Dr. Alpesh Malde: Difference between revisions

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https://maldescientific.com/


'''Alpeshkumar MALDE''' <br>
https://atb.uq.edu.au/
Automated Topology Builder (ATB) and Repository for the GROMOS family of force fields <br>
http://compbio.biosci.uq.edu.au/atb/ <br>
[[Image:Atb.png]] <br>


http://network.nature.com/people/U3E2C3D2E/profile
http://orcid.org/0000-0002-8181-1619


 
http://www.researcherid.com/rid/A-5341-2010
[[Image:2hkz_crystal.png|thumb|Orientation of L-Ser in the crystal structure 2HKZ could explain selectivity over L-Thr but could not explain enantiomeric selectivity towards D-amino acids.]]
[[Image:2hkz_jacs.png|thumb|Thermodynamically stable binding mode revealed by MD simulations and validated by FE calculations could explain both the selectivity as well as the mechanism of enantiomeric selectivity of family of aminoacyl-t-RNA synthetases. http://pubs.acs.org/doi/abs/10.1021/ja9002124]]
 
== Research Interests ==
 
* Small molecule and biomolecular modeling: Molecular dynamics (MD) simulations, free energy (FE) and quantum mechanical (QM) calculations <br>
 
* Force field for heteromolecular ligands and parameterization: Automated force field Topology Builder [http://compbio.biosci.uq.edu.au/atb/ ATB] and Repository <br>
 
* Binding modes of ligands in X-ray crystal complexes <br>
 
* Computational method development in drug design: High throughput free energy calculations <br>
 
== Projects ==
 
* [http://sampl.eyesopen.com/ SAMPL3] challenge  using [http://compbio.biosci.uq.edu.au/atb/ ATB] and GROMOS/GROMACS with G53A6 Force Field [[Image:SAMPL.png|200px|]] <br>
 
* VALIDATION of [http://compbio.biosci.uq.edu.au/atb/ ATB]  [[Image:Atb.png|100px|]] <br>
 
* Deriving force constants for bonded terms from a HESSIAN matrix [[Image:Hessian.png|150px|]]<br>
 
* Modeling family B G-protein Coupled Receptors (B-GPCR):ligand interactions including Gastric Inhibitory pepetide (GIP), Glucagon-like Peptide-1 (GLP-1) and Exenatide (Byetta) [[Image:UQ_GPCR_alpesh.png|100px]] [[Image:byetta.jpg|100px]]] [[Image:gila.jpg|100px]]]<br>
 
* Binding mode of WARFARIN  [[Image:Warfarin.png|150px|]] [[Image:warfarin_2.jpg|150px|]] <br>
 
* Single step high throughput FREE ENERGY calculations [[Image:SSP.png|350px|]] <br>
 
* Force field for BORON and Organoboranes [[Image:Boron.png|50px|]] [[Image:an2690.gif]] <br>
 
== Research Grants ==
“Automated Topology Builder: Force field parameterization and validation for heteromolecules“. University of Queensland Early Career Researcher (UQ-ECR), 2010, AUD 16K <br>
 
“Development of methodology for high throughput free energy calculations in drug design Applications”. Australian Research Council (ARC) Discovery Project, 2009-2011, AUD 259K. <br>
 
“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 <br>
 
== Awards and Fellowships ==
 
'''2011'''<br>
University of Queensland ResTeach Award<br>
'''2010'''<br>
University of Queensland Early Career Researcher (UQ-ECR) Award<br>
'''2009-2011'''<br>
ARC Australian Postdoctoral (ARC-APD) Fellowship <br>
'''2006'''<br>
IBM-Zerner Fellowship, Travel grant from CSIR, India and DST (Department of Science and Technology), India to attend Sanibel Symposium 2006 at Florida, USA <br>
'''2004-2006'''<br>
Senior Research Fellowship from CSIR, India <br>
'''2003-2004'''<br>
Project Associateship from UGC (Universities Grants Commission), India <br>
'''2002-2003'''<br>
Senior Research Fellowship from CSIR, India under NMITLI project on Bioinformatics <br>
'''2000-2001'''<br>
UGC Fellowship during M.S. (Pharm) and Gold Medal for M. S. (Pharm) <br>
'''1999, 2000'''<br>
Best Student Award during Third and Final year B. Pharm <br>
'''1996-2000'''<br>
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 <br>
'''MS (Pharm)''' (Medicinal Chemistry)  National Institute of Pharmaceutical Education and Research (NIPER), India 2001 <br>
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2000 <br>
 
== Positions ==
'''2009-present''' <br>
ARC Australian Postdoctoral (ARC-APD) Fellow, MD group, SCMB, University of Queensland <br>
'''2007-2008''' <br>
Postdoctoral Research Fellow, MD Group, SCMB, University of Queensland <br>
'''2003-2006''' <br>
PhD Student, Bombay College of Pharmacy (University of Mumbai) <br>
'''2002-2003''' <br>
Senior Research Fellow, Dept of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, India <br>
'''2002''' <br>
Chemist, Molecular Modelling and Drug Design Lab, Dr. Reddy’s Research Foundation, Hyderabad, India <br>
'''2000-2001'''<br>
M.S. Student, NIPER, India
 
== Publications ==
 
'''Research Articles'''
 
31. '''Malde AK''' and Mark AE. Challenges in determining the binding modes of non-standard ligands in X-ray crystal complexes. Journal of Computer-Aided Molecular Design, 2011, 25, 1-12.
http://dx.doi.org/10.1007/s10822-010-9397-6
 
30. 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, 2010, 132, 4508-4509 http://dx.doi.org/10.1021/ja905341p
 
29. Verma J, '''Malde A''', Khedkar S, Iyer R, Coutinho E. Local Similarity Index Analysis (LISA) – a 3D-QSAR formalism based on local molecular similarity. Journal of Chemical Information and Modelling, 2009, 49, 2695-2707.
http://dx.doi.org/10.1021/ci900224u
 
28. '''Malde AK''' and Mark AE. The Binding and Enantiomeric Selectivity of Threonyl-tRNA Synthetase. Journal of the American Chemical Society, 2009, 131, 3848-3849.
http://dx.doi.org/10.1021/ja9002124
 
27. Manvar A, '''Malde A''', Verma J, Mishra A, Upadhyay K, Virsodia V, Acharya H, Coutinho E, Shah A. Synthesis, Anti-tubercular Activity and 3D-QSAR Study of Coumarin-4-acetic acid benzylidene hydrazides European Journal of Medicinal Chemistry, 2008, 43, 2395.
http://dx.doi.org/10.1016/j.ejmech.2008.01.016
 
26. 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.
http://dx.doi.org/10.1007/s10822-008-9172-0
 
25. 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.
http://dx.doi.org/10.1021/ci600568u
 
24. Khedkar SA, '''Malde AK''', Coutinho EC. “Inhibition of methionine-S-adenosyltransferase of M. smegmatis and M. tuberculosis: Homology Modelling, Docking and De novo Inhibitor Design”. Internet Electronic Journal of Molecular Design, 2007, 6, 151-166.
 
23. Khedkar SA, '''Malde AK''', Coutinho EC. “CoMFA Study of Distamycin Analogs Binding to the Minor-groove of DNA: A Unified Model for Broad-spectrum Activity”. Journal of Molecular Modeling, 2007, 13, 1099-1108.
http://dx.doi.org/10.1007/s00894-007-0234-3
 
22. '''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.
http://dx.doi.org/10.1021/ct600256s
 
21. '''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.
http://dx.doi.org/10.1002/psc.839
 
20. Pissurlenkar RRS, '''Malde AK''', Khedkar SA, Coutinho EC.  “Encoding Type and Position in Peptide QSAR: Application to peptides binding to Class I MHC Molecule HLA-A*0201”. QSAR and Combinatorial Science (QCS), 2007, 26, 189–203.
http://dx.doi.org/10.1002/qsar.200530184
 
19. '''Malde AK''', Khedkar SA, Coutinho EC. “Isosteres of Peptides – Boron analogs as Dipolar forms of α-amino acids: An Ab Initio Study”. Journal of Physical Organic Chemistry, 2006, 19, 1–10.
http://dx.doi.org/10.1002/poc.1139
 
18. Nayyar A, Monga V, '''Malde A''', Coutinho E, Jain R. “Synthesis, Anti-tuberculosis Activity and 3D-QSAR Study of 4-Adamantan-1-yl group Containing 2-Substituted Quinolines”. Bioorganic & Medicinal Chemistry, 2007, 15, 626-640.
http://dx.doi.org/10.1016/j.bmc.2006.10.064
 
17. '''Malde AK''', Khedkar SA, Coutinho EC. “Stationary points on the PES of N-methoxy Peptides and their Boron Isosteres: An Ab Initio Study”. Journal of Chemical Theory and Computation, 2006, 2, 1664–1674.
http://dx.doi.org/10.1021/ct600192g
 
16. 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.
http://dx.doi.org/10.1007/s10822-006-9051-5
 
15. Jadhav GS, Patel AR, Vavia PR, '''Malde AK''' and Coutinho EC. “Interaction of Valdecoxib with Beta Cyclodextrin: Experimental and Molecular Modeling Studies”. Journal of Inclusion Phenomenon and Macrocyclic Chemistry, 2006, 56, 261-273.
http://dx.doi.org/10.1007/s10847-006-9093-2
 
14. Nayyar A, '''Malde A''', Coutinho E, Jain R. “Synthesis, Anti-tubercular Activity, and 3D-QSAR Study of Ring-Substituted-2/4-Quinolincarbaldehyde Derivatives”. Bioorganic & Medicinal Chemistry, 2006, 14, 7302-7310.
http://dx.doi.org/10.1016/j.bmc.2006.06.049
 
13. '''Malde AK''', Khedkar SA, Coutinho EC. “The ω, φ, and ψ space of N-hydroxy-N-methylacetamide and N-acetyl-N’-hydroxy-N’-methylamide of alanine and their boron isosteres”. Journal of Chemical Theory and Computation, 2006, 2, 312-321.
http://dx.doi.org/10.1021/ct050242v
 
12. Khedkar SA, '''Malde AK''', Coutinho EC. “Topology of Human Methionine S-Adenosyltransferase”. Indian Journal of Chemistry A, 2006, 45A, 138-145.
 
11. 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.
http://dx.doi.org/10.1016/j.bmc.2005.09.018
 
10. Khedkar SA, '''Malde AK''', Coutinho EC. “Modeling Human Neurokinin-1 Receptor Structure using the Crystal Structure of Bovine Rhodopsin”. Internet Electronic Journal of Molecular Design, 2005, 4, 329-341.
 
9. Prabhu A, '''Malde A''', Srivastava S, Coutinho E. “Solution Conformation of Substance P Antagonists – [D-Arg1, D-Trp7,9, Leu11]-SP, [D-Arg1, D-Pro2, D-Trp7,9, Leu11]-SP and [D-Pro2, D-Trp7,9]-SP by CD, NMR and MD simulations”. Peptides, 2005, 26, 875-885.
http://dx.doi.org/10.1016/j.peptides.2004.12.001
 
8. 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.
http://dx.doi.org/10.1016/j.jmgm.2004.11.003
 
7. '''Malde AK''', Khedkar SA, Coutinho EC, Saran A. “Geometry, Transition States and Vibrational Spectra of Boron Isostere of N-methylacetamide by ab initio calculations”. International Journal of Quantum Chemistry, 2005, 102, 734-742.
http://dx.doi.org/10.1002/qua.20446
 
6. Bharatam PV, Iqbal P, '''Malde A''', Tiwari R. “Electron Delocalization in Aminoguanidines”. Journal of Physical Chemistry A, 2004, 108, 10509-10517.
http://dx.doi.org/10.1021/jp049366e
 
5. Mittal S, '''Malde AK''', Selvam C, Arun KHS, Johar PS, Jachak S, Ramarao P, Bharatam PV and Chawla HPS. “Synthesis and Evaluation of S-4-(3-thienyl)phenyl-α-methylacetic acid”. Bioorganic & Medicinal Chemistry Letters, 2004, 14 (4), 979-982.
http://dx.doi.org/10.1016/j.bmcl.2003.11.066
 
4. Chakraborti AK, Gopalakrishnan B, Sobhia ME, '''Malde AK'''. “3D-QSAR Studies of Indole Derivatives as Phosphodiesterase IV Inhibitors”. European Journal of Medicinal Chemistry, 2003, 38 (11,12), 975-982.
http://dx.doi.org/10.1016/j.emech.2003.09.001
 
3. Pal M, Madan M, Padakanti S, Pattabiraman V, Kalleda S, Vanguri A, Mullangi R, Mamidi NVS, Casturi S, '''Malde AK''', Gopalakrishnan B and Yeleswarapu KR. “Synthesis and Cyclooxygenase-2 Inhibiting Property of 1,5-Diarylpyrazoles with Substituted Benzenesulphonamide Moiety as Pharmacophore: Preparation of Sodium Salt for Injectable Formulation”. Journal of Medicinal Chemistry, 2003, 46 (19), 3975-3984.
http://dx.doi.org/10.1021/jm020563g
 
2. Chakraborti AK, Gopalakrishnan B, Sobhia ME, '''Malde AK'''. “Comparative Molecular Field Analysis (CoMFA) of Phthalazine Derivatives as Phosphodiesterase IV Inhibitors”. Bioorganic & Medicinal Chemistry Letters, 2003, 13 (15), 2473-2479.
http://dx.doi.org/10.1016/S0960-894X(03)00493-1
 
1. Chakraborti AK, Gopalakrishnan B, Sobhia 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.
http://dx.doi.org/10.1016/S0960-894X(03)00172-0
 
'''Review Articles'''
 
3. Khedkar SA, '''Malde AK''', Coutinho EC and Srivastava S. “Pharmacophore Modelling in Drug Design and Discovery: An Overview”. [http://www.ingentaconnect.com/content/ben/mc/2007/00000003/00000002/art00008?token=00521b43e7de1ddc26b7e2a46762c6b465d767025704574564524673f7b2f267738703375686f49dd1 Medicinal Chemistry], 2007, 3, 187-197.
 
2. Khedkar SA, '''Malde AK''' and Coutinho EC. “In Silico screening of Ligand Databases: Methods and Applications”. Indian Journal of Pharmaceutical Sciences, 2007, 68, 689-696.
 
1. '''Malde AK''' and Galande A. “Combinatorial Libraries of Peptides, Peptoids and Cyclic Peptides”. Indian Drugs, 1999, 36 (10), 619-627.
 
== Presentations ==
'''Invited talks'''<br>
"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. <br>
 
'''Oral Presentations''' <br>
"Automated Topology Builder (ATB) and Repository for the GROMOS family of force fields". MM 2010 - Advances in Biomolecular and Materials Modelling, 28 Nov - 1 Dec 2010, Monash Institute of Pharmaceutical Sciences, Melbourne, Australia.
 
“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. <br>
 
“Solution conformation of Gastric Inhibitory Polypeptide (GIP) (1-30 amide) by NMR and MD Simulations”. 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. <br>
 
 
'''Poster Presentations'''<br>
“How much can we trust the binding modes of non-standard ligands in X-ray crystal complexes?”. Gordon Research Conference – Computational Chemistry 2010, Aug 29 – Sept 3 at Les Diablerets, Switzerland. <br>
 
“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. <br>
 
“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. <br>
 
“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.<br>
 
“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. <br>
 
“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.<br>
 
== Other Conferences ==
 
10th International NCCR Symposium in Structural Biology, ETH Zurich, 2-3 Sept 2010, Switzerland <br>
 
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 <br>
 
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 <br>
 
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 <br>
 
== Contact Details ==
 
ARC Australian Postdoctoral Fellow <br>
Molecular Dynamics Group <br>
School of Molecular and Microbial Sciences (SMMS) <br>
Molecualr Biosciences building (#76) <br>
The University of Queensland <br>
St. Lucia Campus, Brisbane, QLD 4072 <br>
Australia <br>
'''phone''': +61 7 3365 7562 <br>
'''Fax''': +61 7 3365 3872 <br>
'''email''': a.malde_at_uq.edu.au <br>

Latest revision as of 13:39, 10 July 2018

https://maldescientific.com/

https://atb.uq.edu.au/

http://orcid.org/0000-0002-8181-1619

http://www.researcherid.com/rid/A-5341-2010

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