Dr. Alpesh Malde

Alpeshkumar Malde

Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS - by MD group of Prof. Alan E. Mark at University of Queensland, St. Lucia, QLD 4072, Australia.

http://compbio.chemistry.uq.edu.au/atb/

Research Interests

Computational methods in in Drug Design
Biomolecular and small molecule simulations
Free Energy (FE) Calculations in Drug Design
Molecular Dynamics simulations and Quantum Mechanical calculations
Force field for heteromolecules: parameterization and topology builder

Current Projects

Refinement of ligands in X-ray crystal complexes
Automated force field topology builder for heteromolecules
Solvation Free Energy calculations for a therapeutically relevant fragment library
High throughput free energy calculations for virtual screening in fragment-based drug design

Research Grants

“Development of methodology for high throughput free energy calculations in drug design Applications”. Australian Research Council (ARC) Discovery Project, 2009-2011, AUD 259K.

“Homology modeling of dihydroorotate dehydrogenase from Plasmodium falciparum for the purpose of designing selective inhibitors”, CSIR (Council of Scientific and Industrial Research, India), 2005-2007

Awards and Fellowships

2006
IBM-Zerner Fellowship, Travel grant from CSIR, India and DST (Department of Science and Technology), India to attend Sanibel Symposium 2006 at Florida, USA
2004-2006
Senior Research Fellowship from CSIR, India
2003-2004
Project Associateship from UGC (Universities Grants Commission), India
2002-2003
Senior Research Fellowship from CSIR, India under NMITLI project on Bioinformatics
2000-2001
UGC Fellowship during M.S. (Pharm) and Gold Medal for M. S. (Pharm)
1999, 2000
Best Student Award during Third and Final year B. Pharm
1996-2000
Scholarships during all four years of B. Pharm, IPA (Indian Pharmaceutical Association) Gold Medal.

Academic

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

Positions

2009-present
ARC Australian Postdoctoral Fellow, University of Queensland
2007-2008
Postdoctoral Research Fellow, MD Group, University of Queensland
2003-2006
PhD Student, Bombay College of Pharmacy (University of Mumbai)
2002-2003
Senior Research Fellow, Dept of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, India
2002
Chemist, Molecular Modelling and Drug Design Lab, Dr. Reddy’s Research Foundation, Hyderabad, India
2000-2001
M.S. Student, NIPER, India

Selected Publications

Full list available at: http://network.nature.com/people/U3E2C3D2E/profile

- Malde AK and Mark AE. "X-ray Crystal Complexes: How much can we trust the conformations of non-standard ligands." manuscript in preparation.

- Song B, Kibler P, Malde A, Kodukula K, Galande, A. Design of a short linear peptide that shows hydrogen bond stabilized conformation in water. Journal of the American Chemical Society, submitted.

1. Malde AK and Mark AE. "Binding and Enantiomeric Selectivity of Threonyl-tRNA Synthetase." J. Am. Chem. Soc., 2009, 131 (11), 3848-3849.

2. 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

3. 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

4. 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

5. 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

6. Khedkar SA, Malde AK, Coutinho EC “Pharmacophore Modeling in Drug Discovery and Development: An Overview”. Medicinal Chemistry, 2007, 3, 187–197

7. 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

8. 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

9. 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

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

11. 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

Presentations

Invited talk
"Ligands in X-ray Crystal Complexes: A Drug Design Precautionary Tale". 61st Indian Pharmaceutical Congress 2009, 11-13 December 2009, Ahmedabad, India.

“Comparative Molecular Field Analysis (CoMFA): Method and Applications.” Invited talk at Workshop on Computational techniques in Drug Development at Molecular Mechanisms of Disease and Drug Action (MMDDA-2005) Conference on November 15, 2005 at Saha Institute of Nuclear Physics, Kolkata, India.

Oral Presentations
“Ligands in X-ray Complexes: A Drug Design Precautionary tale”. MM 2009 Molecular Modelling from Dynamical, Biomolecular and Materials Nanotechnology Perspective, 26 – 29 July 2009 at Gold Coast, Australia.

“The Omega Space of N-methylacetamide, N-hydroxy-N-methylacetamide and its Boron Isostere”. Oral presentation at National Symposium on Recent Trends in Molecular and Medical Biophysics (Indian Biophysics Society) organized by University of Pune during January 22 – 25, 2005 at Pune, India.

Poster Presentations
“High Throughput Free Energy Calculations: Application to Solvation Free Energy Estimation”. Poster presentation at World Association of Theoretical and Computational Chemists (WATOC) 2008, during September 14 – 19 at Sydney Convention and Exhibition Center, Australia.

“The ω, φ, and ψ Preferences of Boron Peptides”. Poster presentation at 46th Sanibel Symposium organized by the Quantum Theory Project (QTP) group of University Florida, USA during 26 February – 3 March 2006 at St. Simon’s Island, Georgia, USA.

“Three-dimensional quantitative structure (3D-QSAR) activity relationship studies on ring-substituted quinoline class of anti-tuberculosis agents”. Poster presentation at Molecular Mechanisms of Disease and Drug Action (MMDDA-2005) Conference held during November 16-18, 2005 at Saha Institute of Nuclear Physics, Kolkata, India.

“Electron delocalization in Guanidines”. Poster presentation at 5th National Symposium in Chemistry organized by Chemical Research Society of India (CRSI) held in February 2003 at Chennai, India.

“Computer-aided design of PDE IV inhibitors: Comparative Molecular Field Analysis (CoMFA) of some Thieno[3,2-d]pyrimidine derivatives”. Poster presentation at 54th Indian Pharmaceutical Congress (IPC) held during December 2002 at Pune, India.

Other Conferences

National Symposium on Advances in Magnetic Resonance and its Applications & 12th National Magnetic Resonance Society (NMRS) Meeting during October 8-11, 2005 at Gulmarg, Kashmir and RRL, Jammu, India

XXIst International Conference on Magnetic Resonance in Biological Systems (ICMRBS) organized by Nuclear Magnetic Resonance Society (NMRS) during January 16 –21, 2005 at Hyderabad, India

National Symposium on Cellular and Molecular Biophysics (Indian Biophysics Society); organized by Department of Biophysics, National Institute of Mental Health and Neuro Sciences (NIMHANS) held during January 14-17, 2004 at Bangalore, India

Contact Details

ARC Australian Postdoctoral Fellow
Molecular Dynamics Group
School of Molecular and Microbial Sciences (SMMS)
Chemistry Building (#68)
The University of Queensland
St. Lucia Campus, Brisbane, QLD 4072
Australia

email: a.malde_at_uq.edu.au
Fax: +61 7 3365 3872