Drug Design and Molecular Modelling Centre (DDMM Centre)

The Drug Design and Molecular Modelling Centre (DDMM Centre) at Chitkara College of Pharmacy is an academic and research-focused centre dedicated to advancing the field of drug discovery and development aims to advance research in computer-aided drug design (CADD), molecular modelling, and computational biology. The centre focuses on:

• Accelerating drug discovery through in-silico approaches.
• Facilitating interdisciplinary research in pharmaceutical sciences, bioinformatics, and medicinal chemistry.
• Providing training and resources for academics, researchers, and industry professionals.
• Promoting collaborations with pharmaceutical industries and research institutions.
• Simulate and analyze the interactions between small molecules and biological targets to predict the efficacy and safety of new drugs.

Key Features of DDMM Centre

✔ Advanced Computational Tools & Software

• Molecular Docking: AutoDock, Discovery Studio Client
• Molecular Dynamics: DESMOND, GROMACS, NMDA
• QSAR & Pharmacophore Modelling: Discovery Studio
• ADMET profiling: SwissADME, MolOpt
• GPU-accelerated workstations for simulations.

Key Members of the Centre

Dr. Manjinder Singh
Incharge, DDMM Centre, Associate Professor, Pharmaceutical Chemistry, HOD (Pharm.D, Administration), Deputy Registrar, IQAC

Field of Specialization: Structure based designing and Synthesis of different heterocyclic nucleus, Purification and characterization using various sophisticated techniques, In vitro and In vivo biological evaluation, Computer-aided Drug Designing with Molecular Docking, molecular dynamic analysis, and ADME property calculations and make them clinically appropriate.

Responsibilities: Overseeing research projects, industry collaborations, and academic programs.

Dr. Somdutt Mujwar
Associate Professor, Pharmaceutical Chemistry, Chitkara College of Pharmacy, Chitkara University

Computational drug design, with a particular focus on molecular docking, molecular dynamics simulations, QSAR modelling, ADMET profiling and machine learning approaches for the discovery of novel therapeutic agents. Integrates cheminformatics tools and next-generation computational techniques to streamline the drug discovery pipeline, contributing significantly to the development of targeted and efficient therapeutic interventions.

Dr Pragati Silakari
Assistant Professor, Pharmaceutical Chemistry, Chitkara College of Pharmacy, Chitkara University

Pharmaceutical chemistry, novel drug design, and synthesis of bioactive compounds. Expertise in molecular modeling tools: docking, dynamics, QSAR/QSSR. Structure-activity relationship (SAR) and lead optimization studies.

Dr. Pratibha Sharma
Assistant Professor, Pharmaceutical Chemistry, Chitkara College of Pharmacy, Chitkara University

Drug design and chemical synthesis of heterocyclic compounds with multifunctional therapeutic potential, mainly focused on molecular modelling and computational drug design studies, targeting complex disorders such as Alzheimer’s disease and Rheumatoid arthritis.

✔ Industry & Academic Collaborations

• Partnerships with pharma institutions and industries for drug discovery projects.
• MoUs with national & international research institutes.

✔ Training & Workshops

• Regular workshops on CADD, Bioinformatics, and AI in Drug Discovery.
• Certification courses for students and professionals

Facilities

Software: Biovia Drug Discovery Studio

Purpose of Software Usage

Discovery Studio is a suite of software for simulating small molecule and macromolecule systems. It is developed and distributed by Dassault Systemes BIOVIA. It has various software algorithms developed originally in the scientific community, including CHARMM, MODELLER, DELPHI, ZDOCK, DMol and more. It can be used to do Simulations studies like Molecular Mechanics, Molecular Dynamics, Quantum Mechanics etc.

Discovery Studio is a suite of software used for

• Simulating small molecule and macromolecule systems.
• It can help in designing of Ligand Design,
• Pharmacophore modelling,
• Virtual screening,
• Structure-based Drug Design Including tools for receptor-ligand docking and pose refinement,
• De novo design,
• Macromolecule design and validation,
• Protein- protein docking,
• Membrane-bound proteins,
• ADME studies
• Predictive toxicity.

Software Desmond of Schrodinger for Molecular Dynamics

Schrödinger is the scientific leader in developing state-of-the-art chemical simulation software for use in pharmaceutical, biotechnology, and materials science research. Maestro is the portal to all of Schrödinger’s computational technology – far more than just a user interface, Maestro also helps researchers organize and analyze data. Schrödinger’s computational platforms evaluate compounds in silico, with experimental accuracy on properties such as binding affinity and solubility.

Schrödinger’s products include molecular modeling programs and LiveDesign, an enterprise application designed to facilitate communication among interdisciplinary research teams.

Desmond, a newly developed MD code created by D. E. Shaw Research, provides parallel scalability, simulation throughput, and scientific accuracy to achieve these goals. Molecular dynamics (MD) simulation stands alone as the fundamental computational tool for capturing dynamic events of scientific interest in all these applications.

It can be used for

• Model generation,
• Flexible visualization,
• Quantitative structural analysis,
• Molecular properties
• Calculate the binding energies of Ligand-proteins.
• Predicts dynamic properties such as thermophysical and mechanical properties of materials systems

Workstation

Server 1

Model- HP Z440 Workstation; ;x64 bit OS; RAM 32 GB; Processor: Intel(R) Xeon(R) CPU E5-1620 v3;

Client 3

Acer-i3-514; x64 bit; RAM 8 GB; intel core i3-6100

Expected Outcomes & Achievements:

• Designing of Research Proposal for PhD Students from different courses of Pharmacy. Review and research publications has been communicated. Projects submitted to different agencies like BIRAC, DDH etc using these software’s.
• Research Publications: High-impact papers in SCI/Scopus-indexed journals.
• Patents & Drug Candidates: Novel in-silico-designed molecules for further validation.
• Placements & Internships: Students placed in R&D roles in pharma/biotech firms.

Photographs of Centres with special equipment(s)

WordPress Portfolio

List of Workshops/Conferences/Seminars/Activities conducted under the Centre

• An International Conference on “Recent Innovations in Clinical and Translational Approaches in Pharmaceutical Sciences, November 24th to 25th, 2023.
• An International Conference on “Uplifting the Translational Value of New Drug Molecules in Neuroscience, April 16–17, 2024.
• 5 Day Zonal Centre Program On “Computer Aided Drug Design & Discovery” In association with Makeintern Kshitijz, IIT Kharagpur 2022
• Webinar on ‘Computational Tools in Drug Discovery
• Webinar on ‘Computational approaches in target identification and drug discovery
• An international seminar on ‘Emerging Trends and innovations in Drug delivery & research’
• An International Conference on “Innovation and Advances in Drug Development & Clinical Research (IADDCR-2023), April 24–25, 2023.
• 5 days’ workshop on ‘Computer Aided Drug Discovery and Designing’ Program in collaboration with Zonal Championship Makeintern (E-Cell IIT Kharagpur) 2023
• 5 days’ workshop on ‘CADD’ in collaboration with Zonal Championship Makeintern (E-Cell IIT Kharagpur)
• International Seminar on “Emerging Trends and Innovations in Drug Delivery & Research, 11th November 2022

List of Research/Innovations/Research Publication

• Singh, S., Singh, T. G., Singh, M., Najda, A., Nurzyńska-Wierdak, R., Almeer, R., Kamel, M. & Abdel-Daim, M. M. (2021). Anticonvulsive effects of chondroitin sulfate on pilocarpine and pentylenetetrazole induced epileptogenesis in mice. Molecules, 26(22), 6773
• Bhargava, S. K., Singh, T. G., Mannan, A., Singh, S., Singh, M., & Gupta, S. (2022). Pharmacological evaluation of Thuja occidentalis for the attenuation of neuropathy via AGEs and TNF-α inhibition in diabetic neuropathic rats. Environmental Science and Pollution Research, 29(40), 60542-60557.
• Singh, M., Bhatia, S., Sharma, P., Kaur, M., & Singh, T. G. (2022). Scaffold morphing and in silico studies of potential BACE1 (β‐secretase) inhibitors: A hope for newer dawn in anti‐Alzheimer therapeutics. Alzheimer’s & Dementia, 18, e068799.
• Sharma, P., Singh, M., Singh, V., Singh, T. G., Singh, T., & Ahmad, S. F. (2023). Recent development of novel aminoethyl-substituted chalcones as potential drug candidates for the treatment of alzheimer’s disease. Molecules, 28(18), 6579.
• Sharma, P., Singh, V., & Singh, M. (2023). N‐methylpiperazinyl and piperdinylalkyl‐O‐chalcone derivatives as potential polyfunctional agents against Alzheimer’s disease: Design, synthesis and biological evaluation. Chemical Biology & Drug Design, 102(5), 1155-1175.
• Singh, V., Mujwar, S., Singh, M., Singh, T., & Ahmad, S. F. (2023). Computational studies to understand the neuroprotective mechanism of action basil compounds. Molecules, 28(20), 7005.
• Goyal, S., Singh, M., Thirumal, D., Sharma, P., Mujwar, S., Mishra, K. K., Singh T. & Ahmad, S. F. (2023). In Silico Approaches to Developing Novel Glycogen Synthase Kinase 3β (GSK-3β). Biomedicines, 11(10), 2784.
• Bhatia, S., Singh, M., Sharma, P., Mujwar, S., Singh, V., Mishra, K. K., Singh T., Singh T. & Ahmad, S. F. (2023). Scaffold morphing and in silico design of potential BACE-1 (β-secretase) inhibitors: A hope for a newer dawn in anti-Alzheimer therapeutics. Molecules, 28(16), 6032.
• Kciuk, M., Gielecińska, A., Mujwar, S., Kołat, D., Kałuzińska-Kołat, Ż., Celik, I., & Kontek, R. (2023). Doxorubicin—an agent with multiple mechanisms of anticancer activity. Cells, 12(4), 659.
• Er-Rajy, M., El Fadili, M., Mujwar, S., Zarougui, S., & Elhallaoui, M. (2023). Design of novel anti-cancer drugs targeting TRKs inhibitors based 3D QSAR, molecular docking and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics, 41(21), 11657-11670.
• Fidan, O., Mujwar, S., & Kciuk, M. (2023). Discovery of adapalene and dihydrotachysterol as antiviral agents for the Omicron variant of SARS-CoV-2 through computational drug repurposing. Molecular diversity, 27(1), 463-475.
• Singh, M., Sharma, P., Singh, V., & Singh, T. G. (2023). Potential cognitive enhancers: Discovery and development of multi‐targeting aminoalkyl chalcones. Alzheimer’s & Dementia, 19, e075295.
• Singh, M., Goyal, S., Thirumal, D., Sharma, P., Kaur, M., Singh, V., & Singh, T. G. (2023). Analogues Rescues Tau Pathologies and Memory Deficits Inhibiting GSK‐3 Signaling using Scaffold morphing and in silico approaches. Alzheimer’s & Dementia, 19, e075313.
• Sharma, P., Singh, M., Kaur, P., Silakari, P., Mujawar, S., & Sahu, S. K. (2024). Exploration of Baicalin analogues against main Protease involved in Covid-19 as potential inhibitors involving in silico approaches. In BIO Web of Conferences (Vol. 86, p. 01036). EDP Sciences.
• Singh, J. K., Kaur, S., Chandrasekaran, B., Kaur, G., Saini, B., Kaur, R., Silakari, P., Kaur, N. & Bassi, P. (2024). A QbD-Navigated Approach to the Development and Evaluation of Etodolac–Phospholipid Complex Containing Polymeric Films for Improved Anti-Inflammatory Effect. Polymers, 16(17), 2517.
• Khurana, C., Sapra, V., Silakari, P., Panesar, G., Chaudhary, M., Singh, T. G., & Bedi, O. (2024). Exploration of CHIR99021 by GSK-3β inhibition for triggering the liver regeneration process in partially hepatectomized rats. Journal of Applied Pharmaceutical Science, 14(8), 206-215.
• Grewal, A. K., Dhaliwal, P. K., Silakari, P., Kumar, A., Khan, H., & Singh, T. G. (2024). Neuroprotective role of Piceatannol in Chronic Unpredictable Stress induced memory dysfunction. Alzheimer’s & Dementia, 20, e087954.
• Sharma, K., Singh, M., Sharma, P., Sharma, S. C., Mujwar, S., Kapoor, M., Mishra, K.K. & Wani, T. A. (2024). Design, Synthesis, and Biological Evaluation of Novel Coumarin Analogs Targeted against SARS-CoV-2. Molecules, 29(6), 1406.
• Kandhwal, M., Grewal, A. K., Singh, M., Singh, V., & Singh, T. G. (2024). Neuroprotective Effects of Hesperidin: In-Vitro and In silico Evaluation of Its Antioxidant and Enzyme Inhibitory Activities. Carpathian Journal of Food Science & Technology, 16(4).
• Singh, V., Singh, M., & Shri, R. (2024). Unveiling the Multifaceted Neuroprotection of Dihydroxytrimethoxyflavone: Memory Enhancement Beyond Cholinergic Boost. Alzheimer’s & Dementia, 20, e089173.
• Bhatia, S., Singh, V., Singh, M., Singh, R., Shri, R., & Singh, T. G. (2025). Expatiating the Pivotal Role of Matrix Metalloproteinases and Blood-Brain Barrier Disruption in Ischemic Stroke: Molecular Insights and Therapeutic Targets. In Ischemic Injury (163-179). Apple Academic Press.
• Silakari, P., Piplani, P., Kumar, A. and Grewal, A.K., 2024. Novel piperazine‐benzoquinone derivative as a possible lead molecule selectively targeting AChE for the management of dementia in Alzheimer’s disease. Alzheimer’s & Dementia, 20, p.e087881.
• Singh JK, Kaur S, Chandrasekaran B, Kaur G, Saini B, Kaur R, Silakari P, Kaur N, Bassi P. A QbD-Navigated Approach to the Development and Evaluation of Etodolac–Phospholipid Complex Containing Polymeric Films for Improved Anti-Inflammatory Effect. Polymers. 2024 Sep 4;16(17):2517.
• Khurana, C., Sapra, V., Silakari, P., Panesar, G., Chaudhary, M., Singh, T.G. and Bedi, O., 2024. Exploration of CHIR99021 by GSK-3β inhibition for triggering the liver regeneration process in partially hepatectomized rats. Journal of Applied Pharmaceutical Science, 14(8), pp.206-215.
• Khurana, C., Sapra, V., Silakari, P., Panesar, G., Chaudhary, M., Singh, T.G. and Bedi, O., 2024. Exploration of CHIR99021 by GSK-3β inhibition for triggering the liver regeneration process in partially hepatectomized rats. Journal of Applied Pharmaceutical Science, 14(8), pp.206-215.
• El Fadili, M., Er-Rajy, M., Mujwar, S., Ajala, A., Bouzammit, R., Kara, M., Abuelizz, H.A., Er-Rahmani, S. and Elhallaoui, M., 2024. In silico insights into the design of novel NR2B-selective NMDA receptor antagonists: QSAR modeling, ADME-toxicity predictions, molecular docking, and molecular dynamics investigations. BMC chemistry, 18(1), p.142.
• Singh, V., Shri, R., Sood, P., Singh, M., Singh, T.G., Singh, R., Kumar, A. and Ahmad, S.F., 2024. 5, 7-dihydroxy-3′, 4′, 5′-trimethoxyflavone mitigates lead induced neurotoxicity in rats via its chelating, antioxidant, anti-inflammatory and monoaminergic properties. Food and Chemical Toxicology, 189, p.114747.
• Singh, V., Shri, R., Sood, P., Singh, M., Singh, T.G., Singh, R., Kaur, A., Kumar, A., Singh, T., Ahmad, S.F. and Attia, S.M., 2024. 3-hydroxy-3′, 4′, 5′-trimethoxyflavone protects rats against lead-induced neurotoxicity via chelation and modulating oxidative stress, inflammatory and monoaminergic systems. Journal of Functional Foods, 118, p.106278.
• Choudhary, D., Rani, N. and Kaur, R., 2025. Successful Identification of Key Phytoconstituents of Emblica officinalis as Potential Multitargeting Anti-Inflammatory and Antifungal Agents. Anti-Infective Agents, 23(3), p.E22113525331096.
• Choudhary, D., Kaur, R., Rani, N., Kumar, B., Singh, T.G., Chandrasekaran, B., Rawat, R. and Eyupoglu, V., 2025. Insights into in silico analysis to explore the multitarget antidepressant role of Camellia sinensis. Journal of Biomolecular Structure and Dynamics, pp.1-13.
• Leutcha, Peron Bosco, Hamadou Mamoudou, Yves Oscar Nganso Ditchou, Siddique Akber Ansari, Gabrielle Ange Amang à Ngnoung, Somdutt Mujwar, Jean Domga Taiga et al. “Flavonoids and other constituents from Jacaranda mimosifolia: In vitro analysis, molecular docking, and molecular dynamic simulations of antioxidant and anti-inflammatory activities.” Biomedicine & Pharmacotherapy 182 (2025): 117768.
• Kumari, D., Jamwal, V., Singh, A., Singh, S.K., Mujwar, S., Ansari, M.Y. and Singh, K., 2024. Repurposing FDA approved drugs against Sterol C-24 methyltransferase of Leishmania donovani: a dual in silico and in vitro approach. Acta Tropica, 258, p.107338.
• Aloui, M., Mujwar, S., Er-rajy, M., Abuelizz, H.A., Er-rahmani, S., Zarougui, S. and Menana, E., 2025. In silico design of novel pyridazine derivatives as balanced multifunctional agents against Alzheimer’s disease. Scientific Reports, 15(1), pp.1-27.
• Kaur, A., Kaur, S., Khurana, N., Dhawan, R. K., Singh, S., Singh, M., Mannan A., Mahmoud M. H., Alexiou A., Papadakis, M. and Batiha, G.E.S., & Singh, T. G. (2025). Synergistic approach of alpha-Asarone (α-asarone) with donepezil in mitigating Alzheimer’s disease induced by Aluminium chloride in rats. Journal of Functional Foods, 129, 106847.
• Ez‐zoubi, A., Boutahiri, N., El Fadili, M., Sghyar, R., Mujwar, S., Moustaid, W., El‐Mrabet, A. and Farah, A., 2025. Beta‐Cyclodextrin Inclusion Complexes with Phenolic Synthetic Antioxidants: Synthesis, Spectroscopic Characterisation, Molecular Modeling, and Activity Efficiency. ChemistrySelect, 10(10), p.e202405310.

Patents

• A Quinoline Anti-Tubercular Compound, Compositions and Process of Preparation Thereof; Sandeep Arora, Ritchu Babbar, Vishnu Nayak Badavath. (202111054540)
• Compounds Inhibiting Proteolytic Enzymes for Anti-Sars-Coronavirus (Sars-Cov-2) Activity; Manjinder Singh, Pratibha Sharma, Thakur Gurjeet Singh, Varinder Singh, Maninder Kaur, Sandeep Arora. (202211013566)
• An Α-Amylase And Α–Glucosidase Inhibiting Compound for Management of Diabetes; Manjinder Singh, Varinder Singh, Thakur Gurjeet Singh, Sandeep Arora, Maninder Kaur (202211033588)
• (Un)Substituted Piperazin-1-Yl-Chromen-4-One Compound as Alr-2 Inhibitor and Their Process of Preparation Thereof; Manjinder Singh, Varinder Singh, Thakur Gurjeet Singh, Ravinder Singh, Pragati Silakri (202311002297)
• Acetylcholinesterase Inhibitor Compound as Anti-Alzheimer’s Agent; Rajwinder Kaur, Balraj Saini, Thakur Gurjeet Singh, Manjinder Singh (202311005953)
• Pyrazolo-Benzothiazole Compounds for Management of Alzheimer’s Disease and Method of Their Synthesis; Anju Goyal, Harish Kumar. (202211053077)
• Chromen-4-One Based Aldose Reductase-2 Inhibitor and Use Thereof: Manjinder Singh, Varinder Singh,Thakur Gurjeet Singh, Ravinder Singh,Pragati Silakari (202311006578)
• 10-(2,4-Dichlorobenzyl) Acridin-9(10h)-One for Bacterial Infections; Pragati Silakari, Manjinder Singh, Varinder Singh, Thakur Gurjeet Singh, Amarjot Kaur. (202311005300)
• Anti-Bacterial Compound for Gram-Negative Bacteria; Pragati Silakari, Manjinder Singh, Varinder Singh, Thakur Gurjeet Singh. (202311005299)
• Acridin Compound for Gram-Negative Bacteria; Pragati Silakari, Manjinder Singh, Varinder Singh, Thakur Gurjeet Singh. (202311005298)
• 4-Methoxyphenyl Benzopyran-4-One Based Alr2 Inhibitor; Manjinder Singh, Varinder Singh, Thakur Gurjeet Singh, Ravinder Singh, Pragati Silakri (202411002694)
• Pyrazole Compounds as Anti-Alzheimer’s Agent; Rajwinder Kaur, Thakur Gurjeet Singh, Balraj Saini, Manjinder Singh. (202411018323)
• Anti-Microbial 3, 5- Dinitrosalicylic Acid Phytoconjugate Compounds And Process Of Preparation Thereof; Nidhi Rani, Rajwinder Kaur, Thakur Gurjeet Singh, Varinder Singh, Md Altamash Ahmad, Rashmi Arora, Rupinder Kaur. (202211026261)