Dr. Alpesh Malde

Research Interests

Computational Drug Design
Free Energy (FE) Calculations

Current Projects

FE calculations of Glycogen Phosphorylase inhibitors (antidiabetic agents)
Single step perturbation for virtual screening in fragment-based drug design
FE calculations on Phenylethanolamine N-methyltransferase (PNMT) inhibitors

Research Grants

"Free Energy Perturbation Analysis of glucopyranose analogs as Glycogen Phosphorylase inhibitors Implications for method development and anti-diabetic drug design", 2008, APAC (The Australian Partnership for Advanced Computing), Project n63

Academic

B. Pharm., Bombay College of Pharmacy, University of Mumbai, India 2000
MS (Pharm), (Medicinal Chemistry) National Institute of Pharmaceutical Education and Research (NIPER), India 2001
PhD (Pharmaceutical Chemistry), Bombay College of Pharmacy, University of Mumbai, India 2006

Selected Publications

1. Verma J, Khedkar V, Khedkar SA, Malde AK, Prabhu A, Coutinho EC. “A Comprehensive Analysis of the Thermodynamic Events involved in Ligand-Receptor Binding using CoRIA and its variants”. Journal of Computer-Aided Molecular Design, 2008, 22, 91-104

2. Malde AK, Srivastava SS, Coutinho EC. “Understanding Interactions of Gastric Inhibitory Peptide (GIP) with its Receptor through NMR and Molecular Modelling”. Journal of Peptide Science, 2007, 13, 287-300

3. Khedkar SA, Malde AK, Coutinho EC. “Design of Inhibitors against MurF Enzyme of S. pneumoniae using Docking, 3D-QSAR and De Novo Design” Journal of Chemical Information & Modeling, 2007, 47, 1839-1846

4. Malde AK, Khedkar SA, Coutinho EC. “The B(OH)-NH Isostere is a Surrogate for the Amide bond (CO-NH) in Peptides: An Ab Initio Study”. Journal of Chemical Theory and Computation 2007, 3, 619-627

5. Datar PA, Khedkar SA, Malde AK and Coutinho EC. “Comparative Residue Interaction Analysis (CoRIA): A 3D-QSAR Approach to Explore the Binding Contributions of Active Site Residues with Ligands”. Journal of Computer-Aided Molecular Design, 2006, 20, 343–360

6. Nayyar A, Malde A, Coutinho E, Jain R. “Three-dimensional Quantitative Structure (3D-QSAR) Activity Relationship Studies on Ring-substituted Quinoline Class of Anti-tuberculosis Agents”. Bioorganic & Medicinal Chemistry, 2006, 14, 847-856

7. Khedkar SA, Malde AK, Coutinho EC. “Comparative Protein Modeling of Methionine S-Adenosyltransferase (MAT) Enzyme from M. tuberculosis: A Potential Target for Antituberculosis Drug Discovery”. Journal of Molecular Graphics and Modelling, 2005, 23(4), 355-366

8. Bharatam PV, Iqbal P, Malde A, Tiwari R. “Electron Delocalization in Aminoguanidines”. Journal of Physical Chemistry A, 2004, 108, 10509-10517

9. Chakraborti AK, Gopalakrishnan B, Sobhi ME, Malde AK. “3D-QSAR Studies on Thieno[3,2-d]pyrimidines as Phosphodiesterase IV Inhibitors”. Bioorganic & Medicinal Chemistry Letters, 2003, 13 (8), 1403-1408