Computational Drug Design Lab (CDD)

Brief introduction of the lab

SINES commenced the journey of computational drug design back in 2012. Currently, Computational Drug Design (CDD) research team is composed of 06 doctoral and 12 master students. Following a holistic pharmacoinformatic approach, computational drug design research team combines multi-dimensional annotation, structural modeling of proteins, structure-based drug design, chemometric and machine learning approaches to develop predictive computational systems for transporters, proteins and ion channels. Major purpose of these activities is to design and optimize lead structures with respect to their efficacy and toxicity and to develop multiscale simulation systems for the prediction of drug-efficacy and drug-induced toxicity.

Mission and vision (role)

Rational: Advances in medicine have led to many significant new discoveries, and new insights of the workings of cancers, neurological- , autoimmune- or cardiovascular-, and other devastating diseases. However, still, many of these diseases cannot be effectively treated by existing therapies. And the development of new innovative medicines remains therefore urgent and essential.

First, we need a better understanding of the human pathophysiology and biological pathways underlying specific diseases. This enables us to better predict where to focus time and work that will lead us to viable drugs.

This requires us to develop a better predictability of human pharmacology and drug safety, and much more advanced in vitro and in vivo models translating to the individual
patient. Finally in order to increase the optimal effectiveness, new and more innovative ways for drug delivery are crucial.


At the CDD laboratory, we want to be at the leading edge of new fundamental research on the development of new drugs which are more effective and safer. And additionally develop new innovative ways to apply the right drugs, with the right dosage, at the right place. In this regard we focus on three main lines of research which are described below.

Moreover, as an academic institute, we also focus on the education and training of graduate students in our fields of expertise. And additionally with the added value of CDD being part of the NICHE, we seek active joint research projects.

Envisioned research areas (especially interdisciplinary ones)

Lines of Research: With our set goals, we focus on three main lines of research. Areas that have appeared more sharply into focus over the past few years, and which will steer our research efforts in the coming period.

1. Novel therapeutic modalities and novel concepts in early drug discovery

The first focused area is the development of novel therapeutic techniques and procedures. Including, new innovative concepts in early drug design and discovery in order to better predict ligand-target interactions. For this, we worked on cheminformatics-based identification of new chemical structures with optimal target affinity and specificity. Further, we aim to design cutting-edge formulations and strategies for drug administration. So we can optimize the specific targeting the site of the disease, maximise the desired therapeutic effect, while at the same time minimize the adverse reactions to drugs.

2. Translational Drug Research

Our second line of research is translational in nature. This means we aim at the optimization of the transition from preclinical research towards the stages of pharmacological interventions within the body. Specifically, we are working on innovative bio-pharmaceutical concepts to intervene in auto-immune-like disorders, using biologics such as vaccines and therapeutic proteins. Also, this requires our focus on developing better techniques and methods for predicting the efficacy and drug safety. To achieve this, we develop quantitative systems biology models of health and disease states.

3. Personalized Medicine

Most medical treatments have been designed for the “average patient”, often resulting in a “one-size-fits-all” approach. However, it has become increasingly clear that a much more effective approach is required that takes into account the differences between individuals, their genes, environments, lifestyles, all of which also influences their individual responses to treatment. This calls for a systems-level understanding of diseases, their onset and progressions, aimed at predicting the modulation of disease networks by drugs in cells, organs, and the body as a whole. We aim to develop computational systems pharmacology methods, which will enable us to take into account complex disturbances in biochemical and signaling networks.

Potential student/faculty, funded/non-funded projects of interdisciplinary nature

Lab PI: Dr. Ishrat Jabeen, 12 MS and 06PhD students
1. Probing the Lipophilic Efficiency, Ligand Efficiency and Selectivity Profiles of Inhibitors of Multidrug Transport Proteins” from Higher Education Commission of Pakistan 2012-2013
2. “Pharmacoinformatics Approaches to Design dual Inhibitors of Tyrosine Kinase Domain of IR and IGF-1R” from Higher Education Commission of Pakistan (Amount of PKR 1.3M). 2018-2021.
3. In Silico Modeling of hERG K+ Channel (2014-2020) HEC Funded Phd student Project.
4. Combined Ligand and Structure Based Studies of Modulators of Akt Kinases. NUST Funded Phd student Project.
5. In Silico strategies to predict drug metabolism and drug –drug interactions. HEC Funded Phd student Project.
6. Molecular Modeling Strategies to Design Novel Inhibitors of GAT1. HEC Funded Phd student Project.
7. Synthesis, biological evaluation and in silico studies on inhibitors of IP3R . NUST Funded Phd student Project.
8. Combined Ligand- and Structure- Based Strategies to Design Potential Inhibitors of Multidrug Resistance (MDR) Proteins. NUST Funded Phd student Project.

Key hardware, equipment, software, other resources in the lab (both available and planned)

1. 14 Computers

2. MOE Software

3. Schrodinger Software

4. Gold Software

5. GROMICS Software

6. AMBER Software

7. Pentacle Software

8. Modullar Software


1. Preparatory HPLC

2. Isolation extraction set-up for Venoms and Medicinal Plants

Lab staff and student strength (both available and planned)

Available: Students 18

Names of other NICHE labs with which interdisciplinary collaboration work is expected. Image Analysis Lab i. Any other relevant information

1. Graduates of CDD: More than 50% of the graduates of CDD teams secured fully funded PhD scholarship at top world universities. PhD graduates (05) of CDD are working as data scientists, faculty and Post-doctoral fellows at top local and international organizations.
2. Conferences/Workshops:
1. Symposium of Computer aided drug design approaches, 27 Sep, 2017
2. International Workshop on Rational Drug design approaches, June 15-17, 2021.
3. Webinar on High Performance Computing in Drug Design, May, 17, 2021
4. Invited Speaker at the Molecular Dynamics Simulations workshop at LUMS Lahore, 12-15 Feb 2020
5. Invited Speaker at Current trends in computational sciences seminar at the GCWU Faisalabad, 17 June, 2020
6. Speaker at the supercomputing in modeling and simulation webinar at SINES, NUST, May 2020


The CDD lab offers internship to 5 students/YEAR from different universities. So far 20 students from COMSATS, ISLAMABAD, GC University Faisalabad, Quaid-e-Azam University, and Islamic International University have completed their internship at the CDD lAB