There are 2 ways to go about Ph.D after MBBS. One is the conventional way of completing MBBS, and then MS/MD and then go for Ph.D. The other way is taking advantage of your MBBS qualification and join Institutions which recruit MBBS graduates for their research programmes. One of them in demand always is Rajiv Gandhi Centre for Biotechnology. It is based in Kerala and is under the Govt. of India. Clinical research is another field where there is increased demand for MBBS doctors. ICMR, CIMAP, CCMB hire MBBS graduates for their Clinical research teams. AIIMS, NIMHANS, PGI, TIFR offer courses in this field. There are courses in NanoSciences and Molecular medicine that you can pursue after MBBS. For this you may have to take a little detour and study M.Tech in Nanoscience and then continue with Ph.D in Biomedical Engineering. Then you have Medical Biotechnology, Photothermal therapy, Medical sciences and Technology, Theranostics  and Nanotoxicology.

I hope my answer helps. All the very best for your future endeavors!