 1228–1234.

Shah SZ, Jabbar B, Mirza MU, Waqas M, Aziz S, Halim SA, Ali A, Rafique S, Idrees M, Khalid A, et al. An Immunoinformatics Approach to Design a Potent Multi-Epitope Vaccine against Asia-1 Genotype of Crimean–Congo Haemorrhagic Fever Virus Using the Structural Glycoproteins as a Target. Vaccines. 2023; 11(1):61.

Sarwar S, Abdul Qadir M, Alharthy RD, Ahmed M, Ahmad S, Vanmeert M, Mirza MU, Hameed A. Folate Conjugated Polyethylene Glycol Probe for Tumor-Targeted Drug Delivery of 5-Fluorouracil. Molecules. 2022; 27(6):1780.

Muhammad Usman Mirza, Ida Alanko, Michiel Vanmeert, Kendall M. Muzzarelli, Outi M.H. Salo-Ahen, Iskandar Abdullah, Iulia A. Kovari, Sandra Claes, Steven De Jonghe, Dominique Schols, Raymond F. Schinazi, Ladislau C. Kovari, John F. Trant, Sarfraz Ahmad, Matheus Froeyen,
The discovery of Zika virus NS2B-NS3 inhibitors with antiviral activity via an integrated virtual screening approach, European Journal of Pharmaceutical Sciences, Volume 175, 2022, 106220, ISSN 0928-0987, (

Anwar F, Saleem U, Rehman AU, Ahmad B, Ismail T, Mirza MU, Ahmad S. Acute Oral, Subacute, and Developmental Toxicity Profiling of Naphthalene 2-Yl, 2-Chloro, 5-Nitrobenzoate: Assessment Based on Stress Response, Toxicity, and Adverse Outcome Pathways. Front Pharmacol. 2022 Jan 20;12:810704. doi: 10.3389/fphar.2021.810704. PMID: 35126145; PMCID: PMC8811508.

Fatima I, Ahmad S, Alamri MA, Mirza MU, Tahir Ul Qamar M, Rehman A, Shahid F, Alatawi EA, Alkhayl FFA, Al-Megrin WA, Almatroudi A. Discovery of Rift Valley fever virus natural pan-inhibitors by targeting its multiple key proteins through computational approaches. Sci Rep. 2022 Jun 3;12(1):9260. doi: 10.1038/s41598-022-13267-1. PMID: 35662263; PMCID: PMC9163866.

Alamri MA, Mirza MU, Adeel MM, Ashfaq UA, Tahir ul Qamar M, Shahid F, Ahmad S, Alatawi EA, Albalawi GM, Allemailem KS, et al. Structural Elucidation of Rift Valley Fever Virus L Protein towards the Discovery of Its Potential Inhibitors. Pharmaceuticals. 2022; 15(6):659.

L. Ajmal, A. Hamid, F. Ahmed, R. Safee, U. Chaudhary, K. Iman, et al. Repellent activity of trans-anethole and tea tree oil against Aedes aegypti and their interaction with OBP1, a protein involved in olfaction Entomol Exp Appl, 170 (2022), pp. 547-554

Anwar F, Saleem U, Rehman AU, Ahmad B, Ismail T, Mirza MU, Kee LY, Abdullah I, Ahmad S. Toxicological Screening of 4-Phenyl-3,4-dihydrobenzo[h]quinolin-2(1H)-one: A New Potential Candidate for Alzheimer's Treatment. ACS Omega. 2021 Apr 16;6(16):10897-10909. doi: 10.1021/acsomega.1c00654. PMID: 34056243; PMCID: PMC8153932.

Anwar F, Saleem U, Rehman AU, Ahmad B, Froeyen M, Mirza MU, Kee LY, Abdullah I, Ahmad S. Toxicity Evaluation of the Naphthalen-2-yl 3,5-Dinitrobenzoate: A Drug Candidate for Alzheimer Disease. Front Pharmacol. 2021 May 10;12:607026. doi: 10.3389/fphar.2021.607026. PMID: 34040515; PMCID: PMC8141749.

Ahmad S, Usman Mirza M, Yean Kee L, Nazir M, Abdul Rahman N, Trant JF, Abdullah I. Fragment-based in silico design of SARS-CoV-2 main protease inhibitors. Chem Biol Drug Des. 2021 Oct;98(4):604-619. doi: 10.1111/cbdd.13914. Epub 2021 Jul 2. PMID: 34148292; PMCID: PMC8444677.

Tahir Ul Qamar, Muhammad & Mirza, Usman & Song, Jia-Ming & Junaid Rao, Muhammad & Zhu, Xitong & Chen, Ling-Ling. (2021). Probing the Structural Basis of Citrus Phytochrome B using Computational Modelling and Molecular Dynamics Simulation Approaches. Journal of Molecular Liquids. 340. 10.1016/j.molliq.2021.116895. 

Naheed N, Maher S, Saleem F, Khan A, Wadood A, Rasheed S, Choudhary MI, Froeyen M, Abdullah I, Mirza MU, Trant JF, Ahmad S. New isolate from Salvinia molesta with antioxidant and urease inhibitory activity. Drug Dev Res. 2021 Dec;82(8):1169-1181. doi: 10.1002/ddr.21831. Epub 2021 May 13. PMID: 33983647.

Nisar H, Pasha U, Mirza MU, Abid R, Hanif K, Kadarmideen HN, Sadaf S. Impact of IL-17F 7488T/C Functional Polymorphism on Progressive Rheumatoid Arthritis: Novel Insight from the Molecular Dynamic Simulations. Immunol Invest. 2021 May;50(4):416-426. doi: 10.1080/08820139.2020.1775642. Epub 2020 Jun 16. PMID: 32543936.

Ilyas S, Tabasum R, Iftikhar A, Nazir M, Hussain A, Hussain A, Ali MS, Saleem F, Saleem U, Froeyen M, Abdullah I, Mirza MU, Ahmad S. Effect of Berberis vulgaris L. root extract on ifosfamide-induced in vivo toxicity and in vitro cytotoxicity. Sci Rep. 2021 Jan 18;11(1):1708. doi: 10.1038/s41598-020-80579-5. PMID: 33462261; PMCID: PMC7814047.

Tahir Ul Qamar M, Ahmad S, Khan A, Mirza MU, Ahmad S, Abro A, Chen LL, Almatroudi A, Wei DQ. Structural probing of HapR to identify potent phytochemicals to control Vibrio cholera through integrated computational approaches. Comput Biol Med. 2021 Nov;138:104929. doi: 10.1016/j.compbiomed.2021.104929. Epub 2021 Oct 9. PMID: 34655900.

Tahir Ul Qamar M, Ismail S, Ahmad S, Mirza MU, Abbasi SW, Ashfaq UA, Chen LL. Development of a Novel Multi-Epitope Vaccine Against Crimean-Congo Hemorrhagic Fever Virus: An Integrated Reverse Vaccinology, Vaccine Informatics and Biophysics Approach. Front Immunol. 2021 Jun 16;12:669812. doi: 10.3389/fimmu.2021.669812. PMID: 34220816; PMCID: PMC8242340.

Tahir Ul Qamar M, Ahmad S, Fatima I, Ahmad F, Shahid F, Naz A, Abbasi SW, Khan A, Mirza MU, Ashfaq UA, Chen LL. Designing multi-epitope vaccine against Staphylococcus aureus by employing subtractive proteomics, reverse vaccinology and immuno-informatics approaches. Comput Biol Med. 2021 May;132:104389. doi: 10.1016/j.compbiomed.2021.104389. Epub 2021 Apr 15. PMID: 33866250.

Alamri MA, Tahir Ul Qamar M, Mirza MU, Bhadane R, Alqahtani SM, Muneer I, Froeyen M, Salo-Ahen OMH. Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CLpro. J Biomol Struct Dyn. 2021 Aug;39(13):4936-4948. doi: 10.1080/07391102.2020.1782768. Epub 2020 Jun 24. PMID: 32579061; PMCID: PMC7332866.

Khalid MF, Iman K, Ghafoor A, Saboor M, Ali A, Muaz U, Basharat AR, Tahir T, Abubakar M, Akhter MA, Nabi W, Vanderbauwhede W, Ahmad F, Wajid B, Chaudhary SU. PERCEPTRON: an open-source GPU-accelerated proteoform identification pipeline for top-down proteomics. Nucleic Acids Res. 2021 Jul 2;49(W1):W510-W515. doi: 10.1093/nar/gkab368. PMID: 33999207; PMCID: PMC8262694.


Mirza MU, Froeyen M. Structural elucidation of SARS-CoV-2 vital proteins: Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase. J Pharm Anal. 2020 Aug;10(4):320-328. doi: 10.1016/j.jpha.2020.04.008. Epub 2020 Apr 28. PMID: 32346490; PMCID: PMC7187848.

Salo-Ahen, O., Alanko, I., Rajendra, B., Bonvin, A. M. J. J., Vargas Honorato, R., Hossain, S., Juffer, A., Kabedev, A., Lahtela-Kakkonen, M., Larsen, A. S., Lescrinier, E., Marimuthu, P., Mirza, M. U., Mustafa, G., Nunes-Alves, A., Pantsar, T., Saadabadi, A., Singaravelu, K., & Vanmeert, M. (2020). Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development. Processes, 9(1), Article 71.

Alamri MA, Tahir Ul Qamar M, Mirza MU, Alqahtani SM, Froeyen M, Chen LL. Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches. J Pharm Anal. 2020 Dec;10(6):546-559. doi: 10.1016/j.jpha.2020.08.012. Epub 2020 Aug 28. PMID: 32874702; PMCID: PMC7453225.

Mirza MU, Ahmad S, Abdullah I, Froeyen M. Identification of novel human USP2 inhibitor and its putative role in treatment of COVID-19 by inhibiting SARS-CoV-2 papain-like (PLpro) protease. Comput Biol Chem. 2020 Dec;89:107376. doi: 10.1016/j.compbiolchem.2020.107376. Epub 2020 Sep 13. PMID: 32979815; PMCID: PMC7487165.

Mirza MU, Saadabadi A, Vanmeert M, Salo-Ahen OMH, Abdullah I, Claes S, De Jonghe S, Schols D, Ahmad S, Froeyen M. Discovery of HIV entry inhibitors via a hybrid CXCR4 and CCR5 receptor pharmacophore-based virtual screening approach. Eur J Pharm Sci. 2020 Dec 1;155:105537. doi: 10.1016/j.ejps.2020.105537. Epub 2020 Sep 2. Erratum in: Eur J Pharm Sci. 2021 Jul 1;162:105827. PMID: 32890663; PMCID: PMC7467125.

Rehman HM, Mirza MU, Ahmad MA, Saleem M, Froeyen M, Ahmad S, Gul R, Alghamdi HA, Aslam MS, Sajjad M, et al. A Putative Prophylactic Solution for COVID-19: Development of Novel Multiepitope Vaccine Candidate against SARS-COV-2 by Comprehensive Immunoinformatic and Molecular Modelling Approach. Biology. 2020; 9(9):296.

Maher S, Choudhary MI, Saleem F, Rasheed S, Waheed I, Halim SA, Azeem M, Abdullah IB, Froeyen M, Mirza MU, et al. Isolation of Antidiabetic Withanolides from Withania coagulans Dunal and Their In Vitro and In Silico Validation. Biology. 2020; 9(8):197.

Anwar F, Saleem U, Ahmad B, Ashraf M, Rehman AU, Froeyen M, Kee LY, Abdullah I, Mirza MU, Ahmad S. New naphthalene derivative for cost-effective AChE inhibitors for Alzheimer's treatment: In silico identification, in vitro and in vivo validation. Comput Biol Chem. 2020 Dec;89:107378. doi: 10.1016/j.compbiolchem.2020.107378. Epub 2020 Sep 18. PMID: 33002716.

Khalid H, Landry KB, Ijaz B, Ashfaq UA, Ahmed M, Kanwal A, Froeyen M, Mirza MU. Discovery of novel Hepatitis C virus inhibitor targeting multiple allosteric sites of NS5B polymerase. Infect Genet Evol. 2020 Oct;84:104371. doi: 10.1016/j.meegid.2020.104371. Epub 2020 May 31. PMID: 32485331.

Ali I, Rehman HM, Mirza MU, Akhtar MW, Asghar R, Tariq M, Ahmed R, Tanveer F, Khalid H, Alghamdi HA, et al. Enhanced Thermostability and Enzymatic Activity of cel6A Variants from Thermobifida fusca by Empirical Domain Engineering. Biology. 2020; 9(8):214.

Mirza, M.U.; Ahmad, S.; Abdullah, I.; Froeyen, M. Identification of Novel Human USP2 Inhibitor: Might Involve in SARS-CoV-2 Papain-Like (PLpro) Protease Deubiquitination Activity. Preprints 2020, 2020050136.

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