Hira Khalid

EDUCATION

I am a distinguished biochemistry graduate with a strong academic foundation and focused research expertise in computer-aided drug design (CADD), evidenced by multiple publications in high-impact, peer-reviewed journals. My research contributions reflect a dedication to scientific rigor, innovation, and advancement in molecular science.

RESEARCH, TEACHING, or OTHER INTERESTS

Biochemistry, Clinical Biochemistry, Immunology and Microbiology, Pharmacology, Toxicology and Pharmaceutics

Scopus Publications

Bacterial Metabolite-Derived NDM-1 Inhibitors: A Computational Strategy to Overcome β-Lactam Resistance
Bader S. Alotaibi, Farhat Shabbir, Muhammad Umer Khan, Iqra Ahmad, Hira Khalid, et al.
Probiotics and Antimicrobial Proteins, 2026
Computational Profiling of Asteraceae-Derived Phytochemicals Targeting S-Adenosylhomocysteine Hydrolase (SAHH) of Naegleria fowleri
Hira Khalid, Iqra Ahmad, Muhammad Hassan Butt, Amen Shamim, Umar Nishan, et al.
Chemistryselect, 2025
Primary amoebic meningoencephalitis (PAM) is a rare but fatal disease caused by Naegleria fowleri ( N. fowleri ). This parasitic amoeba has adverse and deadly effects on humans and animals, as it thrives in fresh and warm water environments and has a mortality rate of up to 95%. The pathogen's resistance to current pharmacological regimens, even in combination drug therapies, is a major contribution to its high mortality. The current study aimed to investigate the potential of antiparasitic plants of the Asteraceae family for inhibiting N. fowleri's S‐adenosyl‐homocysteine hydrolase enzyme (Nf‐SAHH). An in‐house library of 716 natural products was obtained from selected ayurvedic antiparasitic plants and virtually screened against Nf‐SAHH. The identified hits were subjected to initial evaluation based on standard drug‐likeness criteria and ligand efficiency. Stability between the interacting residues of the target receptor and the top active ligands was further confirmed by molecular dynamic simulation. Our six top‐screened hits, namely, 3‐hexadecyloxy carbonyl‐5‐(2‐hydroxyethyl)‐4‐methyl imidazolium ion (HCEMI), geranylgeraniol (GGOH), hexadecanoic acid, 2‐hydroxy‐1‐(hydroxymethyl) ethyl ester, (+)‐sesamin (+)‐arborone, and octadecanoic acid 2,3‐dihydroxypropyl ester showed docking score greater than adenosine analogue (Neplanocin A). These inhibitors also adhered to established drug‐likeness criteria, demonstrating favorable ligand efficiency, pharmacophoric and pharmacokinetic properties. They exhibited stable results in molecular dynamics simulations with a broad spectrum of biological activities. Moreover, the concentration–time profile of HCEMI and geranylgeraniol indicated significant concentrations of these metabolites in the brain tissue to bind and inhibit Nf‐SAHH. Their activities extended beyond their robust affinity for the target protein. Predominantly non‐mutagenic, most of the hits possess the capability to permeate the blood–brain barrier (BBB). They inhibit the P‐glycoprotein, making them viable candidates for treating PAM infection. Given their potential to effectively inhibit the Nf‐SAHH protein, these hits warrant further investigation through in vitro and in vivo studies for the development of novel drugs against the PAM infection.
Screening Asian Medicinal Plants for SARS-CoV-2 Inhibitors: A Computational Approach
Hira Khalid, Iqra Ahmad, Asifa Sarfraz, Anwar Iqbal, Umar Nishan, et al.
Chemistry and Biodiversity, 2025
This work aimed to evaluate the antiviral potential of compounds from Asian medicinal plants against SARS‐CoV‐2's main protease and spike glycoprotein, identifying dual inhibitors from these plants that target both proteins through advanced virtual screening, molecular dynamics simulations, and pharmacophore analysis. An in‐house library of 335 antiviral natural products was prepared from the selected medicinal plants. Following the virtual screening of this library against the main protease and spike glycoprotein, top compounds were subjected to downstream analysis for evaluating druggability potential and toxicity analysis. Molecular dynamic simulations were performed to confirm the stability of interactions between the ligands and target proteins. Our analysis demonstrated 67 compounds as dual inhibitors. The six top dual inhibitors, namely trans‐delta‐viniferin, trans‐E‐viniferin, 3,4‐DHPEA‐EDA, oleuropein aglycone, lactucopicrin, and 11β,13‐dihydrolactucopicrin, exhibited superior docking scores and met drug‐likeness criteria, including Lipinski's rule, bioavailability, and favorable ADME and toxicity profiles. Trans‐delta‐viniferin and trans‐E‐viniferin, featuring a stilbene scaffold, emerged as the most promising candidates due to their stable interactions, minimal fluctuations, and consistent hydrogen bonding across SARS‐CoV‐2's Mpro and S‐protein in MD simulations, while 3,4‐DHPEA‐EDA displayed comparatively less stability. All compounds demonstrated key pharmacophoric features and lacked mutagenicity or PAINS alerts, although lactucopicrin and 11β,13‐dihydrolactucopicrin showed risks for hepatotoxicity. Overall, the critical bonding and drug‐like features, biological activity spectra, and favorable medicinal characteristics predict their biological behavior in laboratory testing. Although additional experimental validations are necessary, our findings indicate that the three lead compounds—namely, trans‐delta‐viniferin, trans‐E‐viniferin, and 3,4‐DHPEA‐EDA, isolated from traditional medicinal plants—are promising novel dual inhibitors of two critical SARS‐CoV‐2 proteins.
Phytobioinformatics screening of ayurvedic plants for potential α-glucosidase inhibitors in diabetes management
Hira Khalid, Muhammad Hassan Butt, Aziz ur Rehman Aziz, Iqra Ahmad, Farzana Iqbal, et al.
Current Plant Biology, 2024
Identification of Novel Quinolone and Quinazoline Alkaloids as Phosphodiesterase 10A Inhibitors for Parkinson’s Disease through a Computational Approach
Iqra Ahmad, Hira Khalid, Asia Perveen, Muhammad Shehroz, Umar Nishan, et al.
ACS Omega, 2024
Computer-assisted discovery of natural inhibitors for platelet-derived growth factor alpha as novel therapeutics for thyroid cancer
Hira Khalid, Farah Sattar, Iqra Ahmad, Valdir Ferreira de Paula Junior, Umar Nishan, et al.
Frontiers in Pharmacology, 2024
Platelet-derived growth factor alpha (PDGFRA) plays a significant role in various malignant tumors. PDGFRA expression boosts thyroid cancer cell proliferation and metastasis. Radiorefractory thyroid cancer is poorly differentiated, very aggressive, and resistant to radioiodine therapy. Thus, novel anticancer drugs that inhibit its metastasis are urgently required. In this context, we proposed the PDGFRA inhibitors by an optimized structure-based drug design approach. We performed a virtual screening of metabolites derived from anticancer medicinal plants (Swertia chirayita, Myristica fragrans, and Datura metel) and successfully identified seven hits, namely cis-Grossamide K, Daturafoliside O, N-cis-feruloyltyramine, Maceneolignan H, Erythro-2-(4-allyl-2, 6-dimethoxyphenoxy)-1-(3, 4, 5-trimethoxyphenyl) propan-1, 3-diol, Myrifralignan C, and stigmasteryl-3-O-β-glucoside as potential PDGFRA inhibitors. Not only the top 7 hits exhibited higher docking scores in docking simulation but also optimal drug-likeness and non-toxic profiles in pharmacokinetics analysis among 119 compounds. Our top hits are non-mutagenic, can cross the blood-brain barrier, and inhibit p-glycoprotein, while the N-cis-feruloyltyramine has the potential to become a lead compound. The protein-ligand stability of the top 3 hits, namely cis-Grossamide K, Daturafoliside O, and N-cis-feruloyltyramine, and their interactions at the potential binding site of target protein were confirmed through molecular dynamic simulations. We also analyzed pharmacophoric features for stable binding in the PDGFRA active site. These drug candidates were further characterized to predict their biological activity spectra in the human body and medicinal characteristics to know their extensive behavior in laboratory testing. This study necessitates the in-vitro and in-vivo studies to confirm the potential of our hits for the discovery of novel therapeutics against the thyroid cancer.
Identifying plant-derived antiviral alkaloids as dual inhibitors of SARS-CoV-2 main protease and spike glycoprotein through computational screening
Ramsha Yamin, Iqra Ahmad, Hira Khalid, Asia Perveen, Sumra Wajid Abbasi, et al.
Frontiers in Pharmacology, 2024
COVID-19 is currently considered the ninth-deadliest pandemic, spreading through direct or indirect contact with infected individuals. It has imposed a consistent strain on both the financial and healthcare resources of many countries. To address this challenge, there is a pressing need for the development of new potential therapeutic agents for the treatment of this disease. To identify potential antiviral agents as novel dual inhibitors of SARS-CoV-2, we retrieved 404 alkaloids from 12 selected medicinal antiviral plants and virtually screened them against the renowned catalytic sites and favorable interacting residues of two essential proteins of SARS-CoV-2, namely, the main protease and spike glycoprotein. Based on docking scores, 12 metabolites with dual inhibitory potential were subjected to drug-likeness, bioactivity scores, and drug-like ability analyses. These analyses included the ligand–receptor stability and interactions at the potential active sites of target proteins, which were analyzed and confirmed through molecular dynamic simulations of the three lead metabolites. We also conducted a detailed binding free energy analysis of pivotal SARS-CoV-2 protein inhibitors using molecular mechanics techniques to reveal their interaction dynamics and stability. Overall, our results demonstrated that 12 alkaloids, namely, adouetine Y, evodiamide C, ergosine, hayatinine, (+)-homoaromoline, isatithioetherin C, N,alpha-L-rhamnopyranosyl vincosamide, pelosine, reserpine, toddalidimerine, toddayanis, and zanthocadinanine, are shortlisted as metabolites based on their interactions with target proteins. All 12 lead metabolites exhibited a higher unbound fraction and therefore greater distribution compared with the standards. Particularly, adouetine Y demonstrated high docking scores but exhibited a nonspontaneous binding profile. In contrast, ergosine and evodiamide C showed favorable binding interactions and superior stability in molecular dynamics simulations. Ergosine demonstrated exceptional performance in several key pharmaceutical metrics. Pharmacokinetic evaluations revealed that ergosine exhibited pronounced bioactivity, good absorption, and optimal bioavailability. Additionally, it was predicted not to cause skin sensitivity and was found to be non-hepatotoxic. Importantly, ergosine and evodiamide C emerged as superior drug candidates for dual inhibition of SARS-CoV-2 due to their strong binding affinity and drug-like ability, comparable to known inhibitors like N3 and molnupiravir. This study is limited by its in silico nature and demands the need for future in vitro and in vivo studies to confirm these findings.